1YF2

Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications

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	d1yf2a1	Alpha and beta proteins (a+b)	DNA methylase specificity domain	DNA methylase specificity domain	Type I restriction modification DNA specificity domain	Bipartite methylase S protein MJ0130	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
B	d1yf2b1	Alpha and beta proteins (a+b)	DNA methylase specificity domain	DNA methylase specificity domain	Type I restriction modification DNA specificity domain	Bipartite methylase S protein MJ0130	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Type I restriction modification DNA specificity domain	8021956	4000463	SCOP2 (2022-06-29)
A	SCOP2 Family	Type I restriction modification DNA specificity domain	8021959	4000463	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA methylase specificity domain	8034336	3001742	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA methylase specificity domain	8034339	3001742	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	DNA methylase specificity domain	8034336	3001742	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA methylase specificity domain	8034339	3001742	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	PF01420	e1yf2A2	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: PF01420	ECOD (1.6)
B	PF01420	e1yf2B2	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: PF01420	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.220.20	Alpha Beta	Alpha-Beta Complex	Adenine-n6-DNA-methyltransferase TaqI	Chain A, domain 2	CATH (4.3.0)
A	1.10.287.1120	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Bipartite methylase S protein	CATH (4.3.0)
B	3.90.220.20	Alpha Beta	Alpha-Beta Complex	Adenine-n6-DNA-methyltransferase TaqI	Chain A, domain 2	CATH (4.3.0)
B	1.10.287.1120	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Bipartite methylase S protein	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
A, B	Type I restriction-modification enzyme, S subunit	DNA binding binding organic cyclic compound binding nucleic acid binding	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, B	IPR044946	Type I restriction modification DNA specificity domain superfamily	Homologous Superfamily
A, B	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 R01GM133198.