Catalytic core catalytic domain. Medical search. Frequent questions

The catalytic core domain contains three highly conserved residues Asp64, Asp116 and Glu152 (the DDE motif) that are essential for the catalytic activity of IN. (biomedcentral.com)
Oxr1p belongs to the group of TLDc domain containing proteins that are highly conserved in higher eukaryotes. (upstate.edu)
The primary sequences of ePK catalytic domains are highly conserved, indicating a common ancestry. (dissertation.com)
A highly conserved catalytic Cys, identified as the acylation site, is located near the N terminus of α3. (expasy.org)

10521258 10.1021/bi991362q 1 'High Resolution Structure of the Catalytic Domain of Avian Sarcoma Virus Integrase' J.Mol.Biol. (rcsb.org)

IN is a 32 kDa protein with three distinct structural domains, the N-terminal zinc-binding domain, the central catalytic core domain and the C-terminal domain. (biomedcentral.com)
Click on the protein counts, or double click on taxonomic names to display all proteins containing DEXDc domain in the selected taxonomic class. (embl.de)
We recently described the structure of M. musculus RNF213 (PDB: 6TAX) and characterized its enzymatic activity, revealing it as a large monomeric protein with a functional dynein-like AAA (ATPases Associated with diverse cellular Activities) core that exists alongside a novel E3 ligase module ( 16 ). (biorxiv.org)
This may be explained because the SOS1 protein adopts an auto-inhibited conformation dependent on multiple domain-to-domain interactions that cooperate to block access of the SOS1 catalytic core to its Ras-GTPase targets [7] . (bionity.com)
Starting from a manually aligned and annotated map of 492 typical human protein kinase domains, I first explored the origin of ePKs using a modified BLAST method in various species. (dissertation.com)
BTK, a TEC-family tyrosine kinase activated by the B-cell antigen receptor, contains a variety of regulatory domains and it is subject to complex regulation by membrane phospholipids, protein ligands, phosphorylation, and dimerization. (elifesciences.org)
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)
During a processive reaction, the DNA strand (blue) anneals to the alignment region in the TR (pink), the catalytic TERT protein (grey) reverse transcribes the RNA template (red), adding 6 deoxyribonucleotides (blue) to the DNA strand. (asu.edu)
We also analyzed the evolutionary modularity of a data set of α -amylase catalytic domain homologs, and the dynamic modularity of the Niemann-Pick C1 (NPC1) protein N-terminal domain. (biomedcentral.com)
We still use a similar thought relating protein evolution, since domains are accepted as the protein evolutionary modules, and its modular reuse has been demonstrated in all domains of life [ 2 ]. (biomedcentral.com)
Os08t0125300-01 Integrase, catalytic core domain containing protein. (or.jp)

We have previously determined the structure of various domains within this family and characterized how these proteins heterodimerize, how they bind to DNA but the catalytic reaction remains elusive and what determines the preferential heterodimer formation is also not known. (uu.nl)
There are 499956 DEXDc domains in 496764 proteins in SMART's nrdb database. (embl.de)
Taxonomic distribution of proteins containing DEXDc domain. (embl.de)
The complete taxonomic breakdown of all proteins with DEXDc domain is also avaliable . (embl.de)
Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organisms. (embl.de)
IBR domain is a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. (embl.de)
There are 28130 IBR domains in 15655 proteins in SMART's nrdb database. (embl.de)
Percentage points are related to the number of proteins with IBR domain which could be assigned to a KEGG orthologous group, and not all proteins containing IBR domain. (embl.de)
The normal rate of Ras catalytic GTPase (GTP hydrolysis) activity can be increased by proteins of the RasGAP family, which bind to Ras and increase its catalytic rate by a factor of one thousand - in effect, increasing the rate at which Ras is inactivated. (bionity.com)
There are 1533 E2_bind domains in 1532 proteins in SMART's nrdb database. (embl-heidelberg.de)
Taxonomic distribution of proteins containing E2_bind domain. (embl-heidelberg.de)
The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. (thermofisher.com)
The Telomerase RNP contains two essential core components, the telomerase reverse transcriptase (TERT) and the telomerase RNA (TR), along with other species-specific telomerase associated proteins. (asu.edu)
The NlpC/P60 LRAT-type family includes lecithin-retinol acyltransferase (LRAT), nematode developmental regulator Egl-26, class II tumor suppressor H-rev107 and proteins from poxviruses and animal positive-strand RNA viruses, which share a common catalytic domain fold and the unconventional active site. (expasy.org)
All known catalytic activities require the presence of both proteins. (lu.se)

