1VAS

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
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance 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

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	T4 endonuclease V	8036751	3001328	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth A]	Pyr_excise	e1vasA1	A: alpha arrays	X: T4 endonuclease V (From Topology)	H: T4 endonuclease V (From Topology)	T: T4 endonuclease V	F: Pyr_excise	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	1.10.440.10	Mainly Alpha	Orthogonal Bundle	Endonuclease V	T4 endonuclease V	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF03013	Pyrimidine dimer DNA glycosylase (Pyr_excise)	Pyrimidine dimer DNA glycosylase	Pyrimidine 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

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	DNA (5'-D(APTPCPGPCPGPTPTPGPCPGPCP*T)-3')	-	-	-
B [auth C]	DNA (5'-D(TPAPGPCPGPCPAPAPCPGPCPGP*A)-3')	-	-	-
C [auth A]	PROTEIN (T4 ENDONUCLEASE V (E.C.3.1.25.1))	DNA-(apurinic or apyrimidinic site) endonuclease activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity catalytic activity carbon-oxygen lyase activity pyrimidine dimer DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds deoxyribodipyrimidine endonucleosidase activity endonuclease activity DNA-(apurinic or apyrimidinic site) endonuclease activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity catalytic activity carbon-oxygen lyase activity pyrimidine dimer DNA N-glycosylase activity hydrolase activity, acting on glycosyl bonds hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds deoxyribodipyrimidine endonucleosidase activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR024796	T4 endonuclease V	Homologous Superfamily
C [auth A]	IPR004260	Pyrimidine dimer DNA glycosylase	Family
C [auth A]	IPR021143	Pyrimidine dimer DNA glycosylase, endonuclease V type	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
C [auth A]	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) Search M-CSA Motif + EC 3.2.2.17 EC: 4.2.99.18 (UniProt) Search M-CSA Motif + EC 4.2.99.18

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.