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 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)
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)
Since the last overview of sPLA 2 -binding proteins (sPLA 2 -BPs) 10 years ago, several important discoveries have occurred in this area. (ijbs.com)
Amino acids5
Recurring supersecondary structures characterized by 20 amino acids folding into two alpha helices connected by a non-helical "loop" segment. (wakehealth.edu)
Helix-turn-helix (HTH) consists of two α-helices that constitutes of a right-handed three helical bundle with helices α 2 and α 3 arranged perpendicular to one another joined by a short strand of amino acids (figure below). (vigyansarovar.com)
Helix loop helix are eukaryotic homolog of the HTH motif and are characterized by two ampipathic α -helices (60-90 amino acids) connected by a loop (10-25 amino acids). (vigyansarovar.com)
The two amphipathic helices, particularly the highly conserved hydrophobic amino acids, are thought to mediate dimerization, which is a prerequisite to DNA binding. (vigyansarovar.com)
Amphipathic α-helix - consists of hydrophobic region due to leucine and hydrophilic amino acids outside. (vigyansarovar.com)
Eukaryotic2
The eukaryotic HLH is physically larger than the prokaryotic counterpart HTH motif. (vigyansarovar.com)
The human pathogen Mycoplasma genitalium , a member of the pneumoniae cluster of mycoplasmas, binds to eukaryotic cells by means of its adhesion complex, the Nap. (nature.com)
Consensus sequence1
Using homology modeling and site-directed mutagenesis, we have localized the RNA-binding surface of the Smaug SAM domain and have elaborated the RNAconsensus sequence required for binding. (embl.de)
Regulates1
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)
Protein-protein int1
Helix-turn-helix motif are involved in many processes that includes DNA repair, RNA metabolism, and protein-protein interaction . (vigyansarovar.com)
Ability to bind1
A family of G-protein-coupled receptors that was originally identified by its ability to bind N-formyl peptides such as N-FORMYLMETHIONINE LEUCYL-PHENYLALANINE. (lookformedical.com)
Structural1
DNA binding), and others can be the part of larger structural assemblies. (vigyansarovar.com)
Residues4
In general, transcription factors including this domain are dimeric, each with one helix that contains basic amino acid residues facilitate DNA binding. (vigyansarovar.com)
The motif comprises two α helices, E and F that flank a loop of 12 contiguous residues. (vigyansarovar.com)
Five of the loop residues should contain an oxygen atom and preferably be aspartate or glutamate, as they act as calciumligands (Figure below). (vigyansarovar.com)
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)
Structures3
Supersecondary structures or motifs, are simple and frequent combinations of the secondary structure with a specific geometric arrangement. (vigyansarovar.com)
Both crystal structures and the cryo-EM structure are found in a closed conformation, where the sialic acid binding site in P110 is occluded. (nature.com)
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)
Hydrogen bonds2
α 3 is recognition helix that binds to DNA major groove through a series of hydrogen bonds and various Vander wall forces with exposed bases. (vigyansarovar.com)
b Network of hydrogen bonds in the vicinity of the oligosaccharide-binding site between P140 (blue) and P110N (yellow). (nature.com)
Dimers1
The X-ray structure of the casposase bound to DNA representing the product of integration reveals a tetramer with target DNA bound snugly between two dimers in which single-stranded casposon end binding resembles that of spacer 3'-overhangs. (elifesciences.org)
Glycine2
Residue 6 of the loop must be a glycine because the side chain of any other residue would disturb the structure of the motif. (vigyansarovar.com)
Recently, we determined the crystal structure of the extracellular region of P110 and demonstrated its binding to sialic acid receptors 6 . (nature.com)
Found2
Leucine zipper motifs are usually found as part of a DNA-binding domain in many transcription factors , and are therefore these motifs are involved in regulating gene expression . (vigyansarovar.com)
Now, eight transporters were found to control the uptake and efflux of calcium. (mdpi.com)
Major2
This graph shows the total number of publications written about "Helix-Loop-Helix Motifs" by people in this website by year, and whether "Helix-Loop-Helix Motifs" was a major or minor topic of these publications. (wakehealth.edu)
