3HQF | pdb_00003hqf

Crystal structure of restriction endonuclease EcoRII N-terminal effector-binding domain in complex with cognate DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	Type II restriction endonuclease effector domain	8098211	4000944	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA-binding pseudobarrel domain	8098212	3000213	SCOP2 (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	EcoRII-N	e3hqfA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Type II restriction endonuclease effector domain	F: EcoRII-N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.330.10	Mainly Beta	Beta Barrel	At1g16640 B3 domain	DNA-binding pseudobarrel domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	5'-D(CPGPCPCPAPGPGPGP*C)-3'	-	-	-
B	5'-D(GPCPCPCPTPGPGPCP*G)-3'	-	-	-
A	Restriction endonuclease	DNA binding binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity type II site-specific deoxyribonuclease activity restriction endodeoxyribonuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters DNA binding binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity type II site-specific deoxyribonuclease activity restriction endodeoxyribonuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response DNA restriction-modification system defense response to symbiont response to external stimulus primary metabolic process clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids DNA metabolic process response to biotic stimulus nucleic acid metabolic process nucleobase-containing compound metabolic process DNA modification biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response DNA restriction-modification system defense response to symbiont response to external stimulus primary metabolic process clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids DNA metabolic process response to biotic stimulus nucleic acid metabolic process nucleobase-containing compound metabolic process DNA modification defense response to other organism response to stress macromolecule modification metabolic process cellular process response to external biotic stimulus macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015300	DNA-binding pseudobarrel domain superfamily	Homologous Superfamily
A	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A	IPR038365	EcoRII, C-terminal domain superfamily	Homologous Superfamily
A	IPR023372	Restriction endonuclease, type II, EcoRII, N-terminal	Domain
A	IPR015109	Restriction endonuclease, type II, EcoRII, C-terminal	Domain

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.