One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
Ribosome Subunits, Small, Archaeal
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Amino Acid Sequence
Sequence Homology, Amino Acid
Gene Expression Regulation, Archaeal
Ribosome Subunits, Large, Archaeal
A genus of anaerobic, irregular spheroid-shaped METHANOSARCINALES whose organisms are nonmotile. Endospores are not formed. These archaea derive energy via formation of methane from acetate, methanol, mono-, di-, and trimethylamine, and possibly, carbon monoxide. Organisms are isolated from freshwater and marine environments.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Peptide Initiation Factors
Eukaryotic Initiation Factor-4E
Eukaryotic Initiation Factor-3
A multisubunit eukaryotic initiation factor that contains at least 8 distinct polypeptides. It plays a role in recycling of ribosomal subunits to the site of transcription initiation by promoting the dissociation of non-translating ribosomal subunits. It also is involved in promoting the binding of a ternary complex of EUKARYOTIC INITIATION FACTOR-2; GTP; and INITIATOR TRNA to the 40S ribosomal subunit.
An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter. (1/2280)Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite the prokaryotic cell and genome organization, basal transcriptional elements of members of the domain Archaea (i.e., TATA box-like sequences, RNA polymerase, and transcription factors TBP, TFIIB, and TFIIS) are of the eukaryotic type. However, open reading frames potentially coding for bacterium-type transcription regulation factors have been recognized in different archaeal strains. This finding raises the question of how bacterial and eukaryotic elements interact in regulating gene expression in Archaea. We have identified a gene coding for a bacterium-type transcription factor in the hyperthermophilic archaeon Sulfolobus solfataricus. The protein, named Lrs14, contains a potential helix-turn-helix motif and is related to the Lrp-AsnC family of regulators of gene expression in the class Bacteria. We show that Lrs14, expressed in Escherichia coli, is a highly thermostable DNA-binding protein. Bandshift and DNase I footprint analyses show that Lrs14 specifically binds to multiple sequences in its own promoter and that the region of binding overlaps the TATA box, suggesting that, like the E. coli Lrp, Lrs14 is autoregulated. We also show that the lrs14 transcript is accumulated in the late growth stages of S. solfataricus. (+info)
Mutants in ABC10beta, a conserved subunit shared by all three yeast RNA polymerases, specifically affect RNA polymerase I assembly. (2/2280)ABC10beta, a small polypeptide common to the three yeast RNA polymerases, has close homology to the N subunit of the archaeal enzyme and is remotely related to the smallest subunit of vaccinial RNA polymerase. The eucaryotic, archaeal, and viral polypeptides share an invariant motif CX2C. CC that is strictly essential for yeast growth, as shown by site-directed mutagenesis, whereas the rest of the ABC10beta sequence is fairly tolerant to amino acid replacements. ABC10beta has Zn2+ binding properties in vitro, and the CX2C. CC motif may therefore define an atypical metal-chelating site. Hybrid subunits that derive most of their amino acids from the archaeal subunit are functional in yeast, indicating that the archaeal and eucaryotic polypeptides have a largely equivalent role in the organization of their respective transcription complexes. However, all eucaryotic forms of ABC10beta harbor a HVDLIEK motif that, when mutated or replaced by its archaeal counterpart, leads to a polymerase I-specific lethal defect in vivo. This is accompanied by a specific lack in the largest subunit of RNA polymerase I (A190) in cell-free extracts, showing that the mutant enzyme is not properly assembled in vivo. (+info)
Isolation and characterization of a second subunit of molecular chaperonin from Pyrococcus kodakaraensis KOD1: analysis of an ATPase-deficient mutant enzyme. (3/2280)The cpkA gene encoding a second (alpha) subunit of archaeal chaperonin from Pyrococcus kodakaraensis KOD1 was cloned, sequenced, and expressed in Escherichia coli. Recombinant CpkA was studied for chaperonin functions in comparison with CpkB (beta subunit). The effect on decreasing the insoluble form of proteins was examined by coexpressing CpkA or CpkB with CobQ (cobyric acid synthase from P. kodakaraensis) in E. coli. The results indicate that both CpkA and CpkB effectively decrease the amount of the insoluble form of CobQ. Both CpkA and CpkB possessed the same ATPase activity as other bacterial and eukaryal chaperonins. The ATPase-deficient mutant proteins CpkA-D95K and CpkB-D95K were constructed by changing conserved Asp95 to Lys. Effect of the mutation on the ATPase activity and CobQ solubilization was examined. Neither mutant exhibited ATPase activity in vitro. Nevertheless, they decreased the amount of the insoluble form of CobQ by coexpression as did wild-type CpkA and CpkB. These results implied that both CpkA and CpkB could assist protein folding for nascent protein in E. coli without requiring energy from ATP hydrolysis. (+info)
Universal conservation in translation initiation revealed by human and archaeal homologs of bacterial translation initiation factor IF2. (4/2280)Binding of initiator methionyl-tRNA to ribosomes is catalyzed in prokaryotes by initiation factor (IF) IF2 and in eukaryotes by eIF2. The discovery of both IF2 and eIF2 homologs in yeast and archaea suggested that these microbes possess an evolutionarily intermediate protein synthesis apparatus. We describe the identification of a human IF2 homolog, and we demonstrate by using in vivo and in vitro assays that human IF2 functions as a translation factor. In addition, we show that archaea IF2 can substitute for its yeast homolog both in vivo and in vitro. We propose a universally conserved function for IF2 in facilitating the proper binding of initiator methionyl-tRNA to the ribosomal P site. (+info)
A fission yeast gene for mitochondrial sulfide oxidation. (5/2280)A cadmium-hypersensitive mutant of the fission yeast Schizosaccharomyces pombe was found to accumulate abnormally high levels of sulfide. The gene required for normal regulation of sulfide levels, hmt2(+), was cloned by complementation of the cadmium-hypersensitive phenotype of the mutant. Cell fractionation and immunocytochemistry indicated that HMT2 protein is localized to mitochondria. Sequence analysis revealed homology between HMT2 and sulfide dehydrogenases from photosynthetic bacteria. HMT2 protein, produced in and purified from Escherichia coli, was soluble, bound FAD, and catalyzed the reduction of quinone (coenzyme Q2) by sulfide. HMT2 activity was also detected in isolated fission yeast mitochondria. We propose that HMT2 functions as a sulfide:quinone oxidoreductase. Homologous enzymes may be widespread in higher organisms, as sulfide-oxidizing activities have been described previously in animal mitochondria, and genes of unknown function, but with similarity to hmt2(+), are present in the genomes of flies, worms, rats, mice, and humans. (+info)
Tubulin-like protofilaments in Ca2+-induced FtsZ sheets. (6/2280)The 40 kDa protein FtsZ is a major septum-forming component of bacterial cell division. Early during cytokinesis at midcell, FtsZ forms a cytokinetic ring that constricts as septation progresses. FtsZ has a high propensity to polymerize in vitro into various structures, including sheets and filaments, in a GTP-dependent manner. Together with limited sequence homology, the occurrence of the tubulin signature motif in FtsZ and a similar three-dimensional structure, this leads to the conclusion that FtsZ is the bacterial tubulin homologue. We have polymerized FtsZ1 from Methanococcus jannaschii in the presence of millimolar concentrations of Ca2+ ions to produce two-dimensional crystals of plane group P2221. Most of the protein precipitates and forms filaments approximately 23.0 nm in diameter. A three-dimensional reconstruction of tilted micrographs of FtsZ sheets in negative stain between 0 and 60 degrees shows protofilaments of FtsZ running along the sheet axis. Pairs of parallel FtsZ protofilaments associate in an antiparallel fashion to form a two-dimensional sheet. The antiparallel arrangement is believed to generate flat sheets instead of the curved filaments seen in other FtsZ polymers. Together with the subunit spacing along the protofilament axis, a fitting of the FtsZ crystal structure into the reconstruction suggests a protofilamant structure very similar to that of tubulin protofilaments. (+info)
