2Y7H | pdb_00002y7h

Atomic model of the DNA-bound methylase complex from the Type I restriction-modification enzyme EcoKI (M2S1). Based on fitting into EM map 1534.

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)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8037288	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8037288	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)
C	HsdM_N_1	e2y7hC1	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: HsdM_N_1	ECOD (1.6)
C	N6_Mtase	e2y7hC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (1.6)
B	HsdM_N_1	e2y7hB1	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: HsdM_N_1	ECOD (1.6)
B	N6_Mtase	e2y7hB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (1.6)
A	Methylase_S	e2y7hA3	A: a+b complex topology	X: DNA methylase specificity domain (From Topology)	H: DNA methylase specificity domain (From Topology)	T: DNA methylase specificity domain	F: Methylase_S	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, C	PF02384	N-6 DNA Methylase (N6_Mtase)	N-6 DNA Methylase	-	Family
B, C	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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E	5'-D(GPTPTPGPCPAPCPGPTPCPGPAPCPGP TPTPGPAPAPC)-3'	-	-	-
D	5'-D(GPTPTPCPAPAPCPGPTPCPGPAPCPGP TPGPCPAPAPC)-3'	-	-	-
B, C	TYPE I RESTRICTION ENZYME ECOKI 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex endodeoxyribonuclease complex type I site-specific deoxyribonuclease complex intracellular protein-containing complex endonuclease complex
A	TYPE-1 RESTRICTION ENZYME ECOKI SPECIFICITY PROTEIN	DNA binding binding nucleic acid binding	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 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 metabolic process cellular process response to external biotic stimulus macromolecule metabolic process	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex endodeoxyribonuclease complex type I site-specific deoxyribonuclease complex cytoplasm intracellular protein-containing complex endonuclease complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, C	IPR002052	DNA methylase, N-6 adenine-specific, conserved site	Conserved Site
B, C	IPR003356	DNA methylase, adenine-specific	Domain
B, C	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
B, C	IPR022749	N6 adenine-specific DNA methyltransferase, N-terminal domain	Domain
B, C	IPR051537	DNA Adenine N(4)/N(6)-Methyltransferase	Family
B, C	IPR038333	Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily	Homologous Superfamily
A	IPR044946	Type I restriction modification DNA specificity domain superfamily	Homologous Superfamily
A	IPR051212	Type I restriction enzyme S subunit	Family
A	IPR000055	Type I restriction modification DNA specificity domain	Domain

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.