3HM2

Crystal Structure of Putative Precorrin-6Y C5,15-Methyltransferase Targeted Domain from Corynebacterium diphtheriae

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Precorrin-6Y methyltransferase (CbiT)	8063397	4003082	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063398	3000118	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063398	3000118	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063398	3000118	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063398	3000118	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063398	3000118	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063398	3000118	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063398	3000118	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063398	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	Methyltransf_11_4	e3hm2A1	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	Methyltransf_11_4	e3hm2B1	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	Methyltransf_11_4	e3hm2C1	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)
D	Methyltransf_11_4	e3hm2D1	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)
E	Methyltransf_11_4	e3hm2E1	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)
F	Methyltransf_11_4	e3hm2F1	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)
G	Methyltransf_11_4	e3hm2G1	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)
H	Methyltransf_11_4	e3hm2H1	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	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	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	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
D	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
E	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
F	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
G	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
H	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, D, E A, B, C, D, E, F, G, H	precorrin-6Y C5,15-methyltransferase	catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity transferase activity methyltransferase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	methylation metabolic process cobalamin metabolic process cobalamin biosynthetic process water-soluble vitamin biosynthetic process organonitrogen compound metabolic process tetrapyrrole metabolic process small molecule biosynthetic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process vitamin biosynthetic process vitamin metabolic process tetrapyrrole biosynthetic process methylation metabolic process cobalamin metabolic process cobalamin biosynthetic process water-soluble vitamin biosynthetic process organonitrogen compound metabolic process tetrapyrrole metabolic process small molecule biosynthetic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process vitamin biosynthetic process vitamin metabolic process tetrapyrrole biosynthetic process biosynthetic process small molecule metabolic process cellular process water-soluble vitamin metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR014008	Cobalamin biosynthesis, precorrin-6Y methyltransferase, CbiT subunit	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR035996	Tetrapyrrole methylase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR014777	Tetrapyrrole methylase, subdomain 1	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006365	Cobalamin (vitamin B12) biosynthesis CobL/Precorrin-6Y C(5,15)-methyltransferase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000878	Tetrapyrrole methylase	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012818	Precorrin-6Y methyltransferase	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR050714	Cobalamin biosynthesis 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 R01GM133198.