Its major function is in DNA recognition, as α 3 helix is involved in the recognition and is known as " recognization helix " while another one stabilizes the interaction between DNA and Protein. (vigyansarovar.com)
Here we demonstrate that the sterile-alpha motif (SAM) domain of Smaug functions as an RNA-recognition domain. (embl.de)
Domain4
a P140 contains a large N-terminal domain and a smaller C-terminal domain, which is followed in sequence by a predicted transmembrane helix. (nature.com)
These results suggest that the SAM domain might have a primary role in RNA binding. (embl.de)
The RNA-binding SAM domain of Smaug defines a new family of post-transcriptional regulators. (embl.de)
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)
Shows1
By contrast, the cryo-ET structure shows an open conformation, where the binding site is accessible. (nature.com)
Function1
Some of these motifs are associated with a particular defined function (e.g. (vigyansarovar.com)
Region3
Therefore, entire motif comprising the DNA-binding basic region and the HLH is termed bHLH . (vigyansarovar.com)
This hydrophobic region provides an area for dimerization, allowing the motifs to "zip" together. (vigyansarovar.com)
Furthermore, the hydrophobic leucine region is absolutely required for DNA binding. (vigyansarovar.com)
Content1
As a core metal ion in signaling transduction, calcium content is maintained in dynamic balance under normal circumstances. (mdpi.com)
Form1
Finally, a number of side chains form a hydrophobic core between the α helices and thus must be hydrophobic. (vigyansarovar.com)
Helps1
Most often, one helix is smaller in bHLH, and, because of the flexibility of the loop, helps in dimerization by folding and packing against another helix. (vigyansarovar.com)
AN - coordinate IM with ADENOMA (IM) HN - 2006 BX - Corticotroph Adenoma BX - Pituitary Adenoma, ACTH-Secreting BX - Pituitary Corticotropin-Secreting Adenoma MH - Actin Capping Proteins UI - D051344 MN - D5.750.78.730.32 MN - D12.776.220.525.32 MS - Actin capping proteins are cytoskeletal proteins that bind to the ends of ACTIN FILAMENTS to regulate actin polymerization. (nih.gov)
HN - 2006(1981) BX - Actin-Capping Proteins MH - Actin Depolymerizing Factors UI - D051339 MN - D5.750.78.730.212 MN - D12.776.220.525.212 MS - A family of low MOLECULAR WEIGHT actin-binding proteins found throughout eukaryotes. (nih.gov)
The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. (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)
Its substrate specificity suggests that Tsp may contain a substrate recognition domain, which selectively binds to the nonpolar C-termini of substrate proteins, separate from its catalytic site. (embl.de)
In this work, we show that substrate recognition of Tsp is mediated by a PDZ domain, a small protein module that promotes protein-protein interactions by binding to internal or C-terminal sequences of their partner proteins. (embl.de)
Putative3
Several studies proposed the gating mechanism and putative binding residues by intracellular Ca 2+ . (en-journal.org)
Mouse protein citron, a putative rho/rac effector that binds to the GTP-bound forms of rho and rac. (embl.de)
Systematic deletion mutagenesis of Tsp localized the binding site to amino acids 206-307, a region that completely encompasses the putative PDZ domain (217-301). (embl.de)
Dimer2
These results suggest that LC8 may dissociate from the 320-kDa nNOSalpha dimer upon binding to membrane, thus supporting the view that LC8 may transport nNOSalpha dimer to the varicosity membrane for participation in nitrergic neurotransmission. (embl-heidelberg.de)
Exchange of activating ATP to inactivating ADP triggers short helical segments in the K + -translocating KtrB dimer to organize into two long helices that penetrate deeply into the regulatory RCK domains, thus connecting nucleotide-binding sites and ion gates. (elifesciences.org)
Ligand3
Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. (embl.de)
Here, we present an inactive ADP-bound structure of KtrAB from Vibrio alginolyticus , determined by cryo-electron microscopy, which, combined with EPR spectroscopy and molecular dynamics simulations, uncovers a novel regulatory mechanism for ligand-induced action at a distance. (elifesciences.org)
Initially, binding of a ligand to the RCK domains induces a conformational change. (elifesciences.org)
Mutagenesis1
Site-directed mutagenesis of a surface residue at the peptide binding site of the PDZ domain, valine 229, to Glu or Gln resulted in an increase in the K(M) value but had no effect on the k(cat) value. (embl.de)