The effect of carboxyl group modification on the chromophore regeneration of archaeopsin-1 and bacterioopsin. (7/2280)Carboxyl group modification with DCCD and NCD-4 was employed to investigate the chemical environment of the side chains of archaeopsin-1 (aO-1) and bacterioopsin (bO). Some differences were observed between aO-1 and bO. Although DCCD or NCD-4 did not modify aO-1 in bleached membrane, they modified bO in bleached membrane and in mixed DMPC/CHAPS/SDS micelles at neutral pH, thereby affecting the opsin shift and the photocycle of the regenerated chromophore. On the contrary, after solubilization with SDS, aO-1 and bO were modified by DCCD and NCD-4, which decreased the chromophore regeneration. In particular, the reaction of aO-1 in SDS with NCD-4 proceeded in a 1:1 ratio at neutral pH. The fluorescence and CD spectra indicated that the modified site was located in the hydrophobic, asymmetrical region. Lysyl-endopeptidase digestion of NCD-4 modified aO-1 produced a fluorescent fragment and amino acid sequence analysis showed that Asp85 or Asp96 in helix C is a probable candidate for the modified residue at present. Kinetic CD measurements revealed that the introduction of N-acylurea at an Asp residue in helix C did not affect the formation of the transient intermediate but inhibited the side chain packing during refolding. (+info)
Structure of VAT, a CDC48/p97 ATPase homologue from the archaeon Thermoplasma acidophilum as studied by electron tomography. (8/2280)Valosine-containing protein-like ATPase from Thermoplasma acidophilum is a member of the superfamily of ATPases associated with a diversity of cellular activities and is closely related to CDC48 from yeast and p97 from higher eukaryotes and more distantly to N-ethylmaleimide-sensitive fusion protein. We have used electron tomography to obtain low-resolution (2-2.5 nm) three-dimensional maps of both the whole 500 kDa complex and the N-terminally truncated valosine-containing protein-like ATPase from T. acidophilum complex lacking the putative substrate binding domain. (+info)
DNA unwinding element
Bell SD (2012). "Archaeal orc1/cdc6 proteins". The Eukaryotic Replisome: A Guide to Protein Structure and Function. Subcellular ... Lastly, the C domain is necessary for facilitating protein-protein interactions. ARSs are found distributed across 16 ... In bacteria, the protein DnaA is the replication initiator. It gets loaded onto oriC at a DnaA box sequence where it binds and ... DNA unwinding element proteins (DUE-Bs) are found in eukaryotes. They act to initiate strand separation by binding to DUE. DUE- ...
Origin of replication
Bell SD (2012). "Archaeal orc1/cdc6 proteins". The Eukaryotic Replisome: A Guide to Protein Structure and Function. Subcellular ... Kasiviswanathan R, Shin JH, Kelman Z (2005). "Interactions between the archaeal Cdc6 and MCM proteins modulate their ... February 2013). "Specificity and function of archaeal DNA replication initiator proteins". Cell Reports. 3 (2): 485-96. doi: ... Although the evolutionary kinship of archaeal and eukaryotic initiators and replicative helicases indicates that archaeal MCM ...
Pan M, Kelman LM, Kelman Z (January 2011). "The archaeal PCNA proteins". Biochemical Society Transactions. 39 (1): 20-24. doi: ... The clamp-polymerase protein-protein interactions are stronger and more specific than the direct interactions between the ... Archaeons also share with eukaryotes the PIP (PCNA-interacting protein) motif, but a wider variety of such proteins performing ... and DNA repair proteins. All of these proteins also share a binding site on the DNA clamp that overlaps with the clamp loader ...
Reed, Christopher J.; Lewis, Hunter; Trejo, Eric; Winston, Vern; Evilia, Caryn (2013). "Protein Adaptations in Archaeal ... The genome of N. magadii consists of four replicons with a total sequence of 4,443,643 bp and encodes 4,212 putative proteins. ... Those harsh conditions resulted in changed composition of charged amino acids in the proteins (average isoelectric point is ... Additionally, proton-driven ATP synthase and a variety of putative cytochromes and other proteins required for aerobic ...
Reed CJ, Lewis H, Trejo E, Winston V, Evilia C (2013). "Protein adaptations in archaeal extremophiles". Archaea. 2013: 373275. ... Some acidophilic microorganisms are effective at metal remediation in acidic environments due to proteins found in their ... Chi, A. (2007). "Periplasmic proteins of the extremophile Acidithiobacillus ferrooxidans: a high throughput proteomics analysis ... affecting their protein folding ability under particular conditions. Studying extreme environments on Earth can help ...
"Protein Adaptations in Archaeal Extremophiles". Archaea. 2013: 14. doi:10.1155/2013/373275. PMC 3787623. PMID 24151449. Wong, ... and proteins (i.e. casein) as a carbon source which are oxidized to carbon dioxide via sulphur respiration. T. celer is unable ... Kam-Bo; Bycroft, Mark; Wong, Kam-Bo (March 18, 2003). "Crystal structure of ribosomal protein L30e from the extreme thermophile ... "Effects of Charge-to-Alanine Substitutions on the Stability of Ribosomal Protein L30e from Thermococcus celer". Biochemistry. ...
The archaeal proteins used in these processes are extremely similar to Eukaryotic proteins and so are studied primarily as a ... "CetZ tubulin-like proteins control archaeal cell shape". Nature. Springer Science and Business Media LLC. 519 (7543): 362-365. ... CetZ tubulin-like proteins control archaeal cell shape. Nature 519, 362-365 (2015). https://doi.org/10.1038/nature13983 Garrity ... Due to the salt in method cytoplasmic proteins are structured to fold in the presence of high ionic concentrations. As such, ...
Kinase binding protein CGI-121
This family of proteins also include archaeal homologues. Miyoshi A, Kito K, Aramoto T, Abe Y, Kobayashi N, Ueda N (April 2003 ... In molecular biology, the kinase binding protein CGI-121 family of proteins includes the kinase binding protein CGI-121 and its ... CGI-121 has been shown to bind to the p53-related protein kinase (PRPK). CGI-121 is part of a conserved protein complex, KEOPS ... "Identification of CGI-121, a novel PRPK (p53-related protein kinase)-binding protein". Biochem. Biophys. Res. Commun. 303 (2): ...
Signal recognition particle RNA
Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. Eukaryotic and archaeal 7S RNAs ... The Archaeal SRP contains proteins SRP54 and SRP19. In eukaryotes, the SRP RNA combines with the imported SRP proteins SRP9/14 ... The ribosome resumes protein synthesis, but now the protein is moving through the SRP-receptor transmembrane pore. In this way ... I. Signal recognition protein (SRP) binds to in-vitro-assembled polysomes synthesizing secretory protein". The Journal of Cell ...
... as well as the bacterial protein TubZ, the archaeal protein CetZ, and the FtsZ protein family widespread in bacteria and ... March 2015). "CetZ tubulin-like proteins control archaeal cell shape". Nature. 519 (7543): 362-5. Bibcode:2015Natur.519..362D. ... Tubulin in molecular biology can refer either to the tubulin protein superfamily of globular proteins, or one of the member ... Tubulin is characterized by the evolutionarily conserved Tubulin/FtsZ family, GTPase protein domain. This GTPase protein domain ...
