3HQF

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
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	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	PF09217	e3hqfA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Type II restriction endonuclease effector domain	F: PF09217	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09217	Restriction endonuclease EcoRII, N-terminal (EcoRII-N)	Restriction endonuclease EcoRII, N-terminal	The N-terminal effector-binding domain of the Restriction Endonuclease EcoRII has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, ...	The N-terminal effector-binding domain of the Restriction Endonuclease EcoRII has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

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 National Science Foundation (DBI-1832184), 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 R01GM133198.