3UFB

Crystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	N-6 DNA Methylase-like	8099995	4003146	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8099996	3000118	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	PF12161	e3ufbA2	A: alpha arrays	X: N-terminal helical domain in restriction-modification system methylation subunit-like	H: N-terminal helical domain in restriction-modification system methylation subunit (From Topology)	T: N-terminal helical domain in restriction-modification system methylation subunit	F: PF12161	ECOD (1.6)
A	PF02384	e3ufbA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF02384	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1260.30	Mainly Alpha	Up-down Bundle	Ferritin	N6 adenine-specific DNA methyltransferase, N-terminal domain	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)

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

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 DNA-methyltransferase activity catalytic activity, acting on DNA site-specific DNA-methyltransferase (adenine-specific) activity catalytic activity, acting on a nucleic acid S-adenosylmethionine-dependent methyltransferase 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
A	IPR002052	DNA methylase, N-6 adenine-specific, conserved site	Conserved Site
A	IPR003356	DNA methylase, adenine-specific	Domain
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR038333	Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily	Homologous Superfamily

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.