The eukaryotic signature proteins have no homology to proteins in other domains of life, but appear to be universal among ... The presence of eukaryotic biomarkers in archaea points towards an archaeal origin. The genomes of Asgard archaea have plenty ... Motor proteins of microtubules, dynein and kinesin, and myosin of actin filaments, provide dynamic character of the network. ... They include the proteins of the cytoskeleton, the complex transcription machinery, the membrane-sorting systems, the nuclear ...

... archaeal and plastid-encoded (i.e. chloroplasts, cyanelles, apicoplasts, non-photosynthetic plastids) proteins families or ... protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein ... CATH-Gene3D Describes protein families and domain architectures in complete genomes. Protein families are formed using a Markov ... The proteins in UniProtKB are also the central protein entities in InterPro. Information regarding which signatures ...

Heterotrimeric G proteins 1996 - Green fluorescent protein 1996 - CDK/cyclin complex 1996 - Kinesin motor protein 1997 - GroEL/ ... Archaeal rubredoxins account for many of the highest-resolution small structures in the PDB. 1971 - Insulin (PDB file 1INS) is ... It was used in Anfinsen's seminal research on protein folding which led to the concept that a protein's 3-dimensional structure ... 2000 - AAA+ ATPase 2002 - Ankyrin repeats 2003 - TOP7 protein design 2004 - Cyanobacterial Circadian clock proteins 2004 - ...

Protein pages needing a picture, Protein biosynthesis, Protein domains). ... As a family of elongation factors, EF-Tu also includes its eukaryotic and archaeal homolog, the alpha subunit of eEF-1 (EF-1A ... EF-Tu is a monomeric protein with molecular weight around 43 kDa in Escherichia coli. The protein consists of three structural ... This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. ...

The Putative Bacterial Archaeal Holin (BAH) Family Lysin Lytic cycle Wang IN, Smith DL, Young R (2002). "Holins: the protein ... Examples include the S protein from lambdoid phage 21 and the Hol3626 protein from Clostridium perfringens bacteriophage Ф3626 ... Shi Y, Yan Y, Ji W, Du B, Meng X, Wang H, Sun J (March 2012). "Characterization and determination of holin protein of ... While canonical holins act by forming large pores, pinholins such as the S protein of lambdoid phage 21 act by forming ...

Ensembl Human Protein Reference Database (HPRD) Sequence analysis UniProt List of sequenced eukaryotic genomes List of ... sequenced archaeal genomes RefSeq - the Reference Sequence Database Geneious - includes a GenBank Submission Tool Open science ... annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and ...

... a reaction which is important in de novo purine biosynthesis in archaeal species. In most cases this single-domain protein is ... "Crystal structure of Methanobacterium thermoautotrophicum conserved protein MTH1020 reveals an NTN-hydrolase fold". Proteins. ... The protein is structurally similar to members of the N-terminal nucleophile (NTN) hydrolase superfamily. A deep pocket was in ... This article incorporates text from the public domain Pfam and InterPro: IPR020600 Portal: Biology v t e (Protein domains, EC ...

SecY protein Translocon Protein targeting Osborne AR, Rapoport TA, van den Berg B (2005). "Protein translocation by the Sec61/ ... The eukaryotic Sec61β is however homologous to the archaeal "SecG", leading some authors to refer to the archaeal complex as ... Protein pages needing a picture, Integral membrane proteins, Secretion). ... During protein translocation, the plug is moved out of the way, and a polypeptide chain is moved from the cytoplasmic funnel, ...

The DNA-PKcs protein is the critical element in the center of NHEJ. Using DNA-PKcs KO cell lines or inhibition of DNA-PKcs does ... The archaeal NHEJ system in Methanocella paludicola have a homodimeric Ku, but the three functions of LigD are broken up into ... Ku may function as a docking site for other NHEJ proteins, and is known to interact with the DNA ligase IV complex and XLF. End ... In yeast, Sir2 was originally identified as an NHEJ protein, but is now known to be required for NHEJ only because it is ...

3,928 protein-coding sequences were identified, and 1,822 protein-coding sequences were appointed to one of the 457 RAST ... RAST, Rapid Annotation using Subsystem Technology, is a server that generates bacterial and archaeal genome annotations. The ... The gyrB gene, subunit B protein, is a type II topoisomerase that is essential for DNA replication. This gene is conserved ...

