1NI0 | pdb_00001ni0

Structure of the Y94F mutant of the restriction endonuclease PvuII

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d1ni0c1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	Restriction endonuclease PvuII	Restriction endonuclease PvuII	(Proteus vulgaris ) [TaxId: 585 ],	SCOPe (2.08)
C	d1ni0c2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Proteus vulgaris ) [TaxId: 585 ],	SCOPe (2.08)
B	d1ni0b1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	Restriction endonuclease PvuII	Restriction endonuclease PvuII	(Proteus vulgaris ) [TaxId: 585 ],	SCOPe (2.08)
B	d1ni0b2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Proteus vulgaris ) [TaxId: 585 ],	SCOPe (2.08)
A	d1ni0a1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	Restriction endonuclease PvuII	Restriction endonuclease PvuII	(Proteus vulgaris ) [TaxId: 585 ],	SCOPe (2.08)
A	d1ni0a2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Proteus vulgaris ) [TaxId: 585 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Restriction endonuclease-like	8044434	3000104	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Restriction endonuclease-like	8044434	3000104	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Restriction endonuclease-like	8044434	3000104	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)
C	Endonuc-PvuII	e1ni0C1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: Endonuc-PvuII	ECOD (1.6)
B	Endonuc-PvuII	e1ni0B1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: Endonuc-PvuII	ECOD (1.6)
A	Endonuc-PvuII	e1ni0A1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: Endonuc-PvuII	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.210.10	Alpha Beta	3-Layer(aba) Sandwich	PvuII Endonuclease	Chain A	CATH (4.3.0)
B	3.40.210.10	Alpha Beta	3-Layer(aba) Sandwich	PvuII Endonuclease	Chain A	CATH (4.3.0)
A	3.40.210.10	Alpha Beta	3-Layer(aba) Sandwich	PvuII Endonuclease	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF09225	Restriction endonuclease PvuII (Endonuc-PvuII)	Restriction endonuclease PvuII	Members of this family are predominantly found in prokaryotic restriction endonuclease PvuII. They recognise the double-stranded DNA sequence 5'-CAGCTG-3' and cleave after G-3, resulting in specific double-stranded fragments with terminal 5'-phosphat ...	Members of this family are predominantly found in prokaryotic restriction endonuclease PvuII. They recognise the double-stranded DNA sequence 5'-CAGCTG-3' and cleave after G-3, resulting in specific double-stranded fragments with terminal 5'-phosphates [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Type II restriction enzyme PvuII	DNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule 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 DNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule 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, B, C	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A, B, C	IPR038402	Restriction endonuclease, type II, PvuII superfamily	Homologous Superfamily
A, B, C	IPR015306	Restriction endonuclease, type II, PvuII	Family

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.