"CetZ tubulin-like proteins control archaeal cell shape". Nature. Springer Science and Business Media LLC. 519 (7543): 362-365. ... During cell division, FtsZ is the first protein to move to the division site, and is essential for recruiting other proteins ... Erickson (2009) proposed how the roles of tubulin-like proteins and actin-like proteins in cell division became reversed in an ... Fission (biology) - Biological process Divisome - A protein complex in bacteria responsible for cell division FtsK - Protein ...
Another quarter encodes proteins unique to the archaeal domain. One observation about the genome is that there are many gene ... However, the possibility that the shared presence of these signature proteins in these archaeal lineages is due to lateral gene ... Additionally, 18 proteins which are uniquely found in members of Thermococci, Archaeoglobus and methanogens have been ... A quarter of the genome encodes preserved proteins whose functions are not yet determined, but are expressed in other archaeons ...
Wardleworth BN, Russell RJ, Bell SD, Taylor GL, White MF (September 2002). "Structure of Alba: an archaeal chromatin protein ... Cerchia, Laura (7 August 1999). "An archaeal chaperonin-based reactor for renaturation of denatured proteins. Extremophile". ... One-third of S. solfataricus encoded proteins have no homologs in other genomes. For the remaining encoded proteins, 40% are ... Sulfolobus strains present different peculiar DNA binding proteins, such as the Sso7d protein family. They stabilize the double ...
Magnesium transporter E
Related regions are found also in archaeal and eukaryotic proteins. They have sizes that vary considerably from 311 residues ... These proteins are capable of transporting Mg2+ and Co2+ but not Ni2+. Multiple alignments contain two highly conserved ... The transport reaction catalyzed by MgtE proteins is: Mg2+ (or Co2+) (out) → Mg2+ (or Co2+) (in) Hattori M, Iwase N, Furuya N, ... Kehres and Maguire suggest that the MgtE proteins are secondary carriers with inwardly directed polarity. Hattori et al. have ...
January 2013). "Promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution". Nucleic ... A ribosomal protein (r-protein or rProtein) is any of the proteins that, in conjunction with rRNA, make up the ribosomal ... Ribosomal proteins are among the most highly conserved proteins across all life forms. Among the 40 proteins found in various ... proteins of the eukaryotic small ribosomal subunit proteins are also present in archaea (no ribosomal protein is exclusively ...
"A novel archaeal regulatory protein, Sta1, activates transcription from viral promoters". Nucleic Acids Res. 34 (17): 4837-4845 ... Protein SvtR was the first crenarchaeal RHH regulator characterized in details and also the first viral coded transcriptional ... regulators within the Archaeal domain. It strongly represses the transcription of the minor structural protein and, to a lesser ... In contrast, at least 10% of its genes were predicted to have of different DNA binding motifs in the proteins they code and ...
RNA polymerase II holoenzyme
"Activation of archaeal transcription by recruitment of the TATA-binding protein". Proc. Natl. Acad. Sci. U.S.A. 100 (9): 5097- ... Protein interference is the process where in some signaling protein interacts, either with the promoter or with some stage of ... It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins[ ... In humans, RNAP II consists of seventeen protein molecules (gene products encoded by POLR2A-L, where the proteins synthesized ...
Archaeal transcription factor B
The archaeal counterpart to these two proteins is TFB, which was first identified in the species Pyrococcus woesei in 1992. ... Archaeal transcription factor B (ATFB or TFB) is a protein family of extrinsic transcription factors that guide the initiation ... Articles with short description, Short description matches Wikidata, Transcription factors, Archaeal genes, Archaea proteins, ... TFBN makes up approximately one third of the protein and contains both a B-finger motif (homologous to the TFIIB B-finger) and ...
ISBN 978-1-904455-27-1. O'Connor EM; Shand RF (2002). "Halocins and sulfolobicins: the emerging story of archaeal protein and ... It is a 31 kDa protein that is heat-labile, loses activity when desalted, and exhibits a broad range of inhibition within the ... Production of these archaeal proteinaceous antimicrobials is a nearly universal feature of the rod-shaped haloarchaea. The ... The molecular mass of the mature HalH4 protein is 34.9 kDa (359 amino acids), processed from a preprotein of 39.6 kDa; the ...
TRNA pseudouridine55 synthase
Gurha P, Gupta R (December 2008). "Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA". RNA. 14 (12): ... of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain ... ". Protein Science. 14 (8): 2201-6. doi:10.1110/ps.051493605. PMC 2279332. PMID 15987897. ...
O'Connor EM, Shand RF (2002). "Halocins and sulfolobicins: the emerging story of archaeal protein and peptide antibiotics". ... "Protein-protein interaction between halocin H7 and halobacterial membrane protein". Nippon Yakugakkai Nenkai Koen Yoshishu. 121 ... Some are large proteins, some small polypeptides (microhalocins). This diversity is surprising for a number of reasons, ... Rdest U, Sturm M (1987). "Bacteriocins from halobacteria". In Burgess R (ed.). Protein Purification: Micro to Macro. New York, ...
Archaeal initiation factors
... are proteins that are used during the translation step of protein synthesis in archaea. The ... Not only are archaeal TIF numbers between that of bacteria and eukaryote numbers, but archaeal initiation factors are seen to ... Binds to the 40S small subunit of the ribosome to help guide the start translation of mRNA into proteins. Can substitute for ... Of the three domains of life, archaea, eukaryotes, and bacteria, the number of archaeal TIFs is somewhere between eukaryotes ...
Linker histone H1 variants
Rather than originating from archaeal histones, it probably evolved from a bacterial protein. Unlike core histones featuring a ... Protein Sci. 3 (4): 575-87. doi:10.1002/pro.5560030406. PMC 2142865. PMID 8003976. (Protein families). ... Individual H1 proteins are often referred to as isoforms or variants. The discovery of H1 variants in calf thymus preceded the ... The linker histone H1 is a protein family forming a critical component of eukaryotic chromatin. H1 histones bind to the linker ...
Seitz EM, Brockman JP, Sandler SJ, Clark AJ, Kowalczykowski SC (1998). "RadA protein is an archaeal RecA protein homolog that ... Eukaryotic Rad51 and its related family members are homologous to the archaeal RadA and bacterial RecA recombinases. Rad51 is ...
She is the maintainer of a database of archaeal proteins and their relations. McKay, Kathryn (January 8, 2018), "Focus on NLM ... Makarova's ongoing research involves comparative genomics, and the genetics and protein functions of archaea. ... the use of oligopeptide frequency data to classify proteins. When Makarova's husband moved to the US to work with Eugene Koonin ...
The bacterial and archaeal proteins are in general smaller than the eukaryotic proteins. They have been suggested to traverse ... Two clusters consist exclusively of animal proteins, a third contains several bacterial and archaeal proteins, a fourth ... and prevents protein unfolding. All of the characterized animal proteins catalyze Ca2+:Na+ exchange although some also ... TMS 7 may be close to TMSs 2 and 3 in the 3-D structure of the protein. The Na+:Ca2+ exchanger plays a central role in cardiac ...
"Affinity transfer to the archaeal extremophilic Sac7d protein by insertion of a CDR". Protein Engineering Design and Selection ... These have the ability to act as specific ligands for the proteins of interest that are needed when the fusion of proteins to ... Switching an anti-IgG binding site between archaeal extremophilic proteins results in Affitins with enhanced pH stability. ... which is a hyperthermostable protein. They are artificially binding proteins with high affinity, small size, and low structural ...
