Annotations: 1K98

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1k98a1	All alpha proteins	Methionine synthase domain-like	Methionine synthase domain	Methionine synthase domain	Methionine synthase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1k98a2	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	d1k98a3	Alpha and beta proteins (a+b)	Methionine synthase activation domain-like	Methionine synthase activation domain-like	Methionine synthase SAM-binding domain	Methionine synthase SAM-binding 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)
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)
A	SCOP2B Superfamily	Methionine synthase activation domain-like	8037194	3001398	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		e1k98A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: Cation_efflux	F:	ECOD (20:10:01)
A		e1k98A2	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: CBAH	F:	ECOD (20:10:01)
A		e1k98A3	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: NAD_binding_1	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
A	3.10.196.10	Alpha Beta	Roll	Cobalamin-dependent Methionine Synthase	domain 1	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	1.10.288.10	Mainly Alpha	Orthogonal Bundle	Cobalamin-dependent Methionine Synthase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02965	Vitamin B12 dependent methionine synthase, activation domain (Met_synt_B12)	Vitamin B12 dependent methionine synthase, activation domain		Domain
A	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 b ...	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	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	Methionine synthase	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 transition metal 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 transition metal ion binding zinc ion 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 tetrahydrofolate interconversion one-carbon metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003759	Cobalamin (vitamin B12)-binding module, cap domain	Domain
A	IPR050554	Methionine Synthase/Corrinoid	Family
A	IPR011005	Dihydropteroate synthase-like superfamily	Homologous Superfamily
A	IPR033706	Methionine synthase, B12-binding domain	Domain
A	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
A	IPR003726	Homocysteine-binding domain	Domain
A	IPR004223	Vitamin B12-dependent methionine synthase, activation domain	Domain
A	IPR036589	Homocysteine-binding domain superfamily	Homologous Superfamily
A	IPR000489	Pterin-binding domain	Domain
A	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
A	IPR011822	Cobalamin-dependent methionine synthase	Family
A	IPR036594	Methionine synthase domain	Homologous Superfamily
A	IPR037010	Vitamin B12-dependent methionine synthase, activation domain superfamily	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.