Protein binding can also strip solvent off of DNA and convert it to the A form, as revealed by the structure of several ... A-form DNA is believed to be one of the adaptations of hyperthermophilic archaeal viruses to harsh environmental conditions in ... A-DNA can be derived from a few processes, including dehydration and protein binding. Dehydration of DNA drives it into the A ... In this model, ATP hydrolysis is used to drive protein conformational changes that alternatively dehydrate and rehydrate the ...

The V-Type ATPase is similar to the archaeal (so called) A-Type ATP synthase, a fact that supports an archaeal origin of ... The Vma21 protein assists in assembly of the V-ATPase, and XMEA associated mutations result in decreased activity of the V- ... These associated proteins are essential for Vo domain assembly and are termed Vma12p, Vma21p, and Vma22p. Two of the three ... It has been shown how the V-ATPase structure of the ancestral form consisting of two different proteins evolves into the fungi ...

The prototypical holin is the lambda phage S protein, which assists the lambda phage R protein (lysin). All holins embed ... Quemin ER, Quax TE (5 June 2015). "Archaeal viruses at the cell envelope: entry and egress". Frontiers in Microbiology. 6: 552 ... Unlike most antibiotics, proteins are prone to antibody recognition and binding, which means that lysins could be ineffective ... In order to solve such a problem, phage viruses synthesize another protein called holin which binds to the cell membrane and ...

VP3 is a membrane protein that does not appears to be exposed to the external environment. It may be organised to form a shell ... Infection appears to be productive without lysis of the host like may of the archaeal viruses. Exit is likely to be by budding ... Two of these encode the structural proteins VP3 and VP4. Another (VP8) seems likely to be an ATPase. The functions of the ... The genome does not appear to be associated with a nucleoprotein.[citation needed] The spike protein (VP4) is glycosylated. The ...

The evolutionary structure and range of the histone protein-protein and DNA-protein interactions of the histone fold proteins ... These peptide chains can be found in the archaeal histones, which could have come from eukaryotic H3-H4 tetramer. The archaeal ... When just looking at the histone fold motif in the Drosophila the protein-protein and the protein DNA interaction of the core ... confirmed that a histone-like substructure exists in these proteins, with the individual proteins folding into the canonical ...

... proto-oncogene proteins c-cbl MeSH D08.811.464.938.750.562 - proto-oncogene proteins c-mdm2 MeSH D08.811.464.938.750.750 - skp ... archaeal MeSH D08.811.399.403.741.300 - dna topoisomerases, type ii, bacterial MeSH D08.811.399.403.741.300.500 - dna gyrase ... gtp-binding protein alpha subunits MeSH D08.811.277.040.330.300.200.100.100 - gtp-binding protein alpha subunits, g12-g13 MeSH ... gtp-binding protein alpha subunit, gi2 MeSH D08.811.277.040.330.300.200.100.300 - gtp-binding protein alpha subunits, gq-g11 ...

Archaeal Mevalonate Pathway II). Several key enzymes can be activated through DNA transcriptional regulation on activation of ... SREBP (sterol regulatory element-binding protein-1 and -2). This intracellular sensor detects low cholesterol levels and ... Archaeal Mevalonate Pathway I). A third mevalonate pathway variant found in Thermoplasma acidophilum, phosphorylates mevalonate ...

The recently elucidated archaeal flagellum, or archaellum, is analogous-but not homologous-to the bacterial one. In addition to ... The ion pump later became the motor protein. This was followed by the emergence of the proto-flagellar filament as part of the ... Regarding the origin of the individual protein components, a paper on the evolution of dyneins shows that the more complex ... Gibbons IR (1995). "Dynein family of motor proteins: present status and future questions". Cell Motility and the Cytoskeleton. ...

Tertiary Protein Structure and Folds: section 4.3.2.1. From Principles of Protein Structure, Comparative Protein Modelling, and ... as shown for the 1QRE archaeal carbonic anhydrase at right. Other examples are the lipid A synthesis enzyme LpxA and insect ... However, several notable exceptions include the Outer Surface Protein A (OspA) variants and the Single Layer β-sheet Proteins ( ... Hutchinson EG, Thornton JM (1990). "HERA--a program to draw schematic diagrams of protein secondary structures". Proteins. 8 (3 ...

