Homology domain binds. Medical search. Frequent questions

Oxysterol-binding protein related-proteins (ORPs) 5 and 8 regulate calcium signaling at specific cell compartments. (nih.gov)
The nickel-containing chain of carbon-monoxide dehydrogenase also has a domain with some sequence similarities to the hybrid cluster proteins. (proteininformationresource.org)
Based on primary sequence comparisons, β subunits are predicted to be modular structures composed of five domains (A-E) that are related to the large family of membrane-associated guanylate kinase proteins. (jneurosci.org)
Considering the large number of putative Ras effector proteins, it is highly desirable to develop computational methods to be able to identify true Ras binding molecules. (crg.es)
Based on a limited sequence homology among members of the Ras association (RA) and Ras binding (RB) sub-domain families of the ubiquitin super-family, we have built structural homology models of Ras proteins in complex with different RA and RB domains, using the FOLD-X software. (crg.es)
The homology models are validated by predicting the effect of mutating hot spot residues in the interface, and residues important for the specificity of interaction with different Ras proteins. (crg.es)
The peptides bind to a novel ligand-binding site of the μHD, which is distinct from those of other distantly related μHD-containing proteins. (rcsb.org)
However, these receptors exhibit a high degree of sequence variability at their NH(2)-terminal domain, which suggests the possibility of receptor-specific interactions with co-regulator proteins. (nih.gov)
Recently, the characteristics of a family of soluble carotenoid-binding proteins (Helical Carotenoid Proteins [HCPs]), paralogs of the N-terminal domain of OCP, were described. (nih.gov)
The recruitment of specific cytosolic proteins to intracellular membranes through binding phosphorylated derivatives of phosphatidylinositol (PtdIns) controls such processes as endocytosis, regulated exocytosis, cytoskeletal organization, and cell signaling. (embl.de)
KH domains are found in a wide variety of proteins including ribosomal proteins, transcription factors, and mRNA processing proteins. (novusbio.com)
Receptor dimerization and autophosphorylation attracts proteins containing Src homology 2 (SH2) or phosphotyrosine binding (PTB) domains including adaptor proteins like FRS2 and GRB2. (springer.com)
Different growth factor receptors were known to bind different constellations of SH2 domain-containing proteins. (the-scientist.com)
IRS proteins bind to the phosphorylated residues on the IR and subsequently recruit the regulatory subunit p85 of PI3K. (jci.org)
Domain commonly found in eukaryotic signalling proteins. (embl.de)
The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. (embl.de)
Pleckstrin homology (PH) domains are small modular domains that occur in a large variety of proteins. (embl.de)
Through these interactions, PH domains play a role in recruiting proteins to different membranes, thus targeting them to appropriate cellular compartments or enabling them to interact with other components of the signal transduction pathways. (embl.de)
Pleckstrin is one of the rare proteins to contains two PH domains. (embl.de)
Regulators of small G-proteins like guanine nucleotide releasing factor GNRP (Ras-GRF) (which contains 2 PH domains), guanine nucleotide exchange proteins like vav, dbl, SoS and Saccharomyces cerevisiae CDC24, GTPase activating proteins like rasGAP and BEM2/IPL2, and the human break point cluster protein bcr. (embl.de)
Cytoskeletal proteins such as dynamin (see IPR001401 ), Caenorhabditis elegans kinesin-like protein unc-104 (see IPR001752 ), spectrin beta-chain, syntrophin (2 PH domains) and S. cerevisiae nuclear migration protein NUM1. (embl.de)
Oxysterol binding proteins OSBP, S. cerevisiae OSH1 and YHR073w. (embl.de)
Several S. cerevisiae proteins involved in cell cycle regulation and bud formation like BEM2, BEM3, BUD4 and the BEM1-binding proteins BOI2 (BEB1) and BOI1 (BOB1). (embl.de)
There are 196127 PH domains in 171590 proteins in SMART's nrdb database. (embl.de)
Taxonomic distribution of proteins containing PH domain. (embl.de)
The complete taxonomic breakdown of all proteins with PH domain is also avaliable . (embl.de)
Click on the protein counts, or double click on taxonomic names to display all proteins containing PH domain in the selected taxonomic class. (embl.de)
Platelet activation allows binding of these proteins, which bridges adjacent platelets. (medscape.com)
However, analogous proteins may have structural homology although this is not a prerequisite. (hindawi.com)
START domain-containing proteins (STARDs) are responsible for lipid metabolism. (medsci.org)
The activity of CDKs is controlled by their binding to coactivator subunits termed Cyclins, as well as by CDK inhibitory proteins termed CKIs. (intechopen.com)
Programmable DNA binding proteins have emerged as an exciting platform for engineering synthetic transcription factors for modulating endogenous gene expression 5 - 11 . (cdc.gov)
Among the established custom DNA binding domains, Cas9 is most easily scaled to facilitate genome-scale perturbations 3 , 4 due to its simplicity of programming relative to zinc finger proteins and transcription activator-like effectors (TALEs). (cdc.gov)

