Annotations: 2OKC

Crystal structure of Type I restriction enzyme StySJI M protein (NP_813429.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.20 A resolution

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)
B	d2okcb_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	N-6 DNA Methylase-like	Type I restriction enzyme StySJI M protein	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
A	d2okca1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	N-6 DNA Methylase-like	Type I restriction enzyme StySJI M protein	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	N-6 DNA Methylase-like	8022716	4003146	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8035096	3000118	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8035096	3000118	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	FlaF_Ig-like	e2okcB1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: FlaF_Ig-like	ECOD (v294.2)
A	HsdM_N	e2okcA3	A: beta barrels	X: Four-helical up-and-down bundle	H: N-terminal helical domain in restriction-modification system methylation subunit	T: N-terminal helical domain in restriction-modification system methylation subunit	F: HsdM_N	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.20.1260.30	Mainly Alpha	Up-down Bundle	Ferritin	N6 adenine-specific DNA methyltransferase, N-terminal domain	CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
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, B	PF02384	N-6 DNA Methylase (N6_Mtase)	N-6 DNA Methylase	-	Family
A, B	PF12161	HsdM N-terminal domain (HsdM_N)	HsdM N-terminal domain	This domain is found at the N-terminus of the methylase subunit of Type I DNA methyltransferases. This domain family is found in bacteria and archaea, and is typically between 123 and 138 amino acids in length. The family is found in association with ...	This domain is found at the N-terminus of the methylase subunit of Type I DNA methyltransferases. This domain family is found in bacteria and archaea, and is typically between 123 and 138 amino acids in length. The family is found in association with Pfam:PF02384. Mutations in this region of EcoKI methyltransferase Swiss:P08957 abolish the normally strong preference of this system for methylating hemimethylated substrate [1]. The structure of this domain has been shown to be all alpha-helical.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Type I restriction enzyme StySJI M protein	DNA binding 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	methylation metabolic process cellular process 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 methylation metabolic process cellular process 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 response to external biotic stimulus macromolecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002052	DNA methylase, N-6 adenine-specific, conserved site	Conserved Site
A, B	IPR003356	DNA methylase, adenine-specific	Domain
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR022749	N6 adenine-specific DNA methyltransferase, N-terminal domain	Domain
A, B	IPR051537	DNA Adenine N(4)/N(6)-Methyltransferase	Family
A, B	IPR038333	Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily	Homologous Superfamily

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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.