3UBT

Crystal Structure of C71S Mutant of DNA Cytosine-5 Methyltransferase M.HaeIII Bound to DNA

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 [auth Y]	d3ubty_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	C5 cytosine-specific DNA methylase, DCM	automated matches	Koch-Weeks bacillus (Haemophilus aegyptius ) [TaxId: 197575 ],	SCOPe (2.08)
B [auth A]	d3ubta_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	C5 cytosine-specific DNA methylase, DCM	automated matches	Koch-Weeks bacillus (Haemophilus aegyptius ) [TaxId: 197575 ],	SCOPe (2.08)
C [auth B]	d3ubtb_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	C5 cytosine-specific DNA methylase, DCM	automated matches	Koch-Weeks bacillus (Haemophilus aegyptius ) [TaxId: 197575 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth Y]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8032294	3000118	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8032294	3000118	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8032294	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)
A [auth Y]	DNA_methylase	e3ubtY1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNA_methylase	ECOD (1.6)
B [auth A]	DNA_methylase	e3ubtA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNA_methylase	ECOD (1.6)
C [auth B]	DNA_methylase	e3ubtB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: DNA_methylase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth Y]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A [auth Y]	3.90.120.10	Alpha Beta	Alpha-Beta Complex	DNA Methylase	Chain A, domain 2	CATH (4.3.0)
B [auth A]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B [auth A]	3.90.120.10	Alpha Beta	Alpha-Beta Complex	DNA Methylase	Chain A, domain 2	CATH (4.3.0)
C [auth B]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
C [auth B]	3.90.120.10	Alpha Beta	Alpha-Beta Complex	DNA Methylase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth Y], B [auth A], C [auth B]	PF00145	C-5 cytosine-specific DNA methylase (DNA_methylase)	C-5 cytosine-specific DNA methylase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth Y], B [auth A], C [auth B]	Modification methylase HaeIII	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding DNA (cytosine-5-)-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity	methylation metabolic 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 methylation metabolic 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	-
D, E, F, G, H, D, E, F, G, H, I [auth C]	5'-D(TPGPGPCPCPA)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth Y], B [auth A], C [auth B]	IPR031303	DNA methylase, C-5 cytosine-specific, conserved site	Conserved Site
A [auth Y], B [auth A], C [auth B]	IPR018117	DNA methylase, C-5 cytosine-specific, active site	Active Site
A [auth Y], B [auth A], C [auth B]	IPR001525	C-5 cytosine methyltransferase	Family
A [auth Y], B [auth A], C [auth B]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A [auth Y], B [auth A], C [auth B]	IPR050390	DNA Cytosine-5 Methyltransferase	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 R01GM157729.