3E05 | pdb_00003e05

CRYSTAL STRUCTURE OF Precorrin-6y C5,15-methyltransferase FROM Geobacter metallireducens GS-15

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)
H	d3e05h_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Geobacter metallireducens GS-15 ) [TaxId: 269799 ],	SCOPe (2.08)
G	d3e05g_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Geobacter metallireducens GS-15 ) [TaxId: 269799 ],	SCOPe (2.08)
F	d3e05f_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Geobacter metallireducens GS-15 ) [TaxId: 269799 ],	SCOPe (2.08)
E	d3e05e_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Geobacter metallireducens GS-15 ) [TaxId: 269799 ],	SCOPe (2.08)
D	d3e05d_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Geobacter metallireducens GS-15 ) [TaxId: 269799 ],	SCOPe (2.08)
C	d3e05c_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Geobacter metallireducens GS-15 ) [TaxId: 269799 ],	SCOPe (2.08)
B	d3e05b_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Geobacter metallireducens GS-15 ) [TaxId: 269799 ],	SCOPe (2.08)
A	d3e05a_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	(Geobacter metallireducens GS-15 ) [TaxId: 269799 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063392	3000118	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063392	3000118	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063392	3000118	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063392	3000118	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063392	3000118	SCOP2B (2022-06-29)
C	SCOP2 Family	Precorrin-6Y methyltransferase (CbiT)	8063391	4003082	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063392	3000118	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063392	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8063392	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)
H		e3e05H1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Lipocalin	F:	ECOD (20:10:01)
G		e3e05G1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Lipocalin	F:	ECOD (20:10:01)
F		e3e05F1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Lipocalin	F:	ECOD (20:10:01)
E		e3e05E1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Lipocalin	F:	ECOD (20:10:01)
D		e3e05D1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Lipocalin	F:	ECOD (20:10:01)
C		e3e05C1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Lipocalin	F:	ECOD (20:10:01)
B		e3e05B1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Lipocalin	F:	ECOD (20:10:01)
A		e3e05A1	A: Profilin-like	X: sensor domains	H: sensor domains	T: Resolvase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	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)
F	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)
D	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)
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, C, D, E A, B, C, D, E, F, G, H	Precorrin-6Y C5,15-methyltransferase (Decarboxylating)	catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity transferase activity methyltransferase activity catalytic 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, 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	IPR014776	Tetrapyrrole methylase, subdomain 2	Homologous Superfamily
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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.