Most members contain an N-terminal pleckstrin homology domain and a highly conserved C-terminal OSBP-like sterol-binding domain. (nih.gov)
Pleckstrin homology domain. (embl.de)
phafin 1) is predicted through gene annotation and contains pleckstrin homology domain. (avivasysbio.com)

This is characterized by marked changes in certain residues making up the phosphoinositide-binding site, formation of a short a-helix in variable loop 2, and a movement of variable loop 3 away from the lipid-binding site. (rcsb.org)
Zinc finger UBDs have a broader range of binding modes including interactions with polar residues. (wikipedia.org)
The other cluster was a relatively open 4Fe cluster with a mix of sulfur and oxygen bridging atoms bound by seven amino acid residues including three cysteines, two glutamates, one histidine and a stable persulfido-cysteine, previously seen only as an intermediate active site species (RESID:AA0269). (proteininformationresource.org)
This region includes two folding domains and all seven of the cofactor binding residues observed in the Desulfovibrio vulgaris structure. (proteininformationresource.org)
There are no totally invariant residues within the PH domain. (embl.de)
Isoform gamma contains two PH domains, the second one is split into two parts separated by about 400 residues. (embl.de)
VH is derived from a single protein domain of 35 residues [ 9 ]. (hindawi.com)
A putative chaperone binding domain was identified within the first 100 residues of DspE. (actahort.org)
Based upon this model, 12 amino acids of DspF were identified as putative exposed substrate-binding residues. (actahort.org)
These results demonstrated that DspF residues L32, E39, E44, H55 and F78 are important for virulence, and yeast-two-hybrid experiments showed that DspF residues E39, E44 and H55 are required for binding to DspE. (actahort.org)

Although there is no extended sequence homology between these two different F-actin binding domains, our experiments show that they are functionally equivalent and provide new insights into the mechanism of microfilament severing. (silverchair.com)
The two DPF motifs, which adopt three-dimensional structures stabilized by sequence-specific intramotif and intermotif interactions, are extensively recognized by the μHD and are both required for binding. (rcsb.org)
Based on the amino acid sequence homology and biological activity in macrophages, Shimamoto et al ( 15 ) identified that HLP was identical to MSP ( 15 ). (spandidos-publications.com)
Was this a function of differences in receptor primary sequence, their locations in the cell, or, possibly, the specificity of the protein kinase domain of the receptor? (the-scientist.com)
STAT5 consists of two closely related family members, STAT5A and STAT5B, which exhibit 96% sequence homology and are functionally redundant. (biolegend.com)

We have previously shown that after T-cell antigen receptor stimulation, Lck binds to ZAP-70 via its Src homology 2 (SH2) domain (LckSH2) and, more recently, that Tyr319 of ZAP-70 is phosphorylated in vivo and plays a positive regulatory role. (pasteur.fr)
Steroid receptor family members share significant homology at their DNA and ligand-binding domains. (nih.gov)
When cytokines bind to their cognate receptor, JAKs phosphorylate the cytokine receptor and subsequently the STATs, which then dissociate from the JAK-receptor complex. (medscape.com)
A. Kashishian, A. Kazlauskas, J.A. Cooper, "Phosphorylation sites in the PDGF receptor with different specificities for binding GAP and PI3 kinase in vivo," The EMBO Journal, 11[4]:1373-82, 1992. (the-scientist.com)
Insulin binds to its receptor on POMC and AgRP neurons, stimulating receptor autophosphorylation and activating its signal cascade. (jci.org)
Leptin binds to its receptor, leading to recruitment of JAKs, which phosphorylate the receptor. (jci.org)
The STAT3 monomer binds to the activated leptin receptor and is phosphorylated by JAKs. (jci.org)
Results DIM, but not I3C, increased adipocyte differentiation through upregulation of peroxisome proliferator‐activated receptor γ and CCAAT/enhancer‐binding protein α. (researchgate.net)
Ligand binding to a receptor leads to the recruitment and activation of an IKK complex comprising IKK alpha and/or IKK beta catalytic subunits and two molecules of NEMO. (abcam.com)
In the canonical signaling pathway , binding of a ligand to a cell surface receptor such as a member of the Toll-like receptor superfamily leads to the recruitment of adaptors (such as TRAF) to the cytoplasmic domain of the receptor (Figure 1). (abcam.com)
They are essential for virus-cell receptor binding and the production of structurally complete virus particles. (medsci.org)
11 , 12 Importantly, homology modeling shows that the SARS-CoV-2 binding domain to the ACE2 receptor is structurally similar to SARS-CoV. (medsci.org)
13 , 14 Despite the presence of amino acid mutations in its receptor binding domain, multiple key amino acids are changed. (medsci.org)
Upon activation, STAT5 is phosphorylated by receptor tyrosine kinases and, in turn, forms homodimers or hererodimers with other family members through its SH2 domains. (biolegend.com)

