1M0D

Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions

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)
A	d1m0da_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	Endonuclease I (Holliday junction resolvase)	Endonuclease I (Holliday junction resolvase)	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
B	d1m0db_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	Endonuclease I (Holliday junction resolvase)	Endonuclease I (Holliday junction resolvase)	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
C	d1m0dc_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	Endonuclease I (Holliday junction resolvase)	Endonuclease I (Holliday junction resolvase)	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
D	d1m0dd_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	Endonuclease I (Holliday junction resolvase)	Endonuclease I (Holliday junction resolvase)	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Phage endonuclease I	8029139	4000497	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Restriction endonuclease-like	8041518	3000104	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Restriction endonuclease-like	8041518	3000104	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Restriction endonuclease-like	8041518	3000104	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Restriction endonuclease-like	8041518	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)
A	Phage_endo_I	e1m0dA1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: Phage_endo_I	ECOD (1.6)
B	Phage_endo_I	e1m0dB1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: Phage_endo_I	ECOD (1.6)
C	Phage_endo_I	e1m0dC1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: Phage_endo_I	ECOD (1.6)
D	Phage_endo_I	e1m0dD1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like (From Topology)	T: Restriction endonuclease-like	F: Phage_endo_I	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.91.30	Alpha Beta	3-Layer(aba) Sandwich	Restriction Endonuclease		CATH (4.3.0)
B	3.40.91.30	Alpha Beta	3-Layer(aba) Sandwich	Restriction Endonuclease		CATH (4.3.0)
C	3.40.91.30	Alpha Beta	3-Layer(aba) Sandwich	Restriction Endonuclease		CATH (4.3.0)
D	3.40.91.30	Alpha Beta	3-Layer(aba) Sandwich	Restriction Endonuclease		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05367	Phage endonuclease I (Phage_endo_I)	Phage endonuclease I	The bacteriophage endonuclease I is a nuclease that is selective for the structure of the four-way Holliday DNA junction [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Endodeoxyribonuclease I	DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity double-stranded DNA endonuclease activity catalytic activity DNA nuclease activity DNA binding binding organic cyclic compound binding nucleic acid binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity double-stranded DNA endonuclease activity catalytic activity DNA nuclease activity DNA binding binding organic cyclic compound binding nucleic acid binding endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters crossover junction DNA endonuclease activity DNA endonuclease activity, producing 3'-phosphomonoesters endodeoxyribonuclease activity, producing 5'-phosphomonoesters endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters deoxyribonuclease IV (phage-T4-induced) activity	symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process primary metabolic process symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process DNA integration nucleic acid metabolic process degradation of host chromosome by virus catabolism by virus of host DNA viral process modulation by virus of host process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR008029	Bacteriophage T7, Gp3, endodeoxynuclease I	Family
A, B, C, D	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.