5T67

x-ray structure of the KijD1 C3-methyltransferase from Actinomadura kijaniata in complex with SAH and dTDP-sugar product

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	d5t67a_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	C-3'-methyltransferase-like	automated matches	(Actinomadura kijaniata ) [TaxId: 46161 ],	SCOPe (2.08)
B	d5t67b_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	C-3'-methyltransferase-like	automated matches	(Actinomadura kijaniata ) [TaxId: 46161 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Zinc beta-ribbon	8051771	3001238	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8051770	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CoA-binding Rossmann-fold domain	8051772	3000049	SCOP2B (2022-06-29)
B	SCOP2 Family	C-methyltransferase-associated zinc finger	8050859	4007081	SCOP2 (2022-06-29)
B	SCOP2 Family	C-methyltransferase C-terminal domain-like	8050922	4007110	SCOP2 (2022-06-29)
B	SCOP2 Family	C3-methyltransferase catalytic domain-like	8051769	4007507	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Zinc beta-ribbon	8051771	3001238	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	CoA-binding Rossmann-fold domain	8051772	3000049	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8051770	3000118	SCOP2 (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	Methyltransf_14	e5t67A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Methyltransf_14	ECOD (1.6)
A	Methyltransf_11_3	e5t67A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_3	ECOD (1.6)
A	Methyltransf_13	e5t67A3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Methyltransf_13	ECOD (1.6)
B	Methyltransf_14	e5t67B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: Methyltransf_14	ECOD (1.6)
B	Methyltransf_11_3	e5t67B3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_3	ECOD (1.6)
B	Methyltransf_13	e5t67B1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Methyltransf_13	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.20.50.110	Special	Other non-globular	N-terminal domain of TfIIb	Methyltransferase, zinc-binding domain	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)
A	6.10.250.3100	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	6.20.50.110	Special	Other non-globular	N-terminal domain of TfIIb	Methyltransferase, zinc-binding domain	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)
B	6.10.250.3100	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08421	Putative zinc binding domain (Methyltransf_13)	Putative zinc binding domain	This domain is found at the N-terminus of bacterial methyltransferases and contains four conserved cysteines suggesting a potential zinc binding domain.	Domain
A, B	PF08484	C-methyltransferase C-terminal domain (Methyltransf_14)	C-methyltransferase C-terminal domain	-	Family
A, B	PF13489	Methyltransferase domain (Methyltransf_23)	Methyltransferase domain	This family appears to be a methyltransferase domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Sugar 3-C-methyl transferase	cation binding ion binding binding metal ion binding small molecule binding transferase activity catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR013630	Methyltransferase putative zinc binding domain	Domain
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR038576	Methyltransferase putative zinc binding domain superfamily	Homologous Superfamily
A, B	IPR013691	C-methyltransferase	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.