Seitz EM, Brockman JP, Sandler SJ, Clark AJ, Kowalczykowski SC (May 1998). "RadA protein is an archaeal RecA protein homolog ... DNA repair protein RAD51 homolog 1 is a protein encoded by the gene RAD51. The enzyme encoded by this gene is a member of the ... RAD51 family members are homologous to the bacterial RecA, Archaeal RadA and yeast Rad51. The protein is highly conserved in ... This protein can interact with the ssDNA-binding protein RPA, BRCA2, PALB2 and RAD52. The structural basis for Rad51 filament ...
The larger eukaryotic and archaeal proteins possess N- and C-terminal hydrophilic extensions. Some animal proteins, for example ... Protein families, Membrane proteins, Transmembrane proteins, Transmembrane transporters, Transport proteins, Integral membrane ... The smaller proteins are generally of prokaryotic origin while the larger ones are of eukaryotic origin. Most of them possess ... They are members of the rBAT family of mammalian proteins (TC #8.A.9). Most S. cerevisiae amino acid permeases are members of ...
Haseltine CA, Kowalczykowski SC (May 2009). "An archaeal Rad54 protein remodels DNA and stimulates DNA strand exchange by RadA ... This allows a protein complex including Mre11, known as the MRX complex, to bind to DNA, and begins a series of protein-driven ... RecA protein binds to this strand and is either aided by the RecF, RecO, and RecR proteins or stabilized by them. The RecA ... The proteins of the RecA recombinase family of proteins are thought to be descended from a common ancestral recombinase. The ...
NRC-1. This work showed that its proteins are highly acidic, providing an understanding of how proteins may function in high ... Berquist, Brian R.; DasSarma, Shiladitya (2003-10-15). "An Archaeal Chromosomal Autonomously Replicating Sequence Element from ... Post-genomic research in his laboratory established the core and signature proteins in halophilic Archaea, and the function of ... Capes, Melinda D.; DasSarma, Priya; DasSarma, Shiladitya (2012-01-01). "The core and unique proteins of haloarchaea". BMC ...
To prevent the salting out of proteins, H. salinarum encodes mainly acidic proteins. The average isoelectric point of H. ... Whole proteome comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram- ... salinarum proteins is 5.03. These highly acidic proteins are overwhelmingly negative in charge and are able to remain in ... These proteins form a lattice in the membrane. Sulfate residues are abundant on the glycan chains of the glycoprotein, giving ...
... proteins are of interest for biotechnology and industrial use due to their thermostable nature. One application is ... Sediments from ~90m below the seafloor on the Peruvian continental margin are dominated by intact archaeal tetraethers, and a ... Intracellular proteins are not necessarily stable at low pH however, as Sulfolobus species maintain a significant pH gradient ... They are also unique in the sense that the genes encoding the structural proteins of the virus are constantly transcribed and ...
No archaeal enzymes are known that cleave the β-1,3-glycosidic bonds in pseudopeptidoglycan, but it can be degraded by ... Notably, "formation of the disaccharide moiety of the glycopeptide monomer occurs before the transfer to membrane protein by ... Pseudopeptidoglycan is used by the archaeal cell to determine its shape and provide structure to the cell. It is also used to ... It was thought from these large differences in cell wall chemistry that archaeal cell walls and bacterial cell walls have not ...
Bacterial archaeal holin family
Protein families, Membrane proteins, Transmembrane proteins, Transmembrane transporters, Transport proteins, Integral membrane ... The Putative Bacterial Archaeal Holin (BAH) Family (TC# 9.B.185) consists of several uncharacterized proteins. However, these ... Most BAH proteins are between 125 and 140 amino acyl residues (aas) in length and exhibit 4 transmembrane segments (TMSs), ... Portal: Biology As of this edit, this article uses content from "9.B.185 The Putative Bacterial Archaeal Holin (BAH) Family", ...
In archaea, the small archaeal modifier proteins (SAMPs) share the beta-grasp fold and have been shown to play a ubiquitin-like ... Ubiquitin-like proteins (UBLs) are a family of small proteins involved in post-translational modification of other proteins in ... "The dual role of ubiquitin-like protein Urm1 as a protein modifier and sulfur carrier". Protein & Cell. 2 (8): 612-9. doi: ... One additional protein, known as FUBI, is encoded as a fusion protein in the FAU gene, and is proteolytically processed to ...
The component protein, AbpA, shows homology, both at the sequence and structural level, to the bacterial protein TasA, a major ... "Archaeal bundling pili of Pyrobaculum calidifontis reveal similarities between archaeal and bacterial biofilms". Proceedings of ... It is Gram-negative and its cells are surrounded by an S-layer of protein subunits. P. aerophilum is a hyperthermophilic and ... The aggregation is likely to be mediated by archaeal bundling pili (ABP), which assemble into highly ordered bipolar bundles. ...
List of homing endonuclease cutting sites
RCSB Protein Data Bank. Databases of proteins: Swiss Institute of Bioinformatics (SIB); European Bioinformatics Institute (EBI ... Lykke-Andersen J, Thi-Ngoc HP, Garrett RA (November 1994). "DNA substrate specificity and cleavage kinetics of an archaeal ... Databases of proteins: Database of protein structures, solved at atomic resolution: "PDB". Research Collaboratory for ... Jacquier A, Dujon B (June 1985). "An intron-encoded protein is active in a gene conversion process that spreads an intron into ...
A possible homolog of Dot1 was found in archaea which shows the ability to methylate archaeal histone-like protein in recent ... Proteins in eukaryotic transcription. Advances in Protein Chemistry. Vol. 67. Amsterdam: Elsevier Academic Press. pp. 201-222. ... As indicated by their monikers, these differ in the presence of a SET domain, which is a type of protein domain. Human genes ... Branscombe TL, Frankel A, Lee JH, Cook JR, Yang Z, Pestka S, Clarke S (August 2001). "PRMT5 (Janus kinase-binding protein 1) ...
Four types of archaeal tRNA-intron lyase structures have been identified: α4, α′2, (αβ)2, and 𝜀2. All four structures are ... The homodimeric tRNA-intron lyase, α′2 is composed of two α′ subunits that appear to be a fusion protein made up of two α ... Some introns are found in different parts of tRNA genes, especially in archaeal genomes, but these are minor cases. One main ... One way this has been shown is through the conservation of the overall structure of Archaeal endonuclease in Eukaryotic ...
The origins are generally AT-rich tracts that vary based on the archaeal species. The singular archaeal ORC protein recognizes ... In most eukaryotes it is composed of six ORC proteins (ORC1-6), Cdc6, Cdt1, and a heterohexamer of the six MCM proteins (MCM2-7 ... There is a stoichiometric excess of the MCM proteins over the ORC and Cdc6 proteins, indicating that there may be multiple MCM ... The ORC4 protein is known to bind the AT-rich portion of the origin of replication in S. pombe using AT hook motifs. The ...
... which is now known to be the sequence that interacts with the homologue of the archaeal TATA-binding protein (TBP). Also, even ... there are others that have detected notable differences between archaeal and eukaryotic TBP. The archaea protein exhibits a ... "TATA-binding protein recognition and bending of a consensus promoter are protein species dependent". Biochemistry. 47 (27): ... TATA-binding protein (TBP) can be recruited in two ways, by SAGA, a cofactor for RNA polymerase II, or by TFIID. When promoters ...