This protein has significant homology to forkhead/winged-helix transcription factor family. (lu.se)

This gene encodes a member of the oxysterol-binding protein (OSBP) family, a group of intracellular lipid receptors that play a key role in the maintenance of cholesterol balance in the body. (nih.gov)
The N-terminal A domain differs among the four subtypes of Ca 2+ channel β subunits (β 1 -β 4 ) primarily as the result of two duplications of an ancestral gene containing multiple alternatively spliced exons. (jneurosci.org)
[ 4 ] The genetic defect appears to be a region of the gene encoding the KRT14 nonhelical head (E1/V1) domain located between the microsatellite markers D17S798 and D17S957, which are separated by approximately 26.97 cM. (medscape.com)
The capsid gene of the outbreak strain shares high with the Norwalk virus (GI.1) mainly recognizing saliva amino acid homology with the Kashiwa645 GI.3 strain, pre- from secretors with blood groups A and O, while exhibit- viously shown to recognize nonsecretor saliva, as well as ing low or no binding to saliva to nonsecretors and carriers synthetic Lewis a. (cdc.gov)
Die Popeye domain containing (Popdc)-Gene bilden eine evolutionär stark konservierte Genfamilie mit präferenzieller Expression im Herzen und in der Skelettmuskulatur. (uni-wuerzburg.de)
The Popeye domain containing (Popdc) family is a highly evolutionary conserved gene family, which shows no homology to other genes. (uni-wuerzburg.de)
The expression of Popdc1-LacZ transgene as well as Popdc1 protein was elevated in The Popeye domain containing (Popdc) family is a highly evolutionary conserved gene family, which shows no homology to other genes. (uni-wuerzburg.de)
RelA, c-Rel, and RelB contain C-terminal transcriptional activation domains (TADs), which enable them to activate target gene expression. (abcam.com)

A critical step in our approach is to use different templates of Ras complexes, in order to account for the structural variation among the RA and RB domains. (crg.es)
The automated docking procedure PDZ-DocScheme can serve in the generation of a structural context for validation of PDZ domain specificity from mutagenesis and ligand binding data. (huji.ac.il)
Structural homology between the Rap30 DNA-binding domain and linker histone H5: implications for preinitiation complex assembly. (expasy.org)
To further characterize the DspE-DspF interaction, computational methods were used to create a homology-based structural model of DspF. (actahort.org)

Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac. (embl.de)
The syndrome is caused by a mutation in FOXP3, a putative DNA-binding protein. (lu.se)

Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. (nih.gov)
Phox homology domains specifically bind phosphatidylinositol phosphates. (embl.de)
Here we show that two representative Phox homology (PX) domains selectively bind to specific phosphatidylinositol phosphates. (embl.de)

c-Src tyrosine kinase consists of the N-terminal unique region, the Src homology 3 (SH3), SH2, linker, kinase domain, and the regulatory C-terminal tail. (intechopen.com)

To this end, we have designed a family of docking protocols for PDZ domains (termed PDZ-DocScheme) that is based on simulated annealing molecular dynamics and rotamer optimization, and is applicable to the docking of long peptides (20-40 rotatable bonds) to both known PDZ structures and to the more complicated problem of homology models of these domains. (huji.ac.il)

In general, Janus family tyrosine kinases (JAKs) bind to the intracellular components of cytokine receptors, and are, in turn, bound by STATs upon cytokine signaling. (medscape.com)
The N-terminus is extracellular and glycosylated, while the Cterminus is intracellular and harbours a highly conserved 150 amino acid-long Popeye domain. (uni-wuerzburg.de)

The dimerized STAT5 translocates to the nucleus and binds to the STAT5 response element (TTCXXXGAA). (biolegend.com)