The site itself is composed of the C domain β sheet and particular residues from the N domain. (wikipedia.org)
The interface between the core and terminal domains is composed primarily of small hydrophobic residues. (proteopedia.org)
It has a typical right-hand DNA polymerase fold, with an active site formed by a palm holding the catalytic residues, a thumb that binds the primer:template DNA and fingers interacting with incoming nucleotide, and the N and Exo domains extend from the finger toward the thumb. (cathdb.info)
To our knowledge, there is no other method attempting to identify sub-domain architecture from the correlation among residues. (biomedcentral.com)
We were able to describe functional/structural sub-domain architecture related to key residues for starch cleavage, calcium, and chloride binding sites in the α -amylase, and sterol opening-defining modules and disease-related residues in the NPC1. (biomedcentral.com)

His343 is the catalytic residue in CRAT. (wikipedia.org)
This domain includes a mostly solvent exposed loop (residue 33-43) preceding the beta hairpin containing the flaps (residue 44-63). (proteopedia.org)
Linker regions and domains are labeled, residue numbering shows BTK domain boundaries. (elifesciences.org)
The latter two families were predicted to contain a conserved catalytic triad (Cys, His and a polar third residue) in a circularly permuted catalytic domain where the relative positions of the cysteine and histidine/polar residue are swapped in the primary sequence such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus [ 1 ]. (expasy.org)
The third polar residue in this catalytic triad is a polar residue in the neighboring β3 strand. (expasy.org)

The regulation of PP2A is mainly accomplished by the identity of the regulatory B-type subunit, which determines substrate specificity, subcellular localization and catalytic activity of the PP2A holoenzyme. (ac.be)
Triplet substrates thus resolve a central incongruity of RNA replication, and here allow the ribozyme to synthesise its own catalytic subunit '+' and '-' strands in segments and assemble them into a new active ribozyme. (elifesciences.org)

The conserved Asp25-Thr26-Gly27 catalytic triad, is situated at the interface of the core domains from the two monomers. (proteopedia.org)
Structure/function relationships of adipose phospholipase A2 containing a cys-his-his catalytic triad. (expasy.org)

They consist of a catalytic domain which interacts with the amino acid acceptor-T psi C helix of the tRNA, and a second domain which interacts with the rest of the tRNA structure. (nih.gov)
The helix of the terminal domain packs against several beta-strands of the core domain. (proteopedia.org)
The structure of Pol alpha bound to RNA primer/DNA template shows that, although the palm domain makes a canonical set of interactions with the first 3 bp of the primer-template helix, the thumb domain engages almost exclusively with the RNA primer strand. (cathdb.info)
the SH2 domain opens to allow the B helix of one chain to pack against the β-sheet of the other chain. (elifesciences.org)
In the inactive structure, an incorrect base-pairing, which we call Alt P3, displaces the P3 helix in the catalytic core of the intron. (johnshopkins.edu)

We addressed this by obtaining cryo-EM structures (2.6-3.9 Å) of Candida albicans Kip3 in different catalytic states on the microtubule lattice and on a curved microtubule end mimic. (nature.com)
A lack of high-resolution structures capturing a kinesin-8 motor domain at each major step of its motile and microtubule depolymerization cycles has limited our understanding of the relationship between these two catalytic cycles and the structural elements of the motor domain that control them. (nature.com)
The crystal structures of human cdHDAC7 and its complexes with two hydroxamate inhibitors are the first structures of the catalytic domain of class IIa HDACs and demonstrate significant differences with previously reported class I and class IIb-like HDAC structures. (rcsb.org)
Furthermore, after superposition of the palm domains of Pol II and gp43, the DNAs of the two ternary complexes have nearly identical structures. (cathdb.info)
Structures of the autoinhibited SRC family kinases were solved in 1997 revealing, for the first time, the compact arrangement of the SH3 and SH2 domains assembled onto the distal side of the catalytic kinase domain [ 4 ]. (elifesciences.org)
In Escherichia coli, a proportion of the PNPase is recruited into a multi-enzyme assembly, known as the RNA degradosome, through an interaction with the scaffolding domain of the endoribonuclease RNase E. Here, we report crystal structures of E. coli PNPase complexed with the recognition site from RNase E and with manganese in the presence or in the absence of modified RNA. (port.ac.uk)