Transcription factor II B
TFIIB makes protein-protein interactions with the TATA-binding protein (TBP) subunit of transcription factor IID, and the RPB1 ... It is encoded by the TFIIB gene, and is homologous to archaeal transcription factor B and analogous to bacterial sigma factors ... Tang H, Sun X, Reinberg D, Ebright RH (February 1996). "Protein-protein interactions in eukaryotic transcription initiation: ... In particular the bacterial protein σ70 contains domains that bind the polymerase at the same points as the B-linker, B-ribbon ...
... small archaeal modifier proteins) is performed. The sampylation system only uses E1 to guide proteins to the proteosome. ... coordinating the cellular localization of proteins, activating and inactivating proteins, and modulating protein-protein ... The protein modifications can be either a single ubiquitin protein (monoubiquitylation) or a chain of ubiquitin ( ... The monoubiquitination of a protein can have different effects to the polyubiquitination of the same protein. The addition of a ...
Large-conductance mechanosensitive channel
Protein families, Membrane proteins, Transmembrane proteins, Transmembrane transporters, Transport proteins, Integral membrane ... Although bacterial and archaeal mechanosensitive channels differ in conductive and mechanosensitive properties, they share ... MscL in Pfam UMich Orientation of Proteins in Membranes protein/pdbid-2oar As of this edit, this article uses content from "1.A ... The generalized transport reactions are: (a) proteins (in) → proteins (out) (b) ions (out) ⇌ ions (in) (c) osmolytes (in) ⇌ ...
Protein families, Membrane proteins, Transmembrane proteins, Transmembrane transporters, Transport proteins, Integral membrane ... "Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics". Science. 350 (6259): 434-8. ... Articles with short description, Short description matches Wikidata, Protein pages needing a picture, Articles with imported ...
Seitz EM, Brockman JP, Sandler SJ, Clark AJ, Kowalczykowski SC (1998). "RadA protein is an archaeal RecA protein homolog that ... Bank, RCSB Protein Data. "RCSB Protein Data Bank - RCSB PDB". Archived from the original on 2015-04-18. Retrieved 2018-04-14 ... DNA-binding protein RNA-binding protein Nucleoproteins at the US National Library of Medicine Medical Subject Headings (MeSH) ... Currently, over 2000 RNPs can be found in the RCSB Protein Data Bank (PDB). Furthermore, the Protein-RNA Interface Data Base ( ...
Nucleic acids and proteins from Cenarchaeum symbiosum US WO200018909‐A 2001 EMBO Young Investigator Award 2011 Elected member ... "Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia ... archaea used the newly-isolated Nitrososphaera viennensis EN76 to provide the first description of the genes and proteins ...
"The structure of the soluble domain of an archaeal Rieske iron-sulfur protein at 1.1 A resolution". J Mol Biol. 319 (3): 791- ... Studies of proteins adapted to low pH have revealed a few general mechanisms by which proteins can achieve acid stability. In ... Therefore, intracellular proteins do not need to develop acid stability through evolution. However, other acidophiles, such as ... In this case of kinetic acid stability, protein longevity is accomplished across a wide range of pH, both acidic and basic. ...
Ihara K, Umemura T, Katagiri I, Kitajima-Ihara T, Sugiyama Y, Kimura Y, Mukohata Y (January 1999). "Evolution of the archaeal ... Its cell surface membrane contains Archaerhodopsin-3 (AR3), a photoreceptor protein which harvests the energy from sunlight to ... archaeal, and eukaryal diversity in the intestines of Korean people". Journal of Microbiology. 46 (5): 491-501. doi:10.1007/ ... Its β-galactosidase enzyme has been extensively studied to understand how proteins function in low-temperature, high-saline ...
Hansmann, S; Martin W (2000). "Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is ... Guy L, Ettema TJ (2011). "The archaeal 'TACK' superphylum and the origin of eukaryotes". Trends Microbiol. 19 (12): 580-7. doi: ... Barns, SM; Fundyga RE; Jeffries MW; Pace NR (1994). "Remarkable archaeal diversity detected in a Yellowstone National Park hot ... Korarchaeota is regarded as a phylum, which itself is part of the archaeal TACK superphylum which encompasses Thaumarchaeota ( ...
There are two uncommon amino acids-selenocysteine and pyrrolysine-found in a limited number of proteins and encoded by the stop ... and the archaeal chromosomes. It does not apply to organellar genomes (mitochondria and plastids) smaller than ~20-30 kbp, nor ... there are only 20 amino acids normally present in proteins. ( ...
SurE, survival protein E
Mura C, Katz JE, Clarke SG, Eisenberg D (March 2003). "Structure and function of an archaeal homolog of survival protein E ( ... the protein domain surE refers to survival protein E. It was originally found that cells that did not contain this protein, ... This protein consists of two protein domain. One is a large, globular N-terminal domain and the other is a smaller C-terminal ... Protein families, Bacterial proteins, Protein domains, Bacterial enzymes). ...
Transcription elongation factor A protein 1 is a protein that in humans is encoded by the TCEA1 gene. In other organisms, this ... "The cutting edge of archaeal transcription". Emerging Topics in Life Sciences. 2 (4): 517-533. doi:10.1042/ETLS20180014. PMC ... October 2001). "Protein-protein interaction panel using mouse full-length cDNAs". Genome Research. 11 (10): 1758-65. doi: ... Chen HC, England L, Kane CM (July 1992). "Characterization of a HeLa cDNA clone encoding the human SII protein, an elongation ...
List of sequenced plant genomes
April 2019). "The Genome of Cucurbita argyrosperma (Silver-Seed Gourd) Reveals Faster Rates of Protein-Coding Gene and Long ... List of sequenced eukaryotic genomes List of sequenced animal genomes List of sequenced archaeal genomes List of sequenced ... Proteins. 84 (10): 1517-1533. doi:10.1002/prot.25095. PMC 5026580. PMID 27353064. Zhang H, Du X, Dong C, Zheng Z, Mu W, Zhu M, ...
North American beaver
The protein to calorie ratio of a beaver's diet is 40 mg/calorie in summer and 8 mg/calorie for the rest of the year. In ... Gruninger, Robert J.; McAllister, Tim A.; Forster, Robert J. (May 26, 2016). "Bacterial and Archaeal Diversity in the ... Willow is an important protein source and is likely to be available for the longest period of time in a beaver's habitat ...
An anti-CRISPR protein disables type V Cas12a by acetylation | Nature Structural & Molecular Biology
Here we identify the anti-CRISPR protein AcrVA5 and report the mechanisms by which it inhibits CRISPR-Cas12a. Our structural ... Zhiwei Huang and colleagues report structural and biochemical data showing that the anti-CRISPR protein AcrVA5 functions as an ... Phages use anti-CRISPR proteins to deactivate the CRISPR-Cas system. The mechanisms for the inhibition of type I and type II ... that Lys635 acetylation provides sufficient steric hindrance to prevent dsDNA substrates from binding to the Cas protein. Our ...
Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution | Genome...
Overall, our work encourages a systematic search for composite genes across all archaeal major groups, in order to better ... Amino acid optimizations, which lowered the isoelectric point of haloarchaeal proteins, and abundant lateral gene transfers ... genomes-consistent with a long phylogenetic history involving vertical descent and lateral gene transfer-and encode proteins ... have adjusted their lifestyles by incorporating and recycling laterally acquired bacterial genetic fragments into new archaeal ...
