5T67 | pdb_00005t67

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
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		e5t67A1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F:	ECOD (develop294)
B		e5t67B1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F:	ECOD (develop294)

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)

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.