In this study, we performed mutagenic analyses of the C-terminal region of the catalytic core domain of HIV-1 IN in order to delineate the critical amino acid(s) and/or motif(s) required for the induction of the lethal phenotype in the yeast strain HP16, and to further elucidate the molecular mechanism which causes this phenotype. (biomedcentral.com)
Only two of them however, XPF and MUS81, have nuclease activity mediated by the conserved core nuclease motif (ERKX3D). (uu.nl)
ATP binds to the amino proximal alpha-beta domain, where the Walker A (motif I) and Walker B (motif II) are found. (embl.de)
The N-terminal domain also contains motif III (S-A-T) which was proposed to participate in linking ATPase and helicase activities. (embl.de)
All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain, a DNA binding domain, and binding domains for both dNTP's and pyrophosphate. (cathdb.info)

Rotation of the central stalk against the surrounding alpha3beta3 subunits leads to hydrolysis of ATP in three separate catalytic sites on the beta subunits. (joplink.net)

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)

We unravel a coincident mechanism of lipid-induced activation of PI3KC2α at membranes that involves large-scale repositioning of its Ras-binding and lipid-binding distal Phox-homology and C-C2 domains, and can serve as a model for the entire class II PI3K family. (nature.com)
During catalysis, ATP synthesis in the catalytic domain of F1 is coupled via a rotary mechanism of the central stalk subunits to proton translocation. (joplink.net)
The assembly mechanism of the 19S domain is poorly understood, but Hsp90 is thought to play a role. (tocris.com)
They all share a conserved catalytic core for their phosphotransferase function and often a common activation mechanism by phosphorylation of a variable segment known as the activation T-loop. (dissertation.com)
We discuss the implications of these structural observations for the catalytic mechanism of PNPase, its processive mode of action, and its assembly into the RNA degradosome. (port.ac.uk)

Biochemical and activity-based probe analyses identify a non-canonical zinc finger domain as the E3 active site, which utilizes the strictly conserved Cys4462, not involved in zinc coordination, as the reactive nucleophile. (biorxiv.org)
The cryo-EM structure of the trapped RNF213:E2∼Ub intermediate reveals RNF213 C-terminal domain as the E2 docking site, which positions the ubiquitin-loaded E2 proximal to the catalytic zinc finger, facilitating nucleophilic attack of Cys4462 on the E2∼Ub thioester. (biorxiv.org)

An ATP-dependent 3'-5' DNA helicase which is a component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. (embl.de)
The catalytic core of DNA polymerase is formed from the thumb, palm and finger domains. (cathdb.info)
This superfamily entry represents the palm domain of DNA polymerases B. Members of this superfamily include: DNA Polymerase alpha, delta, epsilon, zeta, DNA polymerase II (Pol II) in E. coli, yeast and Archaea. (cathdb.info)

Our findings show that RNF213 represents an undescribed type of a transthiolation E3 enzyme and is regulated by adenine nucleotide concentration via its ATPase core, possibly allowing it to react to changing metabolic conditions in the cell. (biorxiv.org)

F-type ATPases consist of two structural domains, F1 - containing the extramembraneous catalytic core, and F0 - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. (joplink.net)
Family B DNA polymerases consist of five main structural domains: the N domain, the 3' - 5' Exo (exonuclease) domain, the palm domain, the finger domain and the thumb domain. (cathdb.info)

Together, these data provide the first structural elucidation of full-length BTK and allow a deeper understanding of allosteric control over the BTK kinase domain during distinct stages of activation. (elifesciences.org)

The extracellular domain interacts with one of four ligands identified to date. (medscape.com)
The domain resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains ( PUBMED:15694336 ). (embl-heidelberg.de)