Molecules | Free Full-Text | Genetically Encodable Scaffolds for Optimizing Enzyme Function
The use of protein or nucleic acid scaffolds to enhance enzyme properties has been reported for applications such as microbial ... archaeal ferritin ), 2E0Z (archaeal encapsulin ), 1SHS (heat shock protein ), 4V60 (vault ), and 1R2M ( ... archaeal ferritin ), 2E0Z (archaeal encapsulin ), 1SHS (heat shock protein ), 4V60 (vault ), and 1R2M ( ... à-vis protein scaffolds. A key advantage of protein compartments and scaffolds over lipid-delineated organelles is that protein ...
Protein Expression Facility (PEF) - University of Birmingham
The Protein Expression Facility (PEF) provides a recombinant expression and purification service to the University of ... His experience prior to joining the facility supported research in Cyanobacterial proteins and Photosystem II, Archaeal Cas3 ... Protein Expression Facility Team Protein Expression Specialist. Jamie R. M. Webster. Jamie joined the Protein Expression ... Protein expression and purification training can be requested on a 1-2-1 basis if mentoring is required for a specialist piece ...
Archaeal Proteins Entry term(s). Archaeal Gene Products Archaeal Gene Proteins Archaeal Peptides Gene Products, Archaeal Gene ... Archaeal Gene Products. Archaeal Gene Proteins. Archaeal Peptides. Gene Products, Archaeal. Gene Proteins, Archaeal. ... Proteins found in any species of archaeon.. Annotation:. /drug eff /ultrastruct permitted; /physiol permitted for function ... Proteins found in any species of archaeon. Preferred term. ... Archaeal Proteins - Preferred Concept UI. M0029453. Scope note ...
The COG database: an updated version includes eukaryotes | BMC Bioinformatics | Full Text
... proteins encoded in 66 genomes of unicellular organisms. The euk aryotic o rthologous g roups (KOGs) include proteins from 7 ... The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic ... The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for ... The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) ...
SMART: Pfam domain CTP transf like
... lipopolysaccharide core biosynthesis protein KdtB, the bifunctional protein NadR, archaeal FAD synthase RibL [ (PUBMED:20822113 ... Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, ... Many of these proteins are known to use CTP or ATP and release pyrophosphate. ...
BMRB Entry 16320
Title: Solution structure of an archaeal protein SSO6904 from hyperthermophilic Sulfolobus solfataricus PubMed: 19768683. ... A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules Member of ... "Solution structure and calcium binding of protein SSO6904 from the hyperthermophilic archaeon Sulfolobus solfataricus." ... Proteins 78, 474-479 (2010).. Assembly members:. SSO6904, polymer, 99 residues, 11913.870 Da. ...
Pesquisa | Portal Regional da BVS
Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for ... However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein ... Non-essential ribosomal proteins in bacteria and archaea identified using COGs. Galperin, Michael Y; Wolf, Yuri I; Garushyants ... At least three inserts in the N-terminal domain of the S protein are predicted to lead to escape from neutralizing antibodies, ...
Structural and Functional Characterization of Ribosomal Protein Gene Introns in Sponges | PLOS ONE
Accumulating genomic data suggest that RPG introns in many organisms abound with non-protein-coding-RNAs (ncRNAs). These ... Ribosomal protein genes (RPGs) are a powerful tool for studying intron evolution. They exist in all three domains of life and ... Clouet dOrval B, Bortolin ML, Gaspin C, Bachellerie JP (2001) Box C/D RNA guides for the ribose methylation of archaeal tRNAs ... Some non-protein-coding RNAs (ncRNAs) are transcribed from introns in protein-coding or non-protein-coding genes. The ...
NEW (2008) DeCS DESCRIPTORS WITH SCOPE NOTES (UNIT RECORD FORMAT; 21/02/2008
The small subunit of archaeal RIBOSOMES. It is composed of the 16S RIBOSOMAL RNA and about 28 different RIBOSOMAL PROTEINS. HN ... HN - 2008 BX - Protein Kinase A, Type I BX - Protein Kinase Type I, Cyclic AMP-Dependent MH - Cyclic AMP-Dependent Protein ... They are regulatory proteins that play a role in G-protein-coupled receptor densensitization. HN - 2008 MH - G-Protein-Coupled ... The proteins are usually found in association with TRANSTHYRETIN. AN - RETINOL-BINDING PROTEINS and RETINOL-BINDING PROTEINS, ...
Satoshi Kimura, Ph.D. | Harvard Catalyst Profiles | Harvard Catalyst
REPAIRtoire - a database of DNA repair pathways
A human ortholog of archaeal DNA repair protein Hef is defective in Fanconi anemia complementation group M. Meetei AR, Medhurst ... Edit protein. Protein FULL name:. Fanconi anemia group A protein isoform a [Homo sapiens]. FANCA (Homo sapiens) is product of ... Human diseases related to this protein: * FANCONI ANEMIA (#227650 ) FANCA is involved in:. DDS in Homo sapiens HRR in Homo ... A patient-derived mutant form of the Fanconi anemia protein, FANCA, is defective in nuclear accumulation. Kupfer G, Naf D, ...
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and ... No simple dependence between protein evolutionary rate and the number of protein-protein interactions: only the most prolific ... Protein evolution: Causes of trends in amino-acid gain and loss (Reply).. Nature 442: E12. [PDF] [Google Scholar] ... Evaluating the protein coding potential of exonized transposable element sequences.. Biol Direct. 2: 31. [Abstract] [PDF] [ ...
Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes |...
... and some extracellular electron transfer proteins, such as archaeal type IV pilus (PilTC) and archaeal flagellin (FlaD). ... Archaeal metagenome reads were mostly assigned to Euryarchaeota (0.8-2.3%), which showed a significantly (R2=0.19, P , 0.05) ... Zhang J, Jiao S, Lu Y. Biogeographic distribution of bacterial, archaeal and methanogenic communities and their associations ... Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59-60. ...
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Archaeal 4ME diether G1PC and bacterial transmembrane domains per protein across sequences within a given protein family. ... Abbreviations: ACP-GFP, green fluorescent protein-tagged acyl carrier protein; ADF1, actin-depolymerisation factor 1; BSA, ... and number of their delivery to archaeal 4ME diether G1PC lipids and archaeal sn -G1P lipids. Increased transmission of ... Proceedings of the proteins in the legend (one dot per coefficient, continuous lines are plotted based on a data augmentation ...
Cardiff researcher finds chromatin in volcano - News - Cardiff University
However, we realised that we could also apply this technology to any cell type and decided to investigate an archaeal species ... To our surprise, we found histone proteins that form variably-sized sausages-on-a-string. Humans and archaea last shared a ... In humans this task is fulfilled by proteins called histones, around which DNA molecules are repeatedly wrapped to form chains ...
MonarchBase - Protein-coding gene
IPR003958 Transcription factor CBF/NF-Y/archaeal histone. Orthology group. MCL14844 Nucleotide sequence:. ... tata-binding protein-associated phosphoprotein (dr1) [Aedes aegypti] (1e-63). Best NR hit (blastx) class 2 transcription ... GO:0005515 protein binding. GO:0005634 nucleus. GO:0016563 transcription activator activity. GO:0000122 negative regulation of ... protein Dr1 (6e-44). Best NR hit (blastp) ...
Nature`s Fantastic Four | Max Planck Institute for Terrestrial Microbiology
Reconstructed protein sequences in cyanobacteria reveal that protein interactions can evolve without direct selection pressure ... and Archaeal Enoyl-CoA reductase (AER). ... Its secret lies in the enzymes, proteins that act as catalysts ... In another study, Bernhardsgrütter focused on two candidates for the protein scaffold: Propionyl-CoA synthase (PCS) ...
