5JR3 | pdb_00005jr3

Crystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 4-methylumbelliferone

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
C	d5jr3c1	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	d5jr3c2	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	d5jr3b1	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	d5jr3b2	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)
A	d5jr3a1	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	d5jr3a2	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)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8054284	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8054283	3000118	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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	DnaJ	e5jr3C1	A: a/b three-layered sandwiches	X: Thymine dioxygenase JBP1 DNA-binding domain-like	H: Oligo-peptide binding protein (OPPA) insertion domain	T: Oligo-peptide binding protein (OPPA) insertion domain	F: DnaJ	ECOD (v294.1)
B	DnaJ	e5jr3B1	A: a/b three-layered sandwiches	X: Thymine dioxygenase JBP1 DNA-binding domain-like	H: Oligo-peptide binding protein (OPPA) insertion domain	T: Oligo-peptide binding protein (OPPA) insertion domain	F: DnaJ	ECOD (v294.1)
A	DnaJ	e5jr3A1	A: a/b three-layered sandwiches	X: Thymine dioxygenase JBP1 DNA-binding domain-like	H: Oligo-peptide binding protein (OPPA) insertion domain	T: Oligo-peptide binding protein (OPPA) insertion domain	F: DnaJ	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)

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 protein binding binding protein dimerization activity	methylation metabolic process cellular process aminoglycoside antibiotic biosynthetic process carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process daunorubicin metabolic process small molecule biosynthetic process ketone metabolic process polyketide metabolic process glycoside metabolic process carbohydrate derivative metabolic process antibiotic biosynthetic process glycoside biosynthetic process methylation metabolic process cellular process aminoglycoside antibiotic biosynthetic process carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process daunorubicin metabolic process small molecule biosynthetic process ketone metabolic process polyketide metabolic process glycoside metabolic process carbohydrate derivative metabolic process antibiotic biosynthetic process glycoside biosynthetic process secondary metabolic process antibiotic metabolic process daunorubicin biosynthetic process biosynthetic process polyketide biosynthetic process secondary metabolite biosynthetic process small molecule metabolic process ketone biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR012967	Caffeic acid 3-O-methyltransferase-like, dimerisation domain	Domain
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	IPR016461	O-methyltransferase-like	Family
A, B, C	IPR001077	O-methyltransferase, C-terminal domain	Domain
A, B, C	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily

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.