Yeast saccharomyces protein interaction domains and motifs. Medical search. Frequent questions

Cdc4 was originally identified in the model organism Saccharomyces cerevisiae. (wikipedia.org)
Its 779 amino acids (in S. cerevisiae) are arranged into one F-box domain (approximately 40 amino acids ("F-box" motif)) and 7 WD repeats. (wikipedia.org)
We show here that the SAM domain of Saccharomyces cerevisiae Vts1 binds RNA with the same specificity as Smaug and that Vts1 induces transcript degradation through a mechanism involving the cytoplasmic deadenylase CCR4. (embl.de)
The Saccharomyces cerevisiae branchpoint binding protein (BBP) is a 53 kDa pre-mRNA processing factor with characteristic STARJ/GSG protein organization. (uky.edu)
Structural changes in Mcm5 protein bypass Cdc7-Dbf4 function and reduce replication origin efficiency in Saccharomyces cerevisiae. (yeastgenome.org)
As CXXC1 is orthologous to Saccharomyces cerevisiae Spp1 that links DSB sites to the DSB machinery on the chromosome axis, we propose that these molecular interactions involved in the regulation of meiotic DSB formation are conserved in mouse meiosis. (springer.com)
In Saccharomyces cerevisiae , meiotic DSBs preferentially occur at nucleosome-depleted regions in gene promoters (Ohta et al. (springer.com)
In S. cerevisiae , this interaction is at least in part provided by Spp1 that directly interacts with both methylated H3K4 near DSB sites and the axis-localized protein Mer2 (Acquaviva et al. (springer.com)
Swi2p in Saccharomyces cerevisiae or HRX (ALL-1) in Homo sapiens]. (embl.de)
The pro-region of the Kex2 endoprotease of Saccharomyces cerevisiae is removed by self-processing. (eu.org)
In the yeast Saccharomyces cerevisiae , DNA polymerase ε (Pol ε) synthesizes primarily the leading strand, while DNA polymerase δ (Pol δ) synthesizes primarily the lagging strand and the genes encoding the catalytic subunits of these two polymerases are essential for life. (biomedcentral.com)
In Saccharomyces cerevisiae , the telomere-associated protein Ndj1 is required for bouquet formation. (biorxiv.org)
Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1. (embl-heidelberg.de)
Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. (embl-heidelberg.de)
Here we present genetic results that indicate a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. (embl-heidelberg.de)
Systematic characterization of the protein interaction network and protein complexes in Saccharomyces cerevisiae using tandem affinity purification and mass spectrometry. (leibniz-fli.de)
Collection of domains associated with the protein based on various sources, including the protein coordinates for the domain, a domain Description, a Source and corresponding accession ID, and the number of S. cerevisiae genes that share the same domain. (yeastgenome.org)
A novel cross-phylum family of proteins comprises a KRR1 (YCL059c) gene which is essential for viability of Saccharomyces cerevisiae cells. (nih.gov)

Here we compare the specificity of two budding yeast cyclins, the S-phase cyclin Clb5 and the M-phase cyclin Clb2, in the phosphorylation of 150 Cdk1 (Cdc28) substrates. (nature.com)
Clb5 specificity depended on an interaction between a hydrophobic patch in Clb5 and a short sequence in the substrate (the RXL or Cy motif). (nature.com)
Phosphorylation of Clb5-specific targets during S phase was reduced by replacing Clb5 with Clb2 or by mutating the substrate RXL motif, confirming the importance of Clb5 specificity in vivo . (nature.com)
Figure 2: Clb5 specificity depends on an interaction between the Clb5 hydrophobic patch and an RXL motif in the substrate. (nature.com)
RNA-binding proteins contribute to specificity by interacting with both Ccr4-Not and target mRNAs, but this is not fully understood. (elifesciences.org)
The HMG family of proteins comprises members with multiple HMG domains that bind DNA with low sequence specificity, and members with single HMG domains that recognize specific nucleotide sequences. (embl.de)
We are investigating how Pbx and Meis proteins contribute to the specificity of Hox function in development and how disruption of their activities leads to neoplasia. (stanford.edu)