June 2017 - The proteasome: structure, function, and role in the cell
1 3 The archaeal aIF5A proteins and their modification pathways are poorly characterized. DHS homologs are present in all ... acidocaldariusaIF5A is to date the just archaeal protein that the current presence of the hypusine changes continues to be ... Muscleblind-like (MBNL) proteins are vital RNA processing factors in development. coexpressed. * Post author By globaltechbiz ... Green fluorescent proteins (GFP) labeled pole photoreceptors had been produced by mating with transgenic frogs expressing eGFP ...
Protein BLAST (BLASTp)
We are happy to announce an updated bacterial and archaeal representative genomes collection. The current collection contains a ... Protein BLASTDBs are accession-based. The version 5 BLAST (dbV5) protein databases are now accession-based. You can access ... As we described in a previous post, this means they now contain the GI-less proteins from the NCBI Pathogen Project and other ... As we described in a previous post, this means they now contain the gi-less proteins from the NCBI Pathogen Project and other ...
Diamond Publications - Search Results
... and secondly by generating a chimeric archaeal human protein. Both approaches generate proteins that interact with a fourth BRC ... Abstract: Protein-protein interactions (PPIs) are increasingly important targets for drug discovery. Efficient fragment-based ... Here, we report an approach that exploits protein engineering to "humanise" thermophilic archeal surrogate proteins as targets ... Engineering archeal surrogate systems for the development of protein-protein interaction inhibitors against human RAD51 ...
In silico characterization of bacterial chitinase : illuminating its relationship with archaeal and eukaryotic cousins
Sixty-two chitinase sequences from four different groups of organisms were collected from the RCSB Protein Data Bank. ... In silico characterization of bacterial chitinase : illuminating its relationship with archaeal and eukaryotic cousins. , Login ... In silico characterization of bacterial chitinase : illuminating its relationship with archaeal and eukaryotic cousins. ... In silico characterization of bacterial chitinase : illuminating its relationship with archaeal and eukaryotic cousins. ...
Publications | Mysite
A conserved archaeal pathway for tail-anchored membrane. protein insertion. Traffic. 2011, 12(9):1119-23. ... A second chance for protein targeting/folding: Ubiquitination and deubiquitination of nascent proteins. Bioessays. 2022 Mar 31: ... Culver JA and Mariappan M. Membrane Protein Biogenesis: PAT Complex Pats Membrane Proteins into Shape. ... Tail-Anchored Protein Insertion Under ER Stress Conditions: Calcium is Key, The Yale Undergraduate Research Journal. 2021 Vol ...
How to buy cheap Acyclovir online - Approved Online Pharmacy
However, effects of protein P on other proteins in Arr-B organizations. ResultsCell counts over time influenced their ... Conserved shifts in the last archaeal common ancestor or frequent transporter losses in individual Escherichia coli K-12 using ... Death by protein damage in adult males by exposing them to 25 Gray of gamma radiation and determined reduction in germline ... This may be seen as in Arr-A mode for proteins endowed with strong structural plasticity. Nguyen TT, Zhang X, Yuan Y, Chen J-Q ...
Protein Precursors | Profiles RNS
Archaeal Proteins. *Armadillo Domain Proteins. *Arthropod Proteins. *Avian Proteins. *Bacterial Proteins. *Blood Proteins ... "Protein Precursors" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical ... This graph shows the total number of publications written about "Protein Precursors" by people in this website by year, and ... Below are the most recent publications written about "Protein Precursors" by people in Profiles. ...
... concatenated alignment of 53 archaeal genes based on a subset of the "top-ranked marker proteins" from a recent evaluation ... Pfam: The protein families database. Nucleic Acids Res 42: D222-230. Haft DH, Selengut JD, White O. 2003. The TIGRFAMs database ... and archaeal (RF01959) 16S rRNA models from the RFAM database (Kalvari et al., 2018). Average nucleotide identity ... of protein families. Nucl Acids Res 31: 371-373. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal ...
Soluble expression of recombinant proteins in the cytoplasm of Escherichia coli | Microbial Cell Factories | Full Text
Natural protein sources rarely meet the requirements for quantity, ease of isolation or price and hence recombinant technology ... In spite of all these qualities, expression of recombinant proteins with E. coli as the host often results in insoluble and/or ... Eschericia coli is a frequently used host, since it facilitates protein expression by its relative simplicity, its inexpensive ... Recombinant cell factories are constantly employed for the production of protein preparations bound for downstream purification ...
Archaeal Proteins [D12.776.090] Archaeal Proteins * Armadillo Domain Proteins [D12.776.091] Armadillo Domain Proteins ... biosynthesis:Protein Biosynthesis blood:Blood Proteins cerebrospinal fluid:Cerebrospinal Fluid Proteins deficiency:Protein ... general only; prefer specific protein or specific precoordinated protein group terms such as EYE PROTEINS; BACTERIAL PROTEINS; ... DIETARY PROTEINS; etc.; primary protein structure = AMINO ACID SEQUENCE; protein structure referring to protein architecture = ...
Bacterial and archaeal2
- These novel composite genes were likely advantageous for their hosts, since they show significant residence times in haloarchaeal genomes-consistent with a long phylogenetic history involving vertical descent and lateral gene transfer-and encode proteins with optimized isoelectric points. (biomedcentral.com)
- We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eu k aryotic o rthologous g roups. (biomedcentral.com)
- The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms. (biomedcentral.com)
- The eu k aryotic o rthologous g roups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans , the fruit fly Drosophila melanogaster and Homo sapiens ), one plant, Arabidopsis thaliana , two fungi ( Saccharomyces cerevisiae and Schizosaccharomyces pombe ), and the intracellular microsporidian parasite Encephalitozoon cuniculi . (biomedcentral.com)
- The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies. (biomedcentral.com)
- Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, glycerol-3-phosphate cytidyltransferase [ ( PUBMED:16344011 ) ], ADP-heptose synthase, phosphocholine cytidylyltransferase, lipopolysaccharide core biosynthesis protein KdtB, the bifunctional protein NadR, archaeal FAD synthase RibL [ ( PUBMED:20822113 ) ], and a number whose function is unknown. (embl.de)
- In another study, Bernhardsgrütter focused on two candidates for the protein scaffold: Propionyl-CoA synthase (PCS) and Archaeal Enoyl-CoA reductase (AER). (mpg.de)
- Overall, our work encourages a systematic search for composite genes across all archaeal major groups, in order to better understand the origins of novel prokaryotic genes, and in order to test to what extent archaea might have adjusted their lifestyles by incorporating and recycling laterally acquired bacterial genetic fragments into new archaeal genes. (biomedcentral.com)
- There are a range of different mechanisms that can produce novel genes, including de novo genes, synthesized either partly or completely from non-coding DNA [ 12 ], from the divergence of an existing protein-coding sequence beyond the point at which it is recognizable as a homologue (e.g. following gene duplication events), or by fusion or fission of existing protein-coding sequences [ 13 ]. (biomedcentral.com)
- Ribosomal protein genes (RPGs) are a powerful tool for studying intron evolution. (plos.org)
- Due to the presence of practically the same RPs in all eukaryotes and their ancient origin, ribosomal protein genes (RPGs) are a suitable model for studying intron dynamics  . (plos.org)
- Some non-protein-coding RNAs (ncRNAs) are transcribed from introns in protein-coding or non-protein-coding genes. (plos.org)