A compendium of information regarding PDZ complexes demonstrates that dissimilar C-terminal peptides bind to the same PDZ domain, and different PDZ domains can bind the same peptides. (huji.ac.il)
Adam Kashishian (Fred Hutchinson Cancer Research Center, Seattle): "The question of the specificity of Src homology 2 (SH2) domain/phosphotyrosine interactions has been an important one since the ability of the SH2 domains to bind phosphotyrosine- containing peptides was first shown. (the-scientist.com)

Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. (pdbj.org)

Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids. (embl.de)

We show that a phosphopeptide encompassing the motif harboring Tyr319, YSDP, interacted with LckSH2, although with a lower affinity compared with a phosphopeptide containing the optimal binding motif, YEEI. (pasteur.fr)
Small helical structures are the most common, and examples include ubiquitin-associated domains (UBA), CUE domains, the ubiquitin-interacting motif (UIM), the motif interacting with ubiquitin (MIU), and the VHS protein domain. (wikipedia.org)
One was a 4Fe-4S cubane cluster bound by a novel Cys-2X-Cys-8X-Cys-5X-Cys motif. (proteininformationresource.org)
We have successfully combined two unrelated naturally occurring binding sites, the immunoglobin Fc-binding site of the Z domain and the DNA-binding motif of MyoD bHLH, into a novel stable protein. (hindawi.com)

Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. (crg.es)

These transcription factors share homology through a 300 amino acid N-terminal DNA binding/dimerization domain, called the Rel homology domain (RHD). (abcam.com)

Evidence for functional homology in the F-actin binding domains of gelsolin and alpha-actinin: implications for the requirements of severing and capping. (silverchair.com)
The F-actin binding domains of gelsolin and alpha-actinin compete for the same site on actin filaments with similar binding affinities. (silverchair.com)
Both contain tandem repeats of approximately 125 amino acids, the first of which is shown to contain the actin-binding site. (silverchair.com)
We have replaced the F-actin binding domain in the NH2-terminal half of gelsolin by that of alpha-actinin. (silverchair.com)
The hybrid binds two actin monomers and caps the barbed ends of filaments in the presence or absence of calcium. (silverchair.com)

HGF forms a family with HGF-like protein (HLP), a unique protein with a domain structure similar to that of HGF ( 12 ). (spandidos-publications.com)
The RHD is a platform where family members can form homodimers and heterodimers, enabling them to bind promoters and enhancer regions of genes to modulate their expression. (abcam.com)

Saliva-binding studies have demonstrated that differ- was found between persons of different Lewis or ABO phe- ent NoV strains exhibit different binding patterns ( 14 - 16 ), notypes. (cdc.gov)

In POMC neurons, it diminishes POMC transcription by recruiting Ncor and Hdac1 and by competing with binding sites for phosphorylated STAT3 in the promoter. (jci.org)

Compared with the Desulfovibrio vulgaris hybrid cluster protein, the sequences from Clostridium thermaceticum and Rhodospirillum rubrum have serine rather than glutamate at the seventh binding site (residue 494). (proteininformationresource.org)
As constitutive Alu sequences with high homology were identified at both breakpoints in reversed orientation in the reference genome, we hypothesized that Alu-mediated non-allelic-homologous recombination was responsible for this rearrangement. (bvsalud.org)

It possesses an N-terminal pleckstrin homology (PH) domain that interacts with equal affinity with the second messengers PtdIns(3,4,5)P3 and PtdIns(3,4)P2, generated through insulin and growth factor-mediated activation of phosphoinositide 3-kinase (PI3K). (rcsb.org)
The cap produced by the hybrid binds with lower affinity than that of gelsolin and is not stable: It dissociates from filament ends with a half life of approximately 15 min. (silverchair.com)

Ubiquitin-binding domains (UBDs) are protein domains that recognise and bind non-covalently to ubiquitin through protein-protein interactions. (wikipedia.org)
Most UBDs bind to ubiquitin only weakly, with binding affinities in the low to mid μM range. (wikipedia.org)
and domains similar to those in ubiquitin-conjugating (also known as E2) enzymes. (wikipedia.org)
Most UBDs described to date bind to monoubiquitin and thus do not show a linkage-preference for the differently linked ubiquitin chains. (wikipedia.org)

Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. (embl.de)
Most mutations of FOXP3 are localized in the carboxyl-terminal forkhead DNA binding domain. (lu.se)

