5EEH

Crystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 2-chloro-4-nitrophenol

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	d5eeha1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Plant O-methyltransferase, N-terminal domain	Carminomycin 4-O-methyltransferase	(Streptomyces peucetius ) [TaxId: 1950 ],	SCOPe (2.08)
A	d5eeha2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Plant O-methyltransferase, C-terminal domain	Carminomycin 4-O-methyltransferase	(Streptomyces peucetius ) [TaxId: 1950 ],	SCOPe (2.08)
B	d5eehb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Plant O-methyltransferase, N-terminal domain	Carminomycin 4-O-methyltransferase	(Streptomyces peucetius ) [TaxId: 1950 ],	SCOPe (2.08)
B	d5eehb2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Plant O-methyltransferase, C-terminal domain	Carminomycin 4-O-methyltransferase	(Streptomyces peucetius ) [TaxId: 1950 ],	SCOPe (2.08)
C	d5eehc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Plant O-methyltransferase, N-terminal domain	Carminomycin 4-O-methyltransferase	(Streptomyces peucetius ) [TaxId: 1950 ],	SCOPe (2.08)
C	d5eehc2	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Plant O-methyltransferase, C-terminal domain	Carminomycin 4-O-methyltransferase	(Streptomyces peucetius ) [TaxId: 1950 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8054283	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8054284	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8054284	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8054283	3000118	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8054283	3000118	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8054284	3000034	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	Dimerisation2	e5eehA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Dimerisation2	ECOD (1.6)
A	Methyltransf_11_4	e5eehA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	ECOD (1.6)
B	Dimerisation2	e5eehB2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Dimerisation2	ECOD (1.6)
B	Methyltransf_11_4	e5eehB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	ECOD (1.6)
C	Dimerisation2	e5eehC2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Dimerisation2	ECOD (1.6)
C	Methyltransf_11_4	e5eehC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	1.10.287.1350	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		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)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	1.10.287.1350	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		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)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C	1.10.287.1350	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
C	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, C	PF00891	O-methyltransferase domain (Methyltransf_2)	O-methyltransferase domain	This family includes a range of O-methyltransferases. These enzymes utilise S-adenosyl methionine.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Carminomycin 4-O-methyltransferase DnrK	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity O-methyltransferase activity	methylation metabolic process aminoglycoside antibiotic biosynthetic process glycosyl compound metabolic process cellular biosynthetic process polyketide metabolic process carbohydrate derivative metabolic process antibiotic biosynthetic process secondary metabolic process antibiotic metabolic process cellular ketone metabolic process organic substance metabolic process secondary metabolite biosynthetic process organic substance biosynthetic process methylation metabolic process aminoglycoside antibiotic biosynthetic process glycosyl compound metabolic process cellular biosynthetic process polyketide metabolic process carbohydrate derivative metabolic process antibiotic biosynthetic process secondary metabolic process antibiotic metabolic process cellular ketone metabolic process organic substance metabolic process secondary metabolite biosynthetic process organic substance biosynthetic process small molecule metabolic process carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process daunorubicin metabolic process small molecule biosynthetic process cellular metabolic process glycoside metabolic process glycoside biosynthetic process organic cyclic compound metabolic process daunorubicin biosynthetic process biosynthetic process aminoglycoside antibiotic metabolic process polyketide biosynthetic process organic cyclic compound biosynthetic process cellular process ketone biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR001077	O-methyltransferase domain	Domain
A, B, C	IPR016461	O-methyltransferase COMT-type	Family
A, B, C	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.