3NDC

Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3ndcb_	Alpha and beta proteins (a/b)	Tetrapyrrole methylase	Tetrapyrrole methylase	automated matches	automated matches	Rhodopseudomonas capsulata (Rhodobacter capsulatus SB 1003 ) [TaxId: 272942 ],	SCOPe (2.08)
A	d3ndca1	Alpha and beta proteins (a/b)	Tetrapyrrole methylase	Tetrapyrrole methylase	automated matches	automated matches	Rhodopseudomonas capsulata (Rhodobacter capsulatus SB 1003 ) [TaxId: 272942 ],	SCOPe (2.08)
A	d3ndca2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Rhodopseudomonas capsulata (Rhodobacter capsulatus SB 1003 ) [TaxId: 272942 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Tetrapyrrole methylase	8067842	3000017	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tetrapyrrole methylase	8067842	3000017	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)
B	TP_methylase_C	e3ndcB2	A: a+b two layers	X: Tetrapyrrole methylase C-terminal domain-like	H: Tetrapyrrole methylase C-terminal domain (From Topology)	T: Tetrapyrrole methylase C-terminal domain	F: TP_methylase_C	ECOD (1.6)
B	TP_methylase_N	e3ndcB1	A: a/b three-layered sandwiches	X: Tetrapyrrole methylase N-terminal domain (From Topology)	H: Tetrapyrrole methylase N-terminal domain (From Topology)	T: Tetrapyrrole methylase N-terminal domain	F: TP_methylase_N	ECOD (1.6)
A	TP_methylase_C	e3ndcA2	A: a+b two layers	X: Tetrapyrrole methylase C-terminal domain-like	H: Tetrapyrrole methylase C-terminal domain (From Topology)	T: Tetrapyrrole methylase C-terminal domain	F: TP_methylase_C	ECOD (1.6)
A	TP_methylase_N	e3ndcA1	A: a/b three-layered sandwiches	X: Tetrapyrrole methylase N-terminal domain (From Topology)	H: Tetrapyrrole methylase N-terminal domain (From Topology)	T: Tetrapyrrole methylase N-terminal domain	F: TP_methylase_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.1010.10	Alpha Beta	3-Layer(aba) Sandwich	Cobalt-precorrin-4 Transmethylase	domain 1	CATH (4.3.0)
B	3.30.950.10	Alpha Beta	2-Layer Sandwich	Methyltransferase, Cobalt-precorrin-4 Transmethylase	Domain 2	CATH (4.3.0)
A	3.40.1010.10	Alpha Beta	3-Layer(aba) Sandwich	Cobalt-precorrin-4 Transmethylase	domain 1	CATH (4.3.0)
A	3.30.950.10	Alpha Beta	2-Layer Sandwich	Methyltransferase, Cobalt-precorrin-4 Transmethylase	Domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00590	Tetrapyrrole (Corrin/Porphyrin) Methylases (TP_methylase)	Tetrapyrrole (Corrin/Porphyrin) Methylases	This family uses S-AdoMet in the methylation of diverse substrates. This family includes a related group of bacterial proteins of unknown function, including Swiss:P45528. This family includes the methylase Dipthine synthase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Precorrin-4 C(11)-methyltransferase	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity precorrin-4 C11-methyltransferase activity	methylation metabolic process cobalamin metabolic process cobalamin biosynthetic process cellular biosynthetic process organonitrogen compound biosynthetic process vitamin biosynthetic process cellular nitrogen compound biosynthetic process organic substance metabolic process tetrapyrrole biosynthetic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process small molecule metabolic process methylation metabolic process cobalamin metabolic process cobalamin biosynthetic process cellular biosynthetic process organonitrogen compound biosynthetic process vitamin biosynthetic process cellular nitrogen compound biosynthetic process organic substance metabolic process tetrapyrrole biosynthetic process heterocycle metabolic process organic substance biosynthetic process nitrogen compound metabolic process small molecule metabolic process water-soluble vitamin metabolic process water-soluble vitamin biosynthetic process organonitrogen compound metabolic process tetrapyrrole metabolic process small molecule biosynthetic process cellular metabolic process cellular nitrogen compound metabolic process heterocycle biosynthetic process vitamin metabolic process organic cyclic compound metabolic process biosynthetic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process cellular process cellular aromatic compound metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR035996	Tetrapyrrole methylase superfamily	Homologous Superfamily
A, B	IPR014777	Tetrapyrrole methylase, subdomain 1	Homologous Superfamily
A, B	IPR003043	Uroporphiryn-III C-methyltransferase, conserved site	Conserved Site
A, B	IPR014776	Tetrapyrrole methylase, subdomain 2	Homologous Superfamily
A, B	IPR000878	Tetrapyrrole methylase	Domain
A, B	IPR006362	Cobalamin (vitamin B12) biosynthesis CobM/CbiF, precorrin-4 C11-methyltransferase	Domain

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.