It resides exclusively in the nucleus because of a single monopartite nuclear localisation sequence (NLS) comprising amino acids 82-85 in the N-terminal domain. (wikipedia.org)
Anteroposterior patterning in Drosophila melanogaster is dependent on the sequence-specific RNA-binding protein Smaug, which binds to and regulates the translation of nanos (nos) mRNA. (embl.de)
Using homology modeling and site-directed mutagenesis, we have localized the RNA-binding surface of the Smaug SAM domain and have elaborated the RNA consensus sequence required for binding. (embl.de)
The QUA1 homodimerization motif found upstream of the KH-QUA2 sequence in other STAPJGSG family members is absent in BBP and replaced by a site for the phylogenetically conserved binding partner, Mud2/U2AF65. (uky.edu)
BBP's name reflects the fact that it binds the conserved RNA sequence, UACUAAC, called the branchpoint motif found near the 3' end of yeast introns. (uky.edu)
One pathway, which has been extensively studied in yeast, is mainly guided by chromatin structure and the other, analyzed in detail in mice, is driven by the sequence-specific DNA-binding PR domain-containing protein 9 (PRDM9). (springer.com)
Download DNA or protein sequence, view genomic context and coordinates. (yeastgenome.org)
Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. (yeastgenome.org)
Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein. (yeastgenome.org)
Using pattern searches and position-dependent matrices, we have extracted the AT-hook motifs present in a non-redundant protein sequence database. (embl.de)
We have classified these motifs into three types according to their sequence similarity and have found that they are prevalent in many eukaryotic nuclear proteins in single or multiple copies. (embl.de)
A beta-hairpin comprising the nuclear localization sequence sustains the self-associated states of nucleosome assembly protein 1. (colorado.edu)
The Plus3 domain structure consists of six alpha helices intervened by a sequence of six beta strands in a mixed alpha/beta topology. (embl-heidelberg.de)
Sequence motifs are small sequences capable of acting as binding sites for a particular transcription factor [ 1 ]. (biomedcentral.com)
Exact approaches usually use the consensus sequence for motif representation, employing some mathematical optimization as the search model. (biomedcentral.com)

TWIST belongs to class B bHLH proteins which are known to form stable heterodimers with members of class A bHLH transcription factors including gene products of E12 and E47, respectively. (uni-marburg.de)
The common plant regulatory factors (CPRFs) from parsley are transcription factors with a basic-leucine-zipper motif that bind to cis-regulatory elements frequently found in promoters of light-regulated genes. (embl-heidelberg.de)
These are frequently activated by fusion to other transcriptional proteins resulting in chimeric transcription factors. (stanford.edu)
Transcription factors are specific proteins that bind to distinct sites on the genome. (biomedcentral.com)

Cdc4 recognizes and binds to phosphorylated target proteins. (wikipedia.org)
Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. (embl.de)
The nucleation-enhancing activity of Bud6 requires both a "core" domain that binds to the formin and a "flank" domain that binds monomeric actin. (nih.gov)
one binds in a groove at the barbed end of the actin monomer in a manner closely resembling the helix of WH2 domains, a motif found in many actin nucleation factors. (nih.gov)
Stephen Kowalczykowski (University of California, Davis, USA) described for the first time the purification of this impressive 3,418-amino-acid protein and reported that it binds RAD51 (the human homolog of bacterial RecA) and promotes RAD51 assembly onto single-stranded DNA. (biomedcentral.com)
Carboxyl-terminal domain III of the delta' subunit of the DNA polymerase III holoenzyme binds delta. (colorado.edu)

