2YXD | pdb_00002yxd

Crystal Structure of Cobalamin biosynthesis precorrin 8W decarboxylase (cbiT)

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	d2yxda_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
B	d2yxdb_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)

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)	8063393	4003082	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063394	3000118	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063394	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		e2yxdA1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F:	ECOD (v294.1)
B		e2yxdB1	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F:	ECOD (v294.1)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13847	Methyltransferase domain (Methyltransf_31)	Methyltransferase domain	This family appears to have methyltransferase activity.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Probable cobalt-precorrin-6Y C(15)-methyltransferase [decarboxylating]	transferase activity, transferring one-carbon groups cobalt-precorrin-6B C5-methyltransferase activity transferase activity methyltransferase activity catalytic 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 anaerobic cobalamin biosynthetic 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	IPR025714	Methyltransferase domain	Domain
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR050714	Cobalamin biosynthesis methyltransferase	Family
A, B	IPR023475	Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) CbiT	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.