Skip to main content

 1VAS | pdb_00001vas

ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITION

External Resource: Annotation


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
C [auth A]d1vasa_ All alpha proteins T4 endonuclease V T4 endonuclease V T4 endonuclease V T4 endonuclease V (Tequatrovirus T4 ) [TaxId: 10665 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
C [auth A]SCOP2B SuperfamilyT4 endonuclease V 8036751 3001328 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
C [auth A]Bcl-2e1vasA1 A: alpha arraysX: Urease, gamma-subunitH: p53 tetramerization domainT: p53 tetramerization domainF: Bcl-2ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
C [auth A]1.10.440.10 Mainly Alpha Orthogonal Bundle Endonuclease V T4 endonuclease VCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
C [auth A]PF03013Pyrimidine dimer DNA glycosylase (Pyr_excise)Pyrimidine dimer DNA glycosylasePyrimidine dimer DNA glycosylases excise pyrimidine dimers by hydrolysis of the glycosylic bond of the 5' pyrimidine, followed by the intra-pyrimidine phosphodiester bond. Pyrimidine dimers are the major UV-lesions of DNA. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
C [auth A]PROTEIN (T4 ENDONUCLEASE V (E.C.3.1.25.1)) -
B [auth C]DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3')---
A [auth B]DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3')---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
C [auth A]IPR024796T4 endonuclease VHomologous Superfamily
C [auth A]IPR004260Pyrimidine dimer DNA glycosylaseFamily
C [auth A]IPR021143Pyrimidine dimer DNA glycosylase, endonuclease V typeFamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

ChainsEnzyme NameDescriptionCatalytic Residues
deoxyribonuclease (pyrimidine dimer)  M-CSA #162

Endonuclease V removes pyrimidine dimers in DNA induced by UV radiation. The enzyme first associates with the DNA and locates the damaged site by a scanning mechanism. It catalyses 2 reactions to remove DNA pyrimidine dimers: (1)cleavage of glycosidic bond by pyrimidine dimer glycosylase activity, which hydrolyses the N-glycosyl bond of the 5'-thymidine in the thymine dimer site and (2)incision of the phosphodiester bond at the apyrimidinic site via a beta-elimination reaction by the apurinic/apyrimidinic(AP) endonuclease activity.

Defined by 4 residues: THR:C-1 [auth A-2]ARG:C-21 [auth A-22]GLN:C-22 [auth A-23]ARG:C-25 [auth A-26]
 | 
 
Explore in 3D: M-CSA Motif Definition
Search M-CSA Motif
EC: 3.2.2.17 (UniProt)
EC: 4.2.99.18 (UniProt)