This role involves its DNA-binding domain, which is composed of a tandem array of zinc fingers, and PRDM9-dependent trimethylation of histone H3 at lysine 4. (springer.com)
2010 ). PRDM9 includes several functional domains, such as a DNA-binding zinc finger array, a histone lysine methyltransferase PR/SET (PRDI-BF1 and RIZ1 homology) domain, and a Krüppel-associated box (KRAB)-related domain. (springer.com)
The AT-hook is a small DNA-binding protein motif which was first described in the high mobility group non-histone chromosomal protein HMG-I(Y). Since its discovery, this motif has been observed in other DNA-binding proteins from a wide range of organisms. (embl.de)
Furthermore, AT-hook motifs are frequently associated with known functional domains seen in chromatin proteins and in DNA-binding proteins (e.g. histone folds, homeodomains and zinc fingers). (embl.de)
The high-mobility group (HMG) domain is a DNA-binding motif that is shared abundant non-histone components of chromatin and by specific regulators of transcription and cell differentiation. (embl.de)
The complex regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. (embl-heidelberg.de)
Histone variant H2A.Z (Htz1 in yeast) replaces conventional H2A in many nucleosomes. (sdbonline.org)
Swr1 is required for the deposition of histone H2AZ at specific chromosome locations in vivo, and Swr1 and H2AZ commonly regulate a subset of yeast genes. (sdbonline.org)
The histone H2A.F/Z (H2AZ) variant is a functionally distinct, highly conserved histone subgroup that likely represents a separate evolutionary lineage of histone H2A proteins. (sdbonline.org)
Along with PTMs, the partial or complete disassembly of nucleosomes allows the exchange and degradation of pre-existing histone proteins, with the incorporation of newly synthesised histones onto chromatin that can eventually result in the resetting of previous epigenetic marks. (aging-us.com)
Compared to the canonical ones, histone variants contain limited amino acid differences or unique domains with distinct biochemical properties. (aging-us.com)
These dedicated proteins are generally known as histone chaperones and effectively control histone supply and chromatin dynamics [ 8 ]. (aging-us.com)

E.A. Orabi and A.M. English ( 2018 ) Predicting structural and energetic changes in Met -aromatic motifs on methionine oxidation to the sulfoxide and sulfone , Phys. (concordia.ca)
E.A. Orabi and A.M. English ( 2018 ) Modeling protein S-aromatic motifs reveals their structural and redox flexibility, J. Phys Chem. (concordia.ca)

We find that the fission yeast homologues of Tristetraprolin/TTP and Pumilio/Puf (Zfs1 and Puf3) interact with Ccr4-Not via multiple regions within low-complexity sequences, suggestive of a multipartite interface that extends beyond previously defined interactions. (elifesciences.org)
Known as "destabilising motifs", these sequences attract the attention of a group of proteins called Ccr4-Not. (elifesciences.org)
The enzymes that dephosphorylate these three amino acids are classified into four groups on the basis of specific catalytic signatures/domain sequences and substrate preference. (ac.be)
Mgr2p/Romo1 bridges TIM23 to the presequence translocase-associated motor (PAM) and is thought to regulate the lateral release of proteins harboring stop-transfer sequences. (frontiersin.org)
We have developed an approach for detecting motifs in biopolymers sequences. (biomedcentral.com)

The Eukaryotic Linear Motif resource: 2022 release. (eu.org)

Cdc4 protein interacts with Cdc34, an ubiquitin-conjugating enzyme, and Cdc53 in vivo. (wikipedia.org)
The Bud6 binding site on actin overlaps with that of the formin FH2 domain and is also incompatible with inter-subunit contacts in F-actin, suggesting that Bud6 interacts only transiently with actin monomers during filament nucleation. (nih.gov)
To achieve this, WASP interacts with several other proteins including WIP and myosin, a motor protein that moves along actin filaments to generate mechanical forces. (elifesciences.org)
Yeast Krr1p physically and functionally interacts with a novel essential Kri1p, and both proteins are required for 40S ribosome biogenesis in the nucleolus. (nih.gov)

Furthermore, two more highly conserved TWIST motifs NSEEE and WR were analyzed individually to find out their interacting proteins and their role in regulating the TWIST1 transcriptional activity. (uni-marburg.de)
It contains only a limited number of highly conserved amino acids, among which are three positively charged residues that gave the Plus3 domain its name. (embl-heidelberg.de)
Throughout evolution, eukaryotes adopted a network of highly conserved proteins that buffer the positive charges of histones, maintaining their solubility and, therefore, avoiding aberrant interactions with other cellular components. (aging-us.com)

Stern, B. & Nurse, P. A quantitative model for the cdc2 control of S phase and mitosis in fission yeast. (nature.com)
Fisher, D. L. & Nurse, P. A single fission yeast mitotic cyclin B p34 cdc2 kinase promotes both S-phase and mitosis in the absence of G1 cyclins. (nature.com)

Identifying conserved protein complexes between species by constructing interolog networks. (yeastgenome.org)
The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. (duke.edu)
Triangle network motifs predict complexes by complementing high-error interactomes with structural information. (leibniz-fli.de)
Small angle neutron scattering (SANS) provides unique insight into biomacromolecular complexes by combining solvent contrast variation (H2O:D2O exchange) with either natural contrast between different classes of biomolecules (proteins, RNA/DNA, lipids/detergents) and/or by applying artificial contrast, i.e. deuteration of specific biomolecules. (lu.se)
In a first couple of examples, I will show how distance and shape restraints from SANS have helped to improve the uniqueness of structural models for two multi-protein-RNA complexes, in combination with NMR restraints and building blocks from crystallography [1, 2]. (lu.se)

