7EEW

Crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	B-form DNA mimic Ocr	8041471	3000719	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)
B	PF08684	e7eewB1	A: alpha arrays	X: HTH	H: B-form DNA mimic Ocr (From Topology)	T: B-form DNA mimic Ocr	F: PF08684	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02384	N-6 DNA Methylase (N6_Mtase)	N-6 DNA Methylase	-	Family
A	PF01420	Type I restriction modification DNA specificity domain (Methylase_S)	Type I restriction modification DNA specificity domain	This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host ge ...	This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity subunit (this family), two modification (M) subunits and two restriction (R) subunits [2].	Domain
B	PF08684	DNA mimic ocr (ocr)	DNA mimic ocr	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Type I restriction-modification system methyltransferase subunit	DNA binding binding organic cyclic compound binding nucleic acid binding transferase activity, transferring one-carbon groups N-methyltransferase activity transferase activity methyltransferase activity catalytic activity	methylation metabolic process 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 methylation metabolic process 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 macromolecule metabolic process	-
B	Overcome classical restriction gp0.3	-	symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated evasion of recognition by host innate immune effector response to defenses of other organism symbiont-mediated evasion of host innate immune response response to external stimulus symbiont-mediated evasion of host restriction-modification system response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction evasion of host immune response symbiont-mediated perturbation of host defense response response to host defenses biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated evasion of recognition by host innate immune effector response to defenses of other organism symbiont-mediated evasion of host innate immune response response to external stimulus symbiont-mediated evasion of host restriction-modification system response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction evasion of host immune response modulation by symbiont of host process response to host immune response response to host response to external biotic stimulus modulation of process of another organism modulation by virus of host process virus-mediated perturbation of host defense response viral process modulation by virus of host cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR044946	Type I restriction modification DNA specificity domain superfamily	Homologous Superfamily
A	IPR003356	DNA methylase, adenine-specific	Domain
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR000055	Type I restriction modification DNA specificity domain	Domain
B	IPR036207	B-form DNA mimic Ocr	Homologous Superfamily
B	IPR014798	Protein Ocr	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 R01GM133198.