- 2018) - Archaea reference tree is inferred with IQ-Tree v2.1.2 under the PMSF model from the concatenated alignment of 53 archaeal genes based on a subset of the "top-ranked marker proteins" from a recent evaluation based on minimizing horizontal gene transfer and optimising the recovery of monophyletic lineages (Rinke & Spang et al. (ecogenomic.org)
- To our surprise, we found histone proteins that form variably-sized sausages-on-a-string. (cardiff.ac.uk)
- We chose metabolites with different molecular weight, hydrophobicity, and number of their delivery to archaeal 4ME diether G1PC lipids and archaeal sn -G1P lipids. (silkyence.com)
Maintained in the endoplasmic reticulum1
- 2001 Earlier studies have recommended NFATC1 how the mutant P23H proteins can be misfolded and maintained in the endoplasmic reticulum (ER) (Kaushal and Khorana 1994 Saliba et al. (globaltechbiz.com)
- Ribosome assembly is a complex process that includes coordinated activation of more than 200 non-ribosomal factors and many small nucleolar RNAs (snoRNAs), modification of ribosomal RNA (rRNA) and its correct assembly with ribosomal proteins (RPs)  ,  . (plos.org)
- Identifying 16S rRNA sequences ------------------------------ - Sequences are identified using nhmmer v3.1b2 (Wheeler and Eddy, 2013) with the bacterial (RF00177) and archaeal (RF01959) 16S rRNA models from the RFAM database (Kalvari et al. (ecogenomic.org)
- Evaluation of 16S rRNA Gene Primer Pairs for Monitoring Microbial Community Structures Showed High Reproducibility within and Low Comparability between Datasets Generated with Multiple Archaeal and Bacterial Primer Pairs. (cdc.gov)
- The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. (biomedcentral.com)
- Accumulating genomic data suggest that RPG introns in many organisms abound with non-protein-coding-RNAs (ncRNAs). (plos.org)
- More diverse proteins and organisms in your BLAST results. (nih.gov)
- Sixty-two chitinase sequences from four different groups of organisms were collected from the RCSB Protein Data Bank. (aalto.fi)
- Starting with BLAST+ 2.13.0, the makeblastdb program generates an additional file with the file extension .njs for nucleotide databases or .pjs for protein databases. (nih.gov)
- 30. Sun S, Li X, Mariappan M. Signal sequences encode information for protein folding in the endoplasmic reticulum. (mariappanlab.com)
- Archaeal 4ME diether G1PC and bacterial transmembrane domains per protein across sequences within a given protein family. (silkyence.com)
- Check out our new ClusteredNR database - derived from the default BLAST protein nr database by clustering sequences at 90% identity / 90% length ( details below ). (nih.gov)
- However, we realised that we could also apply this technology to any cell type and decided to investigate an archaeal species that grows in volcanic springs on the island of Kodakara in Japan. (cardiff.ac.uk)
- Green fluorescent proteins (GFP) labeled pole photoreceptors had been produced by mating with transgenic frogs expressing eGFP beneath the opsin promoter (Tam et al. (globaltechbiz.com)
- Protein Precursors" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (wakehealth.edu)
- 21. Sun S and Mariappan M. Lonely ER Membrane Proteins Travel to the Nucleus to Rest in Peace by the Asi Complex. (mariappanlab.com)
- Its secret lies in the enzymes, proteins that act as catalysts to mediate specific chemical reactions, such as the fixation of CO 2 . (mpg.de)
- 29. Heo P, Culver JA, Miao J, Pincet F, Mariappan M. The Get1/2 insertase forms a channel to mediate the insertion of tail-anchored proteins into the ER. (mariappanlab.com)
- 22. Sun S and Mariappan M . C-terminal tail length guides insertion and assembly of membrane proteins. (mariappanlab.com)
- Conserved shifts in the last archaeal common ancestor or frequent transporter losses in individual Escherichia coli K-12 using PCR products. (keynote.cz)
- Their physiology and lifestyle strongly contrast with that of their archaeal ancestors. (biomedcentral.com)
- This graph shows the total number of publications written about "Protein Precursors" by people in this website by year, and whether "Protein Precursors" was a major or minor topic of these publications. (wakehealth.edu)
- The ribosome is a protein-RNA complex, fundamentally the same in all three domains of life, and is the crucial cell component for protein synthesis. (plos.org)
- DNA repair protein that may operate in a postreplication repair or a cell cycle checkpoint function. (genesilico.pl)
- 2004 Tam and Moritz 2006 As seen in additional proteins misfolding disorders long term ER stress because of the build up of mutant proteins ultimately qualified prospects to pole photoreceptor cell loss of life (Lin et al. (globaltechbiz.com)
- In humans this task is fulfilled by proteins called histones, around which DNA molecules are repeatedly wrapped to form chains of structures called nucleosomes. (cardiff.ac.uk)
- It involved numerous genetic events to transform their physiology, as well as amino acid optimizations, which allowed their proteins to remain soluble, resulting in lower isoelectric points than their homologs outside this group [ 3 ]. (biomedcentral.com)
- Fanconi anemia group A protein isoform a [ Homo sapiens ]. (genesilico.pl)
- Here we identify the anti-CRISPR protein AcrVA5 and report the mechanisms by which it inhibits CRISPR-Cas12a. (nature.com)
- Here, we report an approach that exploits protein engineering to "humanise" thermophilic archeal surrogate proteins as targets for small-molecule inhibitor discovery and to exemplify this approach in the development of inhibitors against the PPI between the recombinase RAD51 and tumour suppressor BRCA2. (diamond.ac.uk)
- The Protein Expression Facility (PEF) provides a recombinant expression and purification service to the University of Birmingham Research community. (birmingham.ac.uk)
- The expression systems used by the PEF will enable the recombinant proteins generated to be used in a wide range of downstream applications. (birmingham.ac.uk)
- The PEF provides a central location to undertake recombinant protein expression within a dedicated environment. (birmingham.ac.uk)
- Jamie joined the Protein Expression facility in 2013. (birmingham.ac.uk)
- We deliver a full service for recombinant protein expression and purification, and this will be tailored to needs of the project undertaken. (birmingham.ac.uk)
- Protein expression and purification training can be requested on a 1-2-1 basis if mentoring is required for a specialist piece of work. (birmingham.ac.uk)
- The use of protein or nucleic acid scaffolds to enhance enzyme properties has been reported for applications such as microbial production of chemicals, biosensor development and bioremediation. (mdpi.com)
- As part of the Technology hub the PEF acts as a focal point for advice about all aspects of recombinant protein production. (birmingham.ac.uk)
- Efficient fragment-based drug discovery approaches to tackle PPIs are often stymied by difficulties in the production of stable, unliganded target proteins. (diamond.ac.uk)
- His experience prior to joining the facility supported research in Cyanobacterial proteins and Photosystem II, Archaeal Cas3 and Cas5, the Chromosomal passenger complex and Wallerian Degeneration and since joining the facility has supported colleagues in the college of MDS, LES and School of Chemistry. (birmingham.ac.uk)
- 23. Culver JA and Mariappan M. Membrane Protein Biogenesis: PAT Complex Pats Membrane Proteins into Shape. (mariappanlab.com)
- Phages use anti-CRISPR proteins to deactivate the CRISPR-Cas system. (nature.com)
- As we previously announced , we are offering a ClusteredNR protein database on the web BLAST service that provides faster searches, greater taxonomic reach, and easier to interpret results than the traditional nr database. (nih.gov)
- A cryo-EM structure of the AcrVA5-acetylated MbCas12a reveals that Lys635 acetylation provides sufficient steric hindrance to prevent dsDNA substrates from binding to the Cas protein. (nature.com)