PF06182), appears to be cotrans- cribed with Cphy3780, an ABC-type Na ϩ efflux protein (NCBI accession no. cd03267). (researchgate.net)

I wanted to determine if the TWIST protein or its conserved motifs interact with other regulatory proteins to help to regulate the TWIST transcriptional activity. (uni-marburg.de)
Transcriptional regulation information for a gene, including any predicted DNA binding site motifs ( YeTFaSCo ) for the gene's protein product, as well as any of its targets (genes it regulates) or regulators (genes that regulate it), based on experimental evidence. (yeastgenome.org)
1) Characterize novel families of oncoproteins (Pbx and Meis) that dimerize with and regulate the DNA binding properties of Hox proteins. (stanford.edu)

The prohormone-processing yeast KEX2 protease can act as an intracellular membrane protein or a soluble, secreted endopeptidase. (eu.org)
Deciphering soluble and membrane protein function using yeast systems. (leibniz-fli.de)
D. Martins and A.M. English ( 2014 ) Sod1 oxidation and formation of soluble aggregates in yeast: relevance to sporadic ALS development, Redox Biology 2 , 632-639. (concordia.ca)

Actin-related protein 2/3 (Arp2/3) complex activation by nucleation promoting factors (NPFs) such as WASP, plays an important role in many actin-mediated cellular processes. (elifesciences.org)
Although intracellular signal transduction is often portrayed as a protein kinase 'domino effect', the counterbalancing function of phosphatases, and thus the control of phosphatase activity, is equally relevant to proper regulation of cellular function. (ac.be)
Although viewed as a constitutive housekeeping enzyme in the past, PP2A is a highly regulated phosphatase and is emerging as an important regulator of multiple cellular processes involving protein phosphorylation. (ac.be)
But advances in the understanding of protein phosphatases make now clear that these enzymes are precisely regulated and are as important as kinases in the regulation of cellular processes involving protein phosphorylation. (ac.be)
2 Protein phosphatase 2A (PP2A) is a very abundant - it accounts for as much as 1% of total cellular proteins - ubiquitous and remarkably conserved enzyme. (ac.be)
D. Martins and A.M. English ( 2015 ) Peroxynitrite and hydrogen peroxide elicit a similar cellular stress response mediated by the Ccp1 sensor protein, Free Rad. (concordia.ca)
Our studies have demonstrated that several of the proteins encoded by cellular oncogenes function in fundamental aspects of gene regulation. (stanford.edu)
At the sub-cellular scale, maps document the spatial organization of proteins, RNA, DNA, and metabolites with nanometer precision and temporal acuity on the order of seconds. (stanford.edu)

Journal Article Nucleic Acids Res · August 20, 2021 Chromatin is a tightly packaged structure of DNA and protein within the nucleus of a cell. (duke.edu)

Our results demonstrate that SH3 (Src homology 3) domain-PRM (proline-rich motif) interactions involving multivalent linker proteins play central roles in concentrating NPFs at endocytic sites. (elifesciences.org)
Three of these factors represent new parsley bZIP factors, designated CPRF5-CPRF7, whereas the fourth, named CPRF1-interacting protein (CIP), shows no homology to any other known protein. (embl-heidelberg.de)
Biochemical characterization and homology modeling of a purine-specific ribonucleoside hydrolase from the archaeon Sulfolobus solfataricus: Insights into mechanisms of protein stabilization. (cnr.it)

The second aim of my work was to identify the interacting proteins that could influence the functionality of TWIST using yeast-two-hybrid assay. (uni-marburg.de)
The direct interaction of SEF2 with TWIST was verified in a yeast mating assay and then confirmed in an in vivo NLS-rescue assay using U2-OS cells, showing that SEF2 forms a heterodimer with TWIST protein and co-localized into the nucleus. (uni-marburg.de)
In addition, we identified proteins that interact with the KRAB domain of PRDM9 in yeast two-hybrid assay screens, particularly CXXC1, a member of the COMPASS complex. (springer.com)
An interaction annotation is composed of the interaction type, name of the interactor, assay type (e.g. (yeastgenome.org)

