3BOF | pdb_00003bof

Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+ and Homocysteine

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	d3bofa1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Dihydropteroate synthetase-like	Methyltetrahydrofolate-utiluzing methyltransferases	Cobalamin-dependent methionine synthase MetH, C-terminal domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d3bofa2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Homocysteine S-methyltransferase	Homocysteine S-methyltransferase	Cobalamin-dependent methionine synthase MetH, N-terminal domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d3bofb1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Dihydropteroate synthetase-like	Methyltetrahydrofolate-utiluzing methyltransferases	Cobalamin-dependent methionine synthase MetH, C-terminal domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d3bofb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Homocysteine S-methyltransferase	Homocysteine S-methyltransferase	Cobalamin-dependent methionine synthase MetH, N-terminal domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Methyltetrahydrofolate-utiluzing methyltransferases	8027015	4003343	SCOP2 (2022-06-29)
A	SCOP2 Family	Homocysteine S-methyltransferase	8027017	4002883	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Dihydropteroate synthetase-like	8039394	3000643	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Homocysteine S-methyltransferase	8039396	3001844	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Dihydropteroate synthetase-like	8039394	3000643	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Homocysteine S-methyltransferase	8039396	3001844	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		e3bofA1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: S-methyl_trans	F:	ECOD (20:10:01)
A		e3bofA2	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: Pterin_bind	F:	ECOD (20:10:01)
B		e3bofB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: PF27526	F:	ECOD (20:10:01)
B		e3bofB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Epimerase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.330	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Homocysteine-binding-like domain	CATH (4.3.0)
A	3.20.20.20	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Dihydropteroate synthase-like	CATH (4.3.0)
B	3.20.20.330	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Homocysteine-binding-like domain	CATH (4.3.0)
B	3.20.20.20	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Dihydropteroate synthase-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02574	Homocysteine S-methyltransferase (S-methyl_trans)	Homocysteine S-methyltransferase	-	Family
A, B	PF00809	Pterin binding enzyme (Pterin_bind)	Pterin binding enzyme	This family includes a variety of pterin binding enzymes that all adopt a TIM barrel fold. The family includes dihydropteroate synthase EC:2.5.1.15 as well as a group methyltransferase enzymes including methyltetrahydrofolate, corrinoid iron-sulfur p ...	This family includes a variety of pterin binding enzymes that all adopt a TIM barrel fold. The family includes dihydropteroate synthase EC:2.5.1.15 as well as a group methyltransferase enzymes including methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) Swiss:Q46389 that catalyses a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation. It transfers the N5-methyl group from methyltetrahydrofolate (CH3-H4folate) to a cob(I)amide centre in another protein, the corrinoid iron-sulfur protein. MeTr is a member of a family of proteins that includes methionine synthase and methanogenic enzymes that activate the methyl group of methyltetra-hydromethano(or -sarcino)pterin [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	5-methyltetrahydrofolate S-homocysteine methyltransferase	vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding methionine synthase activity transferase activity, transferring one-carbon groups S-methyltransferase activity transferase activity methyltransferase activity catalytic activity cation binding ion binding vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding methionine synthase activity transferase activity, transferring one-carbon groups S-methyltransferase activity transferase activity methyltransferase activity catalytic activity cation binding ion binding metal ion binding	homocysteine metabolic process oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process folic acid-containing compound metabolic process homocysteine metabolic process oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process folic acid-containing compound metabolic process modified amino acid metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process methylation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003759	Cobalamin (vitamin B12)-binding module, cap domain	Domain
A, B	IPR050554	Methionine Synthase/Corrinoid	Family
A, B	IPR011005	Dihydropteroate synthase-like superfamily	Homologous Superfamily
A, B	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
A, B	IPR003726	Homocysteine-binding domain	Domain
A, B	IPR036589	Homocysteine-binding domain superfamily	Homologous Superfamily
A, B	IPR017215	5-methyltetrahydrofolate-homocysteine S-methyltransferase, bacterial	Family
A, B	IPR000489	Pterin-binding domain	Domain
A, B	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
A, B	IPR036594	Methionine synthase domain	Homologous Superfamily

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.