2J63 | pdb_00002j63

Crystal structure of AP endonuclease LMAP from Leishmania major

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DNase I-like	8079412	4002213	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNase I-like	8079413	3000957	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	DNase I-like	8079413	3000957	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	Asp_Glu_race	e2j63A1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: Asp_Glu_race	ECOD (v294.1)
B	PK_Tyr_Ser-Thr	e2j63B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: PK_Tyr_Ser-Thr	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)
B	3.60.10.10	Alpha Beta	4-Layer Sandwich	Deoxyribonuclease I	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03372	Endonuclease/Exonuclease/phosphatase family (Exo_endo_phos)	Endonuclease/Exonuclease/phosphatase family	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3. ...	This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling [1]. This family includes: AP endonuclease proteins EC:4.2.99.18 e.g Swiss:P27695, DNase I proteins EC:3.1.21.1 e.g. Swiss:P24855, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56 Swiss:O43426, Sphingomyelinase EC:3.1.4.12 Swiss:P11889 and Nocturnin Swiss:O35710.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	AP-ENDONUCLEASE	double-stranded DNA 3'-5' DNA exonuclease activity DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity double-stranded DNA exodeoxyribonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity catalytic activity exonuclease activity double-stranded DNA 3'-5' DNA exonuclease activity DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity double-stranded DNA exodeoxyribonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity catalytic activity exonuclease activity DNA binding binding nucleic acid binding DNA-(apurinic or apyrimidinic site) endonuclease activity DNA endonuclease activity endonuclease activity lyase activity phosphoric ester hydrolase activity phosphoric diester hydrolase activity cation binding ion binding metal ion binding small molecule binding	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 base-excision repair	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR005135	Endonuclease/exonuclease/phosphatase	Domain
A, B	IPR020848	AP endonuclease 1, conserved site	Conserved Site
A, B	IPR004808	AP endonuclease 1	Family
A, B	IPR036691	Endonuclease/exonuclease/phosphatase superfamily	Homologous Superfamily
A, B	IPR020847	AP endonuclease 1, binding site	Binding Site

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.