1BMT

HOW A PROTEIN BINDS B12: A 3.O ANGSTROM X-RAY STRUCTURE OF THE B12-BINDING DOMAINS OF METHIONINE SYNTHASE

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1bmtb1	All alpha proteins	Methionine synthase domain-like	Methionine synthase domain	Methionine synthase domain	Methionine synthase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1bmtb2	Alpha and beta proteins (a/b)	Flavodoxin-like	Cobalamin (vitamin B12)-binding domain	Cobalamin (vitamin B12)-binding domain	Methionine synthase, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1bmta1	All alpha proteins	Methionine synthase domain-like	Methionine synthase domain	Methionine synthase domain	Methionine synthase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1bmta2	Alpha and beta proteins (a/b)	Flavodoxin-like	Cobalamin (vitamin B12)-binding domain	Cobalamin (vitamin B12)-binding domain	Methionine synthase, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Cobalamin (vitamin B12)-binding domain	8039533	3001260	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Methionine synthase alpha-helical domain-like	8039532	3000342	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cobalamin (vitamin B12)-binding domain	8039533	3001260	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Methionine synthase alpha-helical domain-like	8039532	3000342	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	B12-binding_2	e1bmtB1	A: alpha arrays	X: Methionine synthase domain-like (From Topology)	H: Methionine synthase domain-like (From Topology)	T: Methionine synthase domain-like	F: B12-binding_2	ECOD (1.6)
B	B12-binding	e1bmtB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
A	B12-binding_2	e1bmtA1	A: alpha arrays	X: Methionine synthase domain-like (From Topology)	H: Methionine synthase domain-like (From Topology)	T: Methionine synthase domain-like	F: B12-binding_2	ECOD (1.6)
A	B12-binding	e1bmtA2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)
B	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
A	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)
A	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02607	B12 binding domain (B12-binding_2)	B12 binding domain	This B12 binding domain is found in methionine synthase EC:2.1.1.13 Swiss:Q99707, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of Pfam:PF02310. The structure of this domain is known [1], it is a 4 helix ...	This B12 binding domain is found in methionine synthase EC:2.1.1.13 Swiss:Q99707, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of Pfam:PF02310. The structure of this domain is known [1], it is a 4 helix bundle. Many of the conserved residues in this domain are involved in B12 binding, such as those in the MXXVG motif.	Domain
A, B	PF02310	B12 binding domain (B12-binding)	B12 binding domain	This domain binds to B12 (adenosylcobamide)[1-3], it is found in several enzymes, such as glutamate mutase Swiss:Q05488, methionine synthase Swiss:Q99707 and methylmalonyl-CoA mutase Swiss:P22033. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, ...	This domain binds to B12 (adenosylcobamide)[1-3], it is found in several enzymes, such as glutamate mutase Swiss:Q05488, methionine synthase Swiss:Q99707 and methylmalonyl-CoA mutase Swiss:P22033. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	METHIONINE SYNTHASE	vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding methionine synthase activity 5-methyltetrahydrofolate-dependent methyltransferase activity transferase activity, transferring one-carbon groups S-methyltransferase activity transferase activity methyltransferase activity catalytic activity vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding methionine synthase activity 5-methyltetrahydrofolate-dependent methyltransferase activity transferase activity, transferring one-carbon groups S-methyltransferase activity transferase activity methyltransferase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	homocysteine metabolic process organonitrogen compound metabolic process oxoacid metabolic process sulfur amino acid metabolic process cellular 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 organic substance metabolic process metabolic process small molecule metabolic process homocysteine metabolic process organonitrogen compound metabolic process oxoacid metabolic process sulfur amino acid metabolic process cellular 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 organic substance metabolic process metabolic process small molecule metabolic process cellular process sulfur compound metabolic process cellular biosynthetic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process organic substance biosynthetic process methionine biosynthetic process small molecule biosynthetic process L-amino acid biosynthetic process methionine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process organic cyclic compound metabolic process folic acid-containing compound metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process cellular modified amino acid metabolic process methylation tetrahydrofolate interconversion one-carbon metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity 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	IPR011005	Dihydropteroate synthase-like superfamily	Homologous Superfamily
A, B	IPR033706	Methionine synthase, B12-binding domain	Domain
A, B	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
A, B	IPR003726	Homocysteine-binding domain	Domain
A, B	IPR004223	Vitamin B12-dependent methionine synthase, activation domain	Domain
A, B	IPR036589	Homocysteine-binding domain superfamily	Homologous Superfamily
A, B	IPR000489	Pterin-binding domain	Domain
A, B	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
A, B	IPR011822	Cobalamin-dependent methionine synthase	Family
A, B	IPR036594	Methionine synthase domain	Homologous Superfamily
A, B	IPR037010	Vitamin B12-dependent methionine synthase, activation domain superfamily	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	methionine synthase M-CSA #268	Methionine synthase (MetH) is a cobalamin (vitamin B12) and zinc dependent enzyme that catalyses the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. The enzyme's cofactor is re-methylated using methyltetrahydrofolate. During the catalytic cycle, the highly reactive cob(I)alamin intermediate can be oxidised to produce an inactive cob(II)alamin enzyme; the enzyme is then reactivated via reductive methylation by the activation domain.	Defined by 3 residues: ASP:A-107 [auth A-757]HIS:A-109 [auth A-759]SER:A-160 [auth A-810] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.1.1.13 (PDB Primary Data) Search M-CSA Motif + EC 2.1.1.13

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.