7P9Z | pdb_00007p9z

Crystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing adenine opposite to lesion)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DNA-glycosylase	8107826	3000905	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)
A	AGOG	e7p9zA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: DNA-glycosylase	F: AGOG	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09171	N-glycosylase/DNA lyase (AGOG)	N-glycosylase/DNA lyase	This domain is predominantly found in the Archaeal protein N-glycosylase/DNA lyase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth I]	DNA (5'-D(APGPAPAPAPAPAPAP*A)-3')	-	-	-
B	DNA (5'-D(TPTPTP(PED)TPTPTPCP*T)-3')	-	-	-
A	N-glycosylase/DNA lyase	DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity catalytic activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds oxidized base lesion DNA N-glycosylase activity hydrolase activity DNA-(apurinic or apyrimidinic site) endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid DNA nuclease activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity lyase activity catalytic activity carbon-oxygen lyase activity hydrolase activity, acting on glycosyl bonds oxidized base lesion DNA N-glycosylase activity hydrolase activity DNA N-glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process base-excision repair 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
A	IPR015254	N-glycosylase/DNA lyase-like	Family
A	IPR016544	N-glycosylase/DNA lyase	Family
A	IPR011257	DNA glycosylase	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	PED	RESID: AA0494 PSI-MOD : N-(DNA-1',2'-dideoxyribos-1'-ylidene)-L-prolinium MOD:01454

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.