2I2X | pdb_00002i2x

Crystal structure of methanol:cobalamin methyltransferase complex MtaBC from Methanosarcina barkeri

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8106670	3000609	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8106670	3000609	SCOP2B (2022-06-29)
I	SCOP2 Family	MtaB-like	8047303	4005562	SCOP2 (2022-06-29)
I	SCOP2 Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8106670	3000609	SCOP2 (2022-06-29)
O	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8106670	3000609	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8106670	3000609	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8106670	3000609	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8106670	3000609	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8106670	3000609	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	MtaB	e2i2xA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MtaB	ECOD (1.6)
E	MtaB	e2i2xE1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MtaB	ECOD (1.6)
I	MtaB	e2i2xI1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MtaB	ECOD (1.6)
O	MtaB	e2i2xO1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MtaB	ECOD (1.6)
M	MtaB	e2i2xM1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MtaB	ECOD (1.6)
K	MtaB	e2i2xK1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MtaB	ECOD (1.6)
G	MtaB	e2i2xG1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MtaB	ECOD (1.6)
C	MtaB	e2i2xC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MtaB	ECOD (1.6)
B	B12-binding_2	e2i2xB2	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	e2i2xB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
D	B12-binding_2	e2i2xD1	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)
D	B12-binding	e2i2xD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
F	B12-binding_2	e2i2xF1	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)
F	B12-binding	e2i2xF2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
H	B12-binding_2	e2i2xH1	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)
H	B12-binding	e2i2xH2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
J	B12-binding_2	e2i2xJ1	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)
J	B12-binding	e2i2xJ2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
L	B12-binding_2	e2i2xL1	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)
L	B12-binding	e2i2xL2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
P	B12-binding_2	e2i2xP1	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)
P	B12-binding	e2i2xP2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
N	B12-binding_2	e2i2xN1	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)
N	B12-binding	e2i2xN2	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)
D	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)
D	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
F	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)
F	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
H	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)
H	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
J	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)
J	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
L	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)
L	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
P	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)
P	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
N	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (4.3.0)
N	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, C, E, G, I A, C, E, G, I, K, M, O	PF12176	Methanol-cobalamin methyltransferase B subunit (MtaB)	Methanol-cobalamin methyltransferase B subunit	This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 460 amino acids in length. MtaB folds as a TIM barrel and contains a novel zinc-binding motif. Zinc(II) lies at the bottom of a funnel formed at the C ...	This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 460 amino acids in length. MtaB folds as a TIM barrel and contains a novel zinc-binding motif. Zinc(II) lies at the bottom of a funnel formed at the C-terminal beta-barrel end and ligates to two cysteinyl sulfurs (Cys-220 and Cys-269) and one carboxylate oxygen (Glu-164). The function of this protein is to catalyse the cleavage of the C O bond in methanol by an SN2 mechanism. It complexes with MtaA and MtaC to perform this function.	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	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
B, D, F, H, J B, D, F, H, J, L, N, P	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, C, E, G, I A, C, E, G, I, K, M, O	Methyltransferase 1	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	methylation metabolic process cellular process	-
B, D, F, H, J B, D, F, H, J, L, N, P	Methyltransferase 1	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding vitamin binding cobalamin binding tetrapyrrole binding heterocyclic compound binding methionine synthase activity 5-methyltetrahydrofolate-dependent methyltransferase activity transferase activity, transferring one-carbon groups cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding vitamin binding cobalamin binding tetrapyrrole binding heterocyclic compound binding methionine synthase activity 5-methyltetrahydrofolate-dependent methyltransferase activity transferase activity, transferring one-carbon groups S-methyltransferase activity transferase activity methyltransferase activity catalytic activity	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 cellular respiration energy derivation by oxidation of organic compounds alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds methanogenesis hydrocarbon biosynthetic process anaerobic respiration	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O	IPR021079	Methanol-cobalamin methyltransferase, B subunit	Family
B, D, F, H, J B, D, F, H, J, L, N, P	IPR003759	Cobalamin (vitamin B12)-binding module, cap domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR050554	Methionine Synthase/Corrinoid	Family
B, D, F, H, J B, D, F, H, J, L, N, P	IPR012741	Methyltransferase cognate corrinoid protein	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P	IPR036594	Methionine synthase domain	Homologous Superfamily