1DMU

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
Protein Family Annotation
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]	PF14562	e1dmuA1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: PF14562	ECOD (1.6)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF14562	Restriction endonuclease BglI (Endonuc_BglI)	Restriction endonuclease BglI	This restriction endonuclease binds DNA as a dimer. BglI recognises and cleaves the interrupted DNA sequence GCCNNNNNGGC and cleaves between the fourth and fifth unspecified base pair to produce 3' overhanging ends [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth F]	DNA (5'-D(APTPCPGPCPCPTPAPAPTPAPGPGPCPGPAP*T)-3')	-	-	-
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 endodeoxyribonuclease activity, producing 5'-phosphomonoesters hydrolase activity DNA nuclease activity type II site-specific deoxyribonuclease activity restriction endodeoxyribonuclease activity DNA endonuclease activity nuclease activity cation binding ion binding binding metal ion binding small molecule 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	-

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 R01GM133198.