The basic unit of a protein network is the protein-protein interaction (PPI). While there are numerous methods to study PPIs, ... but not archaeal) translation. Although such predictions may be based on single interactions, usually several interactions are ... For instance, even within a proteome two proteins may interact but their paralogs may not. Each protein-protein interactome may ... The yeast interactome, i.e. all protein-protein interactions among proteins of Saccharomyces cerevisiae, has been estimated to ...

Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein . Human AWP1 protein ( ... Archaeal AN1 domains are also linked to transmembrane helices, and domains such as DNAJ and SCP/PR1. These fusions suggest ... Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 ... Duan W, Sun B, Li TW, Tan BJ, Lee MK, Teo TS (October 2000). "Cloning and characterization of AWP1, a novel protein that ...

Whereas most 7-transmembrane proteins are G protein-coupled receptors that open other ion channels indirectly via second ... February 2003). "Archaeal-type rhodopsins in Chlamydomonas: model structure and intracellular localization". Biochemical and ... In terms of structure, channelrhodopsins are retinylidene proteins. They are seven-transmembrane proteins like rhodopsin, and ... This change introduces a further one in the transmembrane protein, opening the pore to at least 6 Å. Within milliseconds, the ...

A sigma factor (σ factor or specificity factor) is a protein needed for initiation of transcription in bacteria. It is a ... It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB. The specific sigma factor used to initiate ... Doing so, other heatshock proteins are expressed, which enable the cell to survive higher temperatures. Some of the enzymes ... Burton SP, Burton ZF (6 November 2014). "The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs". ...

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 ...

The yeast protein, called the nuclear division Rft1 protein (TC# 2.A.66.3.1), is 574 aas with 12 putative TMSs. The homologue ... However, archaeal and eukaryotic homologues are now recognized. The mechanism of energy coupling is not established, but ... Another MVF protein, MurJ, functions as a peptidoglycan biosynthesis protein. A 3-d structural model shows that MurJ contains a ... protein with a cytoplasmic ATP-binding domain (MPA1-C; TC# 3.C.3) as well as an outer membrane auxiliary protein (OMA; TC #3.C. ...

... which is a prerequisite for the next round of protein synthesis. The large ribosomal subunit has a role in protein folding both ... Due to the differences, archaeal 50S are less sensitive to some antibiotics that target bacterial 50S. 50S includes the ... provides a binding site for the G-protein factors (assists initiation, elongation, and termination), and helps protein folding ... The newly synthesized protein needs full access to the large subunit to fold; this process may take a period of time (5 minutes ...

Asgard members encode many eukaryotic signature proteins, including novel GTPases, membrane-remodelling proteins like ESCRT and ... Two other archaeal phyla, both outside of Asgard, were found to also have tails in 2018. In January 2020, scientists found ... These mobile elements do not encode recognizable viral hallmark proteins and could represent either novel types of viruses or ... October 4, 2013). "Quantitative and phylogenetic study of the Deep Sea Archaeal Group in sediments of the Arctic mid-ocean ...

Previously described mRNA, protein and chromosome sequences have the weaknesses of not providing explicit genomic coordinates ... analysis Sequence profiling tool Sequence motif UniProt List of sequenced eukaryotic genomes List of sequenced archaeal genomes ... July 2009). "The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse ... Targeted Loci: This project records molecular markers, specially protein-coding and ribosomal RNA loci that are used for ...

The genus name, Salterprovirus, is derived from salty terminal protein virus, as the linear dsDNA genome has proteins attached ... Hong C, Pietilä MK, Fu CJ, Schmid MF, Bamford DH, Chiu W (February 2015). "Lemon-shaped halo archaeal virus His1 with uniform ... including a gene specifying a protein-primed DNA polymerase (B-family). The ends of the genome have a protein attached. The ... Pietilä MK, Atanasova NS, Oksanen HM, Bamford DH (June 2013). "Modified coat protein forms the flexible spindle-shaped virion ...

Heat shock proteins, Moonlighting proteins, Molecular chaperones, Protein folding). ... While there are differences between eukaryotic, bacterial and archaeal chaperonins, the general structure and mechanism are ... The energy to fold proteins is supplied by non-covalent interactions between the amino acid side chains of each protein, and by ... Molecular chaperones catalyze protein refolding by accelerating partial unfolding of misfolded proteins, aided by energy ...