PROTEIN12
HN - 2006(1981) BX - Cofilins MH - Actin-Related Protein 2 UI - D051377 MN - D5.750.78.730.246.500 MN - D12.776.220.525.246.500 MS - A PROFILIN binding domain protein that is part of the Arp2-3 complex. (nih.gov)
Arp2-3 complex binds WASP PROTEIN and existing ACTIN FILAMENTS, and it nucleates the formation of new branch point filaments. (nih.gov)
HN - 2006 BX - Arp2-3 Complex MH - Actin-Related Protein 3 UI - D051378 MN - D5.750.78.730.246.750 MN - D12.776.220.525.246.750 MS - A component of the Arp2-3 complex that is related in sequence and structure to ACTIN and that binds ATP. (nih.gov)
It is expressed at higher levels than ARP2 PROTEIN and does not contain a PROFILIN binding domain. (nih.gov)
This investigation demonstrates the presence and binding of the protein LC8 (described as "protein inhibitor of nNOS" or PIN in some reports) to different components of neuronal nitric oxide synthase (nNOS) in nitrergic varicosities of mice gut. (embl-heidelberg.de)
Because the Ca 2+ binding motif is embedded inside channel protein according to defined structure, it is still unclear how intracellular Ca 2+ moves to its deep binding pocket effectively. (en-journal.org)
Many eukaryotic protein kinases are activated by phosphorylation on a specific conserved residue in the regulatory activation loop, a post-translational modification thought to stabilize the active DFG-In state of the catalytic domain. (elifesciences.org)
The enzymes that catalyze this process, called protein kinases, are themselves controlled by the phosphorylation of a flexible region called the activation loop. (elifesciences.org)
show that the static model is incorrect in a protein kinase called Aurora A. In this enzyme, the phosphorylated activation loop continues to switch back and forth between active and inactive states. (elifesciences.org)
The isolated PDZ domain (amino acids 206-334) is capable of folding into a well-behaved structure and binds to a nonpolar peptide with a dissociation constant (K(D)) of 1.9 microM, similar to that of the intact Tsp protein. (embl.de)
DEC-205 (CD205), a member of the macrophage mannose receptor protein family, is the prototypic endocytic receptor of dendritic cells, whose ligands include phosphorothioated cytosine-guanosine (CpG) oligonucleotides, a motif often seen in bacterial or viral DNA. (uci.edu)
Structure5
It is related in sequence and structure to ACTIN and binds ATP. (nih.gov)
Recently, the structure determination of a fungal Nectria haematococca TMEM16 (nhTMEM16) scramblase by X-ray crystallography and a mouse ANO1 by cryo-electron microscopy has provided the insight in molecular architecture underlying phospholipid scrambling and Ca 2+ binding. (en-journal.org)
All known cases have a common structure consisting of two perpendicular anti-parallel beta sheets, followed by a C-terminal amphipathic helix. (embl.de)
PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (beta-A to beta-F) and two alpha-helices, A and B, compactly arranged in a globular structure. (embl.de)
The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands. (embl.de)
Inactive1
These studies, along with in vitro nitric oxide assays, show that in gut nitrergic nerve varicosities 1) all cytosolic serine847-phosphorylated nNOS was catalytically inactive and bound with LC8, and 2) membrane-associated nNOS consisted of catalytically active, CaM-bound and catalytically inactive, CaM-lacking, serine847-phosphorylated nNOSalpha dimers, both of which lacked LC8. (embl-heidelberg.de)
Activation2
For many years it had been thought that the purpose of activation loop phosphorylation was to clamp the otherwise flexible activation loop in an active state that allows molecules that need to be phosphorylated to bind to the kinase. (elifesciences.org)
However, new methods and approaches now mean it is possible to visualize how the position of the activation loop changes as it moves in solution. (elifesciences.org)
Forms1
The LC8 immunoprecipitate (IP) showed three nNOS bands, suggesting that LC8 was bound with all three forms of nNOS but dissociated from them during SDS-PAGE. (embl-heidelberg.de)
Site2
Crystal structures of the inhibitors in the nNOS active site confirm the predicted non-intramolecular hydrogen bonded binding mode. (embl-heidelberg.de)
Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids. (embl.de)
Present1
Studies using LC8 IP and supernatant and probed with anti-CaM showed that LC8 was not associated with CaM-bound 320-kDa nNOS but was present in the CaM-lacking fraction. (embl-heidelberg.de)