1NA6 | pdb_00001na6

Crystal structure of restriction endonuclease EcoRII mutant R88A

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	d1na6a1	All beta proteins	DNA-binding pseudobarrel domain	DNA-binding pseudobarrel domain	Type II restriction endonuclease effector domain	Restriction endonuclease EcoRII, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1na6a2	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	Type II restriction endonuclease catalytic domain	Restriction endonuclease EcoRII, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1na6b1	All beta proteins	DNA-binding pseudobarrel domain	DNA-binding pseudobarrel domain	Type II restriction endonuclease effector domain	Restriction endonuclease EcoRII, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1na6b2	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	Type II restriction endonuclease catalytic domain	Restriction endonuclease EcoRII, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Restriction endonuclease-like	8036734	3000104	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA-binding pseudobarrel domain	8036733	3000213	SCOP2B (2022-06-29)
B	SCOP2 Family	Type II restriction endonuclease effector domain	8024354	4000944	SCOP2 (2022-06-29)
B	SCOP2 Family	Type II restriction endonuclease catalytic domain	8024355	4001115	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	DNA-binding pseudobarrel domain	8036733	3000213	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Restriction endonuclease-like	8036734	3000104	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	e1na6A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: EcoRII-N	ECOD (v294.2)
A	EcoRII-C	e1na6A2	A: beta barrels	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: EcoRII-C	ECOD (v294.2)
B	Trypsin	e1na6B1	A: beta barrels	X: Phage tail fiber protein trimerization domain	H: LigT-related	T: LigT-related	F: Trypsin	ECOD (v294.2)
B	RecU	e1na6B2	A: beta barrels	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.2)

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)
A	3.40.91.80	Alpha Beta	3-Layer(aba) Sandwich	Restriction Endonuclease		CATH (4.3.0)
B	2.40.330.10	Mainly Beta	Beta Barrel	At1g16640 B3 domain	DNA-binding pseudobarrel domain	CATH (4.3.0)
B	3.40.91.80	Alpha Beta	3-Layer(aba) Sandwich	Restriction Endonuclease		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Restriction endonuclease EcoRII	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, B	IPR015300	DNA-binding pseudobarrel domain superfamily	Homologous Superfamily
A, B	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A, B	IPR038365	EcoRII, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR023372	Restriction endonuclease, type II, EcoRII, N-terminal	Domain
A, B	IPR015109	Restriction endonuclease, type II, EcoRII, C-terminal	Domain

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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.