3EVY

Crystal structure of a fragment of a putative type I restriction enzyme R protein from Bacteroides fragilis

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	HsdR C-terminal domain-like	8047102	4005449	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	HsdR C-terminal domain-like	8091626	3002528	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	HsdR C-terminal domain-like	8091626	3002528	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	PF12008	e3evyA1	A: alpha arrays	X: HSDR subunit helical domain (From Topology)	H: HSDR subunit helical domain (From Topology)	T: HSDR subunit helical domain	F: PF12008	ECOD (1.6)
B	PF12008	e3evyB1	A: alpha arrays	X: HSDR subunit helical domain (From Topology)	H: HSDR subunit helical domain (From Topology)	T: HSDR subunit helical domain	F: PF12008	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.58.910	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	1.20.58.910	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF12008	Type I restriction and modification enzyme - subunit R C terminal (EcoR124_C)	Type I restriction and modification enzyme - subunit R C terminal	This enzyme has been characterised and shown to belong to a new family of the type I class of restriction and modification enzymes. This family is involved in bacterial defence by making double strand breaks in specific double stranded DNA sequences, ...	This enzyme has been characterised and shown to belong to a new family of the type I class of restriction and modification enzymes. This family is involved in bacterial defence by making double strand breaks in specific double stranded DNA sequences, e.g. that of invading bacteriophages. EcoR124 is made up of three subunits, HsdR, HsdS and HsdM. The R subunit has ATPase and restriction endonuclease activity. This domain is the C terminal of the R subunit [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Putative type I restriction enzyme R protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid endodeoxyribonuclease activity, producing 5'-phosphomonoesters hydrolase activity DNA nuclease activity ATP-dependent activity ATP-dependent activity, acting on DNA restriction endodeoxyribonuclease activity DNA endonuclease activity type I site-specific deoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA DNA translocase activity 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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR007409	Restriction endonuclease, type I, HsdR, N-terminal	Domain
A, B	IPR004473	Restriction endonuclease, type I, HsdR	Family
A, B	IPR040980	SWI2/SNF2 ATPase	Domain
A, B	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B	IPR022625	Type I restriction enzyme R protein, C-terminal	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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 R01GM133198.