CRAT contains two domains, an N domain and a C domain, and is composed of 20 α helices and 16 β strands. (wikipedia.org)
The N domain consists of an eight-stranded β sheet flanked on both sides by eight α helices. (wikipedia.org)
A six-stranded mixed β sheet and eleven α helices comprise the enzyme's C domain. (wikipedia.org)

Interestingly, the E1'sUbc12 binding domain resembles ubiquitin and recruits Ubc12 in a manner mimickingubiquitin's interactions with ubiquitin binding domains. (embl-heidelberg.de)

The carboxy-terminal alpha-beta domain is structurally very similar to the proximal one even though it is bereft of an ATP-binding site, suggesting that it may have originally arisen through gene duplication of the first one. (embl.de)

On the way to activation, disassembly of the SH3-SH2- kinase core opens a new autoinhibitory site on the kinase domain for PHTH domain binding that is ultimately released upon interaction of PHTH with PIP3. (elifesciences.org)

This domain is quite crucial in dimer formation and stabilization of an active PR. (proteopedia.org)
This domain is quite useful in dimer stabilization, as well as the catalytic site stability. (proteopedia.org)
Membrane-induced dimerization activates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to trans-autophosphorylation. (elifesciences.org)
The compact structure of the SH3-SH2-kinase region of BTK is exacted from the domain swapped dimer structure (PDB: 4XI2) solved by Wang et al. (elifesciences.org)

NPC1 N-terminus is the first luminal domain which binds to cholesterol and its oxygenated derivatives. (biomedcentral.com)

These data reveal that the microtubule depolymerization activity of kinesin-8 originates from conformational changes of its motor core that are amplified by dynamic contacts between its extended loop-2 and tubulin. (nature.com)
Here, we characterize the structure and enzymatic activity of the catalytic domain of human HDAC7 (cdHDAC7). (rcsb.org)
When mediated by nutrient levels, the process is reversible and catalytic-activity dependent. (upstate.edu)
Several group VIII transition metal (Fe, Co, and Ni) nitrides are studied as core materials, with Ir/Fe 4 N core-shell particles showing enhancement in both OER activity and stability. (osti.gov)
Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. (thermofisher.com)
Catalytic activity is encoded in the second exon, and the active cysteine is encoded by the seventh exon. (medscape.com)

The TR component contains a template region that is complementary to the telomeric DNA sequence, while TERT contains the catalytic reverse transcriptase domain responsible for nucleotide addition. (asu.edu)

Subunits alpha and beta form the catalytic core in F1. (joplink.net)
The 20S catalytic domain is barrel-shaped and consists of seven structurally similar α- and β-subunits. (tocris.com)
EXOSC2 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC4 and EXOSC7. (thermofisher.com)

Overall, this study demonstrates that three mutations located in the C-terminal region of the catalytic core domain of HIV-1 IN inhibit the IN-induced lethal phenotype in yeast by inhibiting the binding of IN to the host chromatin. (biomedcentral.com)
Classical MEN2A is associated with germline missense mutations in RET codons 609, 611, 618, or 620 of exon 10 or codon 634 of exon 11, which map to the receptor's extracellular cysteine-rich domain. (medscape.com)
Biochemically, these mutations have been shown to similarly effect aberrant activation of the catalytic domain towards Ras-GTPases. (bionity.com)

The gene is 160 kilobases in length and has 15 exons and 14 introns with specific structural and functional domains. (medscape.com)

We used the traditional framework of core functions of public health -assessment, policy development and assurance-to structure the interviews and to summarize the feedback we received. (cdc.gov)

Subsequent entry of ATP initiates closing of the nucleotide-binding pocket and docking of a short peptide, known as the neck-linker, along the side of the motor domain. (nature.com)

RET consists of 3 domains, including a cysteine-rich extracellular receptor domain, a hydrophobic transmembrane domain, and an intracellular tyrosine kinase catalytic domain. (medscape.com)

In addition to these catalytic roles, PI3KC2α is also required for genome stability by acting as a scaffold at the mitotic spindle during cell division 26 . (nature.com)
In situ X-ray absorption fine structure measurements are used to determine the structure and stability of the core-shell catalysts under OER conditions. (osti.gov)

The nearest full-length structure of BTK to date consists of the autoinhibited SH3-SH2-kinase core. (elifesciences.org)

