1DMU | pdb_00001dmu

Crystal structure of the restriction endonuclease BglI (e.c.3.1.21.4) bound to its dna recognition sequence

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth A]	d1dmua_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	Restriction endonuclease BglI	Restriction endonuclease BglI	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2 Family	Restriction endonuclease BglI	8032055	4000531	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Restriction endonuclease-like	8044433	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)
B [auth A]		e1dmuA1	A: Restriction endonuclease-like	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Endonuc_BglI	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	3.40.600.20	Alpha Beta	3-Layer(aba) Sandwich	ECO RV Endonuclease	Chain A	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A]	BGLI RESTRICTION ENDONUCLEASE	cation binding ion binding 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 cation binding ion binding 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	-
A [auth F]	DNA (5'-D(APTPCPGPCPCPTPAPAPTPAPGPGPCPGPAP*T)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR043121	Restriction endonuclease, type II, BglI superfamily	Homologous Superfamily
B [auth A]	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
B [auth A]	IPR011543	Restriction endonuclease, type II, BglI	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
B [auth A]	type II site-specific deoxyribonuclease, BgII M-CSA #495	The type-II restriction enzymes catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. This is a large group of enzymes which require only Mg(II) and recognise specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition site. This entry represents the BgII family (IPR011543) which recognises the GCCNNNNNGGC motif and cleaves after N-4.	Defined by 4 residues: ASP:B-116 [auth A-116]ASP:B-142 [auth A-142]ILE:B-143 [auth A-143]LYS:B-144 [auth A-144] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.1.21.4 (PDB Primary Data) Search M-CSA Motif + EC 3.1.21.4

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.

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