Molecular analysis suggested that Esc2p contributed to silencing in a manner similar to Sir1p and probably helped recruit or stabilize the other Sir proteins, while Htz1p present at HMR assembled a specialized chromatin structure necessary for silencing (Dhillon, 2000). (sdbonline.org)
Given the considerable stability of the nucleosome, eukaryotic cells employ a staggering array of interconnected molecular mechanisms that locally modify the electrostatic interaction between the highly basic histones and the negatively charged DNA molecules. (aging-us.com)
Detection and molecular characterization of a novel BRAF activated domain mutation in follicular variant of papillary thyroid carcinoma. (cnr.it)

In the present work, the crystal structure of Bud32/Cgi121 in complex with ADP revealed that ADP is bound in the catalytic site of Bud32 in a canonical manner characteristic of Protein Kinase A (PKA) family proteins. (nih.gov)
Identification of a cyclin-cdk2 recognition motif present in substrates and p21-like cyclin-dependent kinase inhibitors. (nature.com)

The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. (embl.de)
Post-Transcriptional Regulation by STAR Proteins: Control of RNA Metabolism in Development and Disease (pp. 123-141). (uky.edu)
Short conserved domain in transcriptional regulators. (embl-heidelberg.de)
Isolation and characterization of four novel parsley proteins that interact with the transcriptional regulators CPRF1 and CPRF2. (embl-heidelberg.de)
We are studying the effects and consequences of protein fusion on the transcriptional and transforming activities of these proteins using in vitro and animal models. (stanford.edu)
We demonstrate here that GSK-3 maintains the MLL leukemia stem cell transcriptional program by promoting the conditional association of CREB and its coactivators TORC and CBP with homedomain protein MEIS1, a critical component of the MLL-subordinate program, which in turn facilitates HOX-mediated transcription and transformation. (stanford.edu)
Furthermore, the transcriptional responses of B5 at different temperature by using rice straw as sole carbon sources were also analyzed, based on which the mechanism of lignocellulose degradation at high temperature was revealed that B5 could resist the heat by up-regulating the heat shock proteins (HSP) and then secrete various Carbohydrate-Active enzymes (CAZymes) to realize energy balance. (researchsquare.com)

Evolutionary alignment of Twist proteins from different species, indicate TWIST contain 4 additional conserved regions such as NSEEE, NLS1, NLS2, and WR-domain besides the bHLH motif. (uni-marburg.de)
3,4 BBP/SF1 is essential for viability in organisms spanning the evolutionary spectrum from yeast to Caenorhabditis elegans to mice. (uky.edu)
We have developed in previous work two approaches called Discovery Motifs by Evolutionary Computation (DMEC) [ 17 ] and Discovery Motifs by Memetic Algorithms (DMMA) [ 18 ]. (biomedcentral.com)

Consequently, motif quality is a major determinant of mRNA stability for Puf3 targets in vivo and can be used for the prediction of mRNA targets. (elifesciences.org)

We constructed a model of yeast KEOPS that provides structural insight into the role of Gon7. (nih.gov)
Protein Phosphatase 2A (PP2A) is a widely expressed family of protein phosphatases made of a core dimer, composed of a catalytic (C) subunit and a structural (A) subunit, in association with a third variable regulatory (B) subunit. (ac.be)

In budding yeast, the actin-binding protein Bud6 cooperates with formins Bni1 and Bnr1 to catalyze the assembly of actin filaments. (nih.gov)
Here, we describe the structure of the Bud6 flank domain in complex with actin. (nih.gov)
In yeast, Arp2/3-mediated actin filament assembly drives endocytic membrane invagination and vesicle scission. (elifesciences.org)
These studies provide evidence that WASP and WIP play central roles in establishment of a robust multivalent SH3 domain-PRM network in vivo, giving actin assembly onset at endocytic sites a switch-like behavior. (elifesciences.org)
Actin is one of the most abundant proteins in yeast, mammalian and other eukaryotic cells. (elifesciences.org)
In yeast, a member of the WASP family of proteins promotes the assembly of actin filaments around the site where endocytosis will occur. (elifesciences.org)
However, it was not clear how these proteins work together to trigger actin filaments to assemble at the right place and time. (elifesciences.org)
suggest that WASP and WIP play key roles in establishing the network of proteins needed for actin filaments to assemble during endocytosis. (elifesciences.org)
These attachment sites are linked to actin-bundles that surround the nucleus via an Ndj1-Mps3-Csm4 protein bridge that spans the inner and outer nuclear membranes. (biorxiv.org)