Complexes of Vps34, the sole class III PI3K member, produce PI 3-phosphate (PI(3)P) in the endolysosomal system and during autophagy to regulate vesicle-mediated sorting en route to lysosomes 1 . (nature.com)

On straight tubulin protofilaments in the microtubule lattice, loop-2-tubulin contacts inhibit conformational changes in the motor core, but in the ADP-Pi state these contacts are relaxed, allowing neck-linker docking for motility. (nature.com)
CryoEM reconstructions support conformational heterogeneity in the PHTH-PRR region wherein the globular PHTH domain adopts a range of states arrayed around the autoinhibited SH3-SH2-kinase core. (elifesciences.org)

Tissue transglutaminase (tTGase), also known as TGase 2, has four distinct domains: N-terminal β-sandwich, catalytic core and two C-terminal β-barrel domains. (biovendor.com)

Precisely how the BTK N-terminal domains (the Pleckstrin homology/Tec homology (PHTH) domain and proline-rich regions (PRR) contain linker) contribute to BTK regulation remains unclear. (elifesciences.org)

The proteasome complex is composed of a 20S catalytic core and one or two terminal 19S regulatory units. (tocris.com)

Assembly of the 20S domain is very complex and requires extrinsic (e.g. (tocris.com)
Here we engineered the catalytic core complex and the RNA binding domain, and evaluated the capability of using these materials for inhibitor development. (duke.edu)
We report here the crystal structure of a complex between the C-terminal domain from NEDD8's heterodimeric E1 (APPBP1-UBA3) and the catalytic core domain of NEDD8's E2 (Ubc12). (embl-heidelberg.de)

Their catalytic function however depends on heterodimer formation with the non-catalytic family members. (uu.nl)

The TEC and SRC kinases share the SH3-SH2-kinase domain arrangement (the 'Src module') ( Fig. 1a ). (elifesciences.org)

Furthermore, a different active site topology results in modified catalytic properties and in an enlarged active site pocket. (rcsb.org)
5 ]. The three domains (SH3, SH2, kinase), the SH2-kinase linker, the activation loop and the active site are labeled. (elifesciences.org)

Neck-linker docking in the microtubule-bound motor domain propels the second, microtubule-unbound, motor domain towards the microtubule plus-end, enabling a single stepping event. (nature.com)
c) Structure of the BTK PHTH domain bound to IP4 (PDB: 1B55) [ 8 ]. (elifesciences.org)

Here, the pantothenic arm's terminal thiol group and the ε2 nitrogen on the catalytic His343 side chain form a hydrogen bond. (wikipedia.org)
Our study identified three HIV-1 IN mutants, V165A, A179P and KR186,7AA, located in the C-terminal region of the catalytic core domain of IN that do not induce the lethal phenotype in yeast. (biomedcentral.com)
These results demonstrate that the C-terminal region of the catalytic core domain of HIV-1 IN is important for binding to host chromatin and is crucial for both viral replication and the promotion of the IN-induced lethal phenotype in yeast. (biomedcentral.com)

Presented here is a framework to reduce Ir loading by combining core-shell iridium/metal nitride morphologies using in situ experiments and density functional theory (DFT) calculations. (osti.gov)

The interactions between the thumb domain and the RNA primer are concentrated in a contiguous region of five nucleotides, from position two to six of the RNA primer and involve solely the ribose and phosphate moieties of the RNA backbone. (cathdb.info)

This entry represents the DNA-binding domain of classical SF1 and SF2 helicases. (embl.de)
One-half of the domain swapped BTK structure represents the current model for autoinhibited BTK and closely resembles the compact structure of autoinhibited SRC kinases ( Fig. 1b ). (elifesciences.org)

Anatomy12

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Analytical, Diagnostic and Therapeutic Techniques and Equipment34

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Disciplines and Occupations1

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Highly conserved4

Structure of the Catalytic Domain1

Protein11

Proteins15

Residues5

Residue5

Subunit2

Triad2

Helix5

Structures6

Motif5

Hydrolysis1

Sequences1

Mechanism5

Zinc finger2

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ATPase1

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Helices3

Ubiquitin1

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Disassembly1

Dimer4

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Activity6

Sequence1

Subunits3

Mutations3

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Cysteine-rich1

Stability2

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