3NJR | pdb_00003njr

Crystal structure of C-terminal domain of precorrin-6Y C5,15-methyltransferase from Rhodobacter capsulatus

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)
B	d3njrb1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Rhodobacter capsulatus SB 1003 ) [TaxId: 272942 ],	SCOPe (2.08)
B	d3njrb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Rhodobacter capsulatus SB 1003 ) [TaxId: 272942 ],	SCOPe (2.08)
A	d3njra1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Rhodobacter capsulatus SB 1003 ) [TaxId: 272942 ],	SCOPe (2.08)
A	d3njra2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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	S-adenosyl-L-methionine-dependent methyltransferases	8063396	3000118	SCOP2B (2022-06-29)
A	SCOP2 Family	Precorrin-6Y methyltransferase (CbiT)	8063395	4003082	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063396	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)
B	Flavin_Reduct	e3njrB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (v294.1)
A	Pro_isomerase	e3njrA1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Pro_isomerase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	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	Precorrin-6y methylase	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity precorrin-6Y C5,15-methyltransferase (decarboxylating) activity catalytic activity, acting on a protein protein methyltransferase activity	methylation metabolic process cellular process cobalamin metabolic process cobalamin biosynthetic process water-soluble vitamin biosynthetic process tetrapyrrole metabolic process small molecule biosynthetic process vitamin biosynthetic process vitamin metabolic process tetrapyrrole biosynthetic process biosynthetic process small molecule metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR014008	Cobalamin biosynthesis, precorrin-6Y methyltransferase, CbiT subunit	Family
A, B	IPR035996	Tetrapyrrole methylase superfamily	Homologous Superfamily
A, B	IPR014777	Tetrapyrrole methylase, subdomain 1	Homologous Superfamily
A, B	IPR006365	Cobalamin (vitamin B12) biosynthesis CobL/Precorrin-6Y C(5,15)-methyltransferase	Family
A, B	IPR000878	Tetrapyrrole methylase	Domain
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR012818	Precorrin-6Y methyltransferase	Domain
A, B	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.