M. Kathiresan and A.M. English ( 2016 ) Targeted proteomics identify metabolism-dependent interactors of yeast cytochrome c peroxidase: Implications in stress response and heme trafficking , Metallomics 8 , 434 -443. (concordia.ca)

Widespread domain in signalling and nuclear proteins. (embl.de)

CDK phosphorylation regulates Mcm3 degradation in budding yeast. (yeastgenome.org)
Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex. (yeastgenome.org)
Using cryo-electron microscopy and biochemical analysis we discovered that an interaction between the HBRCT domain of Dbf4 with Mcm2 serves as an anchoring point, which supports binding of DDK across the MCM2-7 double-hexamer interface and phosphorylation of Mcm4 on the opposite hexamer. (imperial.ac.uk)
1 Reversible protein phosphorylation is an important regulatory mechanism that controls the activities of a myriad of proteins and is thus involved in virtually every major physiological process. (ac.be)
4 While proteins can be phosphorylated on nine amino acids, serine, threonine and tyrosine phosphorylation are by far the most predominant in eukaryotic cells. (ac.be)

The Clb5-specific targets include several proteins (Sld2, Cdc6, Orc6, Mcm3 and Cdh1) involved in early S-phase events. (nature.com)
DSB sites are preferentially located within chromatin loops, while several proteins that are required for DSB formation (Rec114, Mei4, and Mer2) localize on the chromosome axis (Blat et al. (springer.com)

For membrane proteins, a third mechanism, based on the interaction of their transmembrane domain (TMD) with lipid microdomains, must also be considered. (biologists.com)
In this Commentary, I review evidence in favor of the idea that partitioning of TMDs into bilayer domains that are endowed with distinct physico-chemical properties plays a pivotal role in the transport of membrane proteins within the early secretory pathway. (biologists.com)
The combination of such self-organizational phenomena with canonical intermolecular interactions is most likely to control the release of membrane proteins from the ER into the secretory pathway. (biologists.com)
This result and other findings suggested that Mgr2p controls the lateral release of inner membrane proteins harboring a stop-transfer signal that follows an N-terminal amino acid signal. (frontiersin.org)

This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologues. (embl.de)
Classification of nonenzymatic homologues of protein kinases. (leibniz-fli.de)

Donaldson, A. D. The yeast mitotic cyclin Clb2 cannot substitute for S phase cyclins in replication origin firing. (nature.com)
Changing protein-DNA interactions promote ORC binding-site exchange during replication origin licensing. (yeastgenome.org)
DNA replication origins retain mobile licensing proteins. (yeastgenome.org)
Recombination and Pol ζ Rescue Defective DNA Replication upon Impaired CMG Helicase-Pol ε Interaction. (yeastgenome.org)
Yeast heterochromatin regulators Sir2 and Sir3 act directly at euchromatic DNA replication origins. (yeastgenome.org)
HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. (embl.de)
The MCM2-7 protein complex is the precursor of the replicative helicase that unwinds DNA in front of the active replication complex. (biomedcentral.com)
Botchan's work further indicates that Cdc45 has a structure similar to the bacterial recombination protein RecJ, linking replication and recombination. (biomedcentral.com)
Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. (lookformedical.com)

The structure reveals that Cdc6 contributes to origin DNA recognition via its winged helix domain (WHD) and its initiator-specific motif. (imperial.ac.uk)
Alanine scanning of MS2 coat protein reveals protein-phosphate contacts involved in thermodynamic hot spots. (colorado.edu)

Cdc4 (cell division control protein 4) is a substrate recognition component of the SCF (SKP1-CUL1-F-box protein) ubiquitin ligase complex, which acts as a mediator of ubiquitin transfer to target proteins, leading to their subsequent degradation via the ubiquitin-proteasome pathway. (wikipedia.org)
Thus, Sic1 protein degradation is necessary to enter S-phase. (wikipedia.org)
Together these proteins shorten the end of the mRNAs, preparing the molecules for degradation. (elifesciences.org)

Here we report the cryo-EM structure at 3.3 Å resolution of the yeast ORC-Cdc6 bound to an 85-bp ARS1 origin DNA. (imperial.ac.uk)
Cdc6 binding rearranges a short α-helix in the Orc1 AAA+ domain and the Orc2 WHD, leading to the activation of the Cdc6 ATPase and the formation of the three sites for the recruitment of Mcm2-7, none of which are present in ORC alone. (imperial.ac.uk)

PRDM9 is a member of the PRDM family of transcription regulators, but unlike other family members, it contains a Krüppel-associated box (KRAB)-related domain that is predicted to be a potential protein interaction domain. (springer.com)
Many of these proteins are regulators of gene expression. (embl.de)

Crystal structure and mechanism of the Escherichia coli ArnA (PmrI) transformylase domain. (colorado.edu)
This dual sorting mechanism is currently being investigated, and in yeast appears to be regulated by a recently discovered subunit, the Mgr2 protein. (frontiersin.org)

The Nanos protein gradient in Drosophila, required for proper abdominal segmentation, is generated in part via translational repression of its mRNA by Smaug. (embl.de)
The second screening of the yeast clones suggested some promising candidates protein as interacting partners with the NSEEE motif such as ETV5, SURF4, Spastin, Metalloproteinase 2, and ALR-like protein mRNA. (uni-marburg.de)
When a cell needs to make a particular protein, it first copies the instructions from the matching gene into a molecule known as a messenger RNA (or an mRNA for short). (elifesciences.org)
The more mRNA copies it makes, the more protein it can produce. (elifesciences.org)
A simple way to control protein production is to raise or lower the number of these mRNA messages, and living cells have lots of ways to make this happen. (elifesciences.org)

A single-stranded DNA-binding protein that is found in EUKARYOTIC CELLS. (lookformedical.com)

The coat on the budding vesicle comprises two layers, an inner layer of adaptor proteins (gray ovals) and an outer layer that forms a polyhedral cage. (biologists.com)

In Cdc4, the substrate binding domain is built on WD40 domains, which use repeats of 40 amino acids), each forming four anti-parallel beta-strands, to assemble the blades of a so-called beta-propeller. (wikipedia.org)
This substrate interaction region is located C-terminally. (wikipedia.org)
Cdc4 assists there by recruiting target molecules via its C-terminal substrate interaction domain (WD40 repeat domain) to the ubiquitination machinery. (wikipedia.org)

PACE4 (paired basic amino acid cleaving system 4, SPC4) is a calcium-dependent serine endoprotease that can cleave precursor protein at their paired basic amino acid processing sites. (eu.org)
Furin (PACE, paired basic amino acid cleaving enzyme, membrane associated receptor protein) is serine endoprotease responsible for processing a variety of substrates (proparathyroid hormone, transforming growth factor beta 1 precursor, proalbumin, pro-beta-secretase, membrane type-1 matrix metalloproteinase, beta subunit of pro-nerve growth factor and von Willebrand factor). (eu.org)
Yeast prohormone processing enzyme (KEX2 gene product) is a Ca2+-dependent serine protease. (eu.org)
Yeast KEX2 genes encodes an endopeptidase homologous to subtilisin-like serine proteases. (eu.org)

Yeast Stn1 promotes MCM to circumvent Rad53 control of the S phase checkpoint. (yeastgenome.org)

PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. (springer.com)
Here, we show that truncation of the KRAB domain of mouse PRDM9 leads to loss of PRDM9 function and altered meiotic prophase and gametogenesis. (springer.com)
Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs), generated by SPO11 and accessory proteins (de Massy 2013 ). (springer.com)
Here we identified Nup2 in a pool of enriched proteins that co-purify with tagged Ndj1 from meiotic cell extracts. (biorxiv.org)

In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. (embl.de)
The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. (embl.de)
These results suggest that the SAM domain might have a primary role in RNA binding. (embl.de)
Residues that compose the RNA-binding surface are conserved in a subgroup of SAM domain-containing proteins, suggesting that the function of the domain is conserved from yeast to humans. (embl.de)
This includes a central RNA binding site composed of an extended Type I KH domain with an adjacent QUA2 motif. (uky.edu)
Rymond, Brian C. / The branchpoint binding protein : In and out of the spliceosome cycle . (uky.edu)
High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. (embl.de)
AT-hook motifs identified in a wide variety of DNA-binding proteins. (embl.de)
In general, it appears that the AT-hook motif is an auxiliary protein motif cooperating with other DNA-binding activities and facilitating changes in the structure of the DNA either as a polypeptide on its own [e.g. (embl.de)
It is most interesting that this motif seems to be quite specific to known or predicted chromosomal/DNA-binding proteins, suggesting that it may act as a versatile minor groove tether. (embl.de)
This state is determined, in part, by the dynamic binding of proteins to the DNA. (duke.edu)
A ubiquitously expressed telomere-binding protein that is present at TELOMERES throughout the cell cycle. (lookformedical.com)
It is structurally different from TELOMERIC REPEAT BINDING PROTEIN 1 in that it contains basic N-terminal amino acid residues. (lookformedical.com)
Histones are evolutionarily conserved DNA-binding proteins. (aging-us.com)
Continued development of an empirical function for predicting and rationalizing protein-protein binding affinities. (leibniz-fli.de)
E.A. Orabi and A.M. English ( 2016 ) Sulfur-Aromatic Interactions: Modeling Cysteine and Methionine Binding toTyrosinate and Histidinium Ions to Assess Their Influence on Protein Electron Transfer , Isr. (concordia.ca)
Binding sites motifs as predicted by YeTFaSCo . (yeastgenome.org)

The aim of my work is to characterize functional domains in TWIST protein, and to determine the interacting partner for TWIST and its motifs particularly NSEEE and WR. (uni-marburg.de)
First, I focused on functional characterization of the NLS1 and NLS2 domains as potential nuclear localization signals in TWIST. (uni-marburg.de)

Additionally, to understand the role of the TWIST NLS2 in nuclear localization, amino acid at positions 73, 76 and 77 were substituted in this motif. (uni-marburg.de)

The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [ ( PUBMED:9007998 ) ] involved in many biological processes. (embl.de)

Two-hybrid screens using CPRF1 and CPRF2 as "baits" resulted in the isolation of four novel parsley proteins which interact with either CPRF1 or CPRF2 in vivo. (embl-heidelberg.de)

M. Kathiresan, D.Martins and A.M. English ( 2014 ) Respiration triggers heme transfer from cytochrome c peroxidase to catalase in yeast mitochondria , Proc. (concordia.ca)

We discuss the possible roles of the newly identified proteins in CPRF1- and CPRF2-dependent target gene expression. (embl-heidelberg.de)

Downstream of KH-QUA2 are two CCHC-type zinc knuckles and a proline-rich C-terminal interaction domain (Fig. 1A). (uky.edu)

Analysis of food proteins and peptides by mass spectrometry-based techniques. (cnr.it)

The biogenesis of most proteins in the mitochondrial matrix and the inner membrane relies on the function of the TIM23 complex. (frontiersin.org)

Crystal structure of Escherichia coli ArnA (PmrI) decarboxylase domain. (colorado.edu)

The experiments show that WASP, myosin and WIP are recruited to sites where endocytosis is about to occur through specific interactions with other proteins. (elifesciences.org)

Anatomy20

Organisms18

Chemicals and Drugs88

Analytical, Diagnostic and Therapeutic Techniques and Equipment30

Phenomena and Processes98

Disciplines and Occupations2

Technology, Industry, Agriculture1

Information Science8

Health Care1

Cerevisiae18

Specificity7

Sequence15

Transcription Factors4

Binds6

Histone12

20182

Sequences5

20221

Interacts4

Highly conserved3

Fission yeast2

Complexes5

Accession1

Regulate3

Soluble3

Cellular8

Nucleic Aci1

Homology3

Assay4

Molecular3

Kinase2

Transcriptional7

Evolutionary3

Major determinant1

Structural2

Actin9

Metabolism1

Nuclear proteins1

Phosphorylation5

Several proteins2

Membrane proteins4

Homologues2

Replication9

Reveals2

Degradation3

Cdc62

Regulators2

Mechanism2

MRNA5

Eukaryotic cells1

Comprises1

Substrate3

Serine4

Promotes1

Meiotic4

Binding17

Functional2

Amino Acid1

Putative1

Vivo1

Cytochrome1

Gene Expression1

Zinc1

Mass spectrometry1

Biogenesis1

Escherichia1

Occur1