Here we have identified Ran-binding protein in the microtubule-organizing center (RanBPM) to be a novel AR-interacting protein by yeast two-hybrid assay and have confirmed this interaction by glutathione S-transferase- and His-tagged pull-down assays. (nih.gov)
In addition, the double mutant (Y42A/L48Q) of the PX domain of Vam7p, reported to cause vacuolar trafficking defects in yeast, has a dramatically decreased level of binding to PtdIns-3-P. These data reveal that the membrane targeting function of the Vam7p PX domain is based on its ability to associate with PtdIns-3-P, analogous to the function of FYVE domains. (embl.de)
Members of a subfamily of these enzymes share a specific domain that was first identified in the yeast Sac1 protein [1]. (embl.de)
Yeast-two-hybrid experiments were conducted to map the chaperone binding domain of DspE. (actahort.org)

abstract = "PDZ domains are important scaffolding modules that typically bind to the C-termini of their interaction partners. (huji.ac.il)

Therefore, amino acids in multifunctional docking sites of Met have been exchanged with specific binding motifs for downstream adaptor molecules in order to investigate the signaling potential of the HGF‑Met signaling pathway. (spandidos-publications.com)

A nonsense mutation in a corresponding region of KRT5 has been found in Dowling-Degos disease and a missense mutation in the V1 domain of KRT5 has been described in patients with epidermolysis bullosa with mottled pigmentation. (medscape.com)
The BRCA2 R3052W mutation fails to complement chemotherapeutic sensitivity and homology-directed repair functions in BRCA2 knockout cells. (frontiersin.org)
Mutation of either Tyr740 or 751 strongly reduced binding of an SH2 protein. (the-scientist.com)

Oxysterol binding protein-related protein-5 is related to invasion and poor prognosis in pancreatic cancer. (nih.gov)
Oxysterol-binding protein-related protein 5 (ORP5) promotes cell proliferation by activation of mTORC1 signaling. (nih.gov)

The binding of PKB to PtdIns(3,4,5)P3/PtdIns(3,4)P2 recruits PKB from the cytosol to the plasma membrane and is also thought to induce a conformational change that converts PKB into a substrate that can be activated by the phosphoinositide-dependent kinase 1 (PDK1). (rcsb.org)
The protein kinase B/AKT and phosphoinositide-dependent protein kinase 1 (PDK1) bind to PIP 3 via their pleckstrin homology (PH) domains. (jci.org)

It may binds to two Zn++ ions through its FYVE zinc finger domain. (avivasysbio.com)

The BRCA2 R3052W mutated protein exacerbates genome instability, is unable to rescue homology-directed repair, and fails to complement cell survival following exposure to PARP inhibitors and crosslinking drugs. (frontiersin.org)

Tyrosine 319 in the interdomain B of ZAP-70 is a binding site for the Src homology 2 domain of Lck. (pasteur.fr)
Several structures of such complexes have been solved, revealing a conserved binding site in the PDZ domain and an extended conformation of the bound peptide. (huji.ac.il)
Discovery and mechanism of a pH-dependent dual-binding-site switch in the interaction of a pair of protein modules. (pdbj.org)

This region is an homology domain that is observed in at least four homeomorphic superfamilies [8] and is presented as an alignment in Figure 1. (proteininformationresource.org)
Their μ homology domains (μHDs) interact with the C-terminal region of an endocytic scaffold protein, Eps15, containing fifteen Asp-Pro-Phe (DPF) motifs. (rcsb.org)

Based on these results, we can establish energy thresholds above, or below which, we can predict with 96% confidence that a RA/RB domain will or will not interact with Ras. (crg.es)

(A) BRCA2 protein schematic depicting domain organization: N-terminus, BRC repeats DNA binding domain (DBD), and C-terminal domain (CTD). (frontiersin.org)

Solution studies with CD also provided evidence of conformational changes taking place upon binding of Ins(1,3,4,5)P4 to the PH domain of PKB. (rcsb.org)

Anatomy20

Organisms11

Chemicals and Drugs110

Analytical, Diagnostic and Therapeutic Techniques and Equipment34

Phenomena and Processes78

Information Science4

Health Care1

Proteins33

Pleckstrin homolo3

Residues10

Sequence5

Receptor14

Significant homology1

Gene8

Structural4

Putative2

Phox3

Kinase domain1

Simulated annealing1

Intracellular2

Nucleus1

Peptides2

Superfamily1

Phosphatidylinositol1

Motif4

Prediction1

Dimerization1

Actin5

Family2

Exhibit1

Stat31

Sequences2

Affinity2

Ubiquitin4

Mutations2

Yeast4

Abstract1

Amino acids1

Mutation3

Oxysterol2

Phosphoinositide2

Zinc1

Genome1

Site3

Region2

Interact1

Repeats1

Evidence1