DB code: M00145

CATH domain 2.40.50.100 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
3.90.226.10 : 2-enoyl-CoA Hydratase; Chain A, domain 1 Catalytic domain
3.90.226.10 : 2-enoyl-CoA Hydratase; Chain A, domain 1
3.20.20.- : TIM Barrel
E.C. 2.1.3.1
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
2.40.50.100 : OB fold (Dihydrolipoamide Acetyltransferase, E2P) M00163 M00222 M00188 M00189 T00223 M00190 M00191 M00208
3.90.226.10 : 2-enoyl-CoA Hydratase; Chain A, domain 1 M00122 S00849 D00254

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P02904 Methylmalonyl-CoA carboxyltransferase 1.3S subunit
EC 2.1.3.1
Biotin carboxyl carrier protein of transcarboxylase
Transcarboxylase, 1.3S subunit
PF00364 (Biotin_lipoyl)
[Graphical View]
Q8GBW6 Methylmalonyl-CoA carboxyltransferase 12S subunit
EC 2.1.3.1
Transcarboxylase 12S subunit
PF01039 (Carboxyl_trans)
[Graphical View]

KEGG enzyme name
methylmalonyl-CoA carboxytransferase
transcarboxylase
methylmalonyl coenzyme A carboxyltransferase
methylmalonyl-CoA transcarboxylase
oxalacetic transcarboxylase
methylmalonyl-CoA carboxyltransferase
methylmalonyl-CoA carboxyltransferase
(S)-2-methyl-3-oxopropanoyl-CoA:pyruvate carboxyltransferase
(S)-2-methyl-3-oxopropanoyl-CoA:pyruvate carboxytransferasecarboxytransferase [incorrect]

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P02904 BCCP_PROFR (S)-methylmalonyl-CoA + pyruvate = propanoyl- CoA + oxaloacetate. Transcarboxylase is composed of three subunits: 1.3S, 5S, and 12S. The core of the enzyme is composed of six 12S subunits. On each side of the core there are three pairs of 5S subunits. Each 5S dimer is attached to the core by two 1.3S subunits. Thus the total number of chains is 30 (6 + 12 + 12).
Q8GBW6 12S_PROFR (S)-methylmalonyl-CoA + pyruvate = propanoyl- CoA + oxaloacetate. Homohexamer. Transcarboxylase is composed of three subunits: 1.3S, 5S, and 12S. The core of the enzyme is composed of six 12S subunits. On each side of the core there are three pairs of 5S subunits. Each 5S dimer is attached to the core by two 1.3S subunits. Thus the total number of chains is 30 (6 + 12 + 12).

KEGG Pathways
Map code Pathways E.C.
MAP00640 Propanoate metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00120 C00175 C00038 C00683 C00022 C00100 C00036
E.C.
Compound Biotin Cobalt Zinc (S)-2-Methyl-3-oxopropanoyl-CoA Pyruvate Propanoyl-CoA Oxaloacetate
Type amide group,amine group,fatty acid,sulfide group heavy metal heavy metal amine group,carbohydrate,carboxyl group,nucleotide ,peptide/protein,sulfide group carbohydrate,carboxyl group amine group,carbohydrate,nucleotide ,peptide/protein,sulfide group carbohydrate,carboxyl group
ChEBI 15956
48828
29105
15466
32816
15539
30744
PubChem 171548
104729
32051
11966111
439291
1060
439164
92753
970
1dczA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1dd2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1on3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:MCA Analogue:DXX Unbound Unbound
1on3B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:MCA Analogue:DXX Unbound Unbound
1on3C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:MCA Analogue:DXX Unbound Unbound
1on3D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:MCA Analogue:DXX Unbound Unbound
1on3E01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:MCA Analogue:DXX Unbound Unbound
1on3F01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:MCA Analogue:DXX Unbound Unbound
1on9A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:MCA Unbound Unbound Unbound
1on9B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:MCA Unbound Unbound Unbound
1on9C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:MCA Unbound Unbound Unbound
1on9D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:MCA Unbound Unbound Unbound
1on9E01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:MCA Unbound Unbound Unbound
1on9F01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:MCA Unbound Unbound Unbound
1on3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:_CD Unbound Unbound Unbound Unbound Unbound
1on3B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1on3C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:_CD Unbound Unbound Unbound Unbound Unbound
1on3D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1on3E02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:_CD Unbound Unbound Unbound Unbound Unbound
1on3F02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1on9A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:_CD Unbound Unbound Unbound Unbound Unbound
1on9B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1on9C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:_CD Unbound Unbound Unbound Unbound Unbound
1on9D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1on9E02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:_CD Unbound Unbound Unbound Unbound Unbound
1on9F02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1dczA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1dd2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1on3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 185 ALA 143;ALA 180;GLY 182;ALA 183
1on3B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 185 ALA 143;ALA 180;GLY 182;ALA 183
1on3C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 185 ALA 143;ALA 180;GLY 182;ALA 183
1on3D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 185 ALA 143;ALA 180;GLY 182;ALA 183
1on3E01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 185 ALA 143;ALA 180;GLY 182;ALA 183
1on3F01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 185 ALA 143;ALA 180;GLY 182;ALA 183
1on9A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 185 ALA 143;ALA 180;GLY 182;ALA 183
1on9B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 185 ALA 143;ALA 180;GLY 182;ALA 183
1on9C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 185 ALA 143;ALA 180;GLY 182;ALA 183
1on9D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 185 ALA 143;ALA 180;GLY 182;ALA 183
1on9E01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 185 ALA 143;ALA 180;GLY 182;ALA 183
1on9F01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain TYR 185 ALA 143;ALA 180;GLY 182;ALA 183
1on3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 388(metal binding) GLY 414
1on3B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 388(metal binding) GLY 414
1on3C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 388(metal binding) GLY 414
1on3D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 388(metal binding) GLY 414
1on3E02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 388(metal binding) GLY 414
1on3F02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 388(metal binding) GLY 414
1on9A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 388(metal binding) GLY 414
1on9B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 388(metal binding) GLY 414
1on9C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 388(metal binding) GLY 414
1on9D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 388(metal binding) GLY 414
1on9E02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 388(metal binding) GLY 414
1on9F02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 388(metal binding) GLY 414

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[12]
Fig.7, p.4638-4639 2
[16]
Fig.6, p.2340-2341

References
[1]
Resource
Comments
Medline ID
PubMed ID 3910092
Journal Biochemistry
Year 1985
Volume 24
Pages 6163-9
Authors Hoving H, Crysell B, Leadlay PF
Title Fluorine NMR studies on stereochemical aspects of reactions catalyzed by transcarboxylase, pyruvate kinase, and enzyme I
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 3735431
Journal J Mol Biol
Year 1986
Volume 188
Pages 495-8
Authors Skrzypczak-Jankun E, Tulinsky A, Fillers JP, Kumar KG, Wood HG
Title Preliminary crystallographic data and quaternary structural implications of the central subunit of the multi-subunit complex transcarboxylase
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2269346
Journal FEBS Lett
Year 1990
Volume 277
Pages 156-8
Authors Bendrat K, Berger S, Buckel W, Etzel WA, Rohm KH
Title Carbon-13 labelled biotin--a new probe for the study of enzyme catalyzed carboxylation and decarboxylation reactions
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 1526981
Journal J Biol Chem
Year 1992
Volume 267
Pages 