6U7T
MutY adenine glycosylase bound to DNA containing a transition state analog (1N) paired with d(8-oxo-G)
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | HhH-GPD | e6u7tA2 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: DNA-glycosylase | F: HhH-GPD | ECOD (1.6) |
A | NUDIX_4 | e6u7tA1 | A: a+b two layers | X: beta-Grasp | H: Nudix (From Topology) | T: Nudix | F: NUDIX_4 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 1.10.1670.10 | Mainly Alpha | Orthogonal Bundle | Endonuclease Iii, domain 2 | Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) | CATH (utative) |
A | 1.10.340.30 | Mainly Alpha | Orthogonal Bundle | Endonuclease III | domain 1 | CATH (utative) |
A | 3.90.79.10 | Alpha Beta | Alpha-Beta Complex | Nucleoside Triphosphate Pyrophosphohydrolase | Nucleoside Triphosphate Pyrophosphohydrolase | CATH (utative) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00633 | Helix-hairpin-helix motif (HHH) | Helix-hairpin-helix motif | - | Motif | |
PF10576 | Iron-sulfur binding domain of endonuclease III (EndIII_4Fe-2S) | Iron-sulfur binding domain of endonuclease III | Escherichia coli endonuclease III (EC 4.2.99.18) [1] is a DNA repair enzyme that acts both as a DNA N-glycosylase, removing oxidised pyrimidines from DNA, and as an apurinic/apyrimidinic (AP) endonuclease, introducing a single-strand nick at the site ... | Domain | |
PF14815 | NUDIX domain (NUDIX_4) | NUDIX domain | Domain | ||
PF00730 | HhH-GPD superfamily base excision DNA repair protein (HhH-GPD) | HhH-GPD superfamily base excision DNA repair protein | This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate [2]. This includes endonucle ... | Domain | |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR003265 | HhH-GPD domain | Domain | |
IPR000445 | Helix-hairpin-helix motif | Conserved Site | |
IPR023170 | Helix-hairpin-helix, base-excision DNA repair, C-terminal | Homologous Superfamily | |
IPR044298 | Adenine/Thymine-DNA glycosylase | Family | |
IPR015797 | NUDIX hydrolase-like domain superfamily | Homologous Superfamily | |
IPR029119 | Adenine DNA glycosylase, C-terminal | Domain | |
IPR005760 | A/G-specific adenine glycosylase MutY | Family | |
IPR011257 | DNA glycosylase | Homologous Superfamily | |
IPR003651 | Endonuclease III-like, iron-sulphur cluster loop motif | Conserved Site |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
adenine DNA glycosylase M-CSA #807 | Oxidative DNA damage is caused by reactive oxygen species that are generated during aerobic respiration and immune response. The oxidative lesions in DNA caused are repaired by the base excision repair pathway. Hydroxyl radicals rapidly react with guanine C8 producing a steady state level of mutagenic 8-oxoguanines in cells. It also creates 8-oxo-GTP that, like 8-oxoguanines in DNA template, is often mispaired with adenine by replicative polymerases, creating A-T to C-G and G-C to T-A transversion mutations. DNA glycosylase MutY recognises the mutational intermediate 8-oxoguanine-adenine mispair and excises adenine from the mispair. This creates an abasic site that is then processed by the multi-enzyme base excision repair pathway. The sequence of MutY is conserved from bacteria to humans suggesting its fundamental importance in DNA repair. Mutations of MutY increases transversion frequencies and hence cancer susceptibility in human. MutY belongs to the base excision repair glycosylases superfamily which includes both pure DNA glycosylases and DNA glycosylase/lyases. The most conserved structural element in this family is the Helix-hairpin-Helix (HhH) motif. A revised MutY reaction mechanism was published in 2016, which involves a covalent intermediate and two oxocarbenium ion-like transition states. There is sufficient structural, mutagenesis and biochemical date to support the proposed mechanism described. | EC: 3.2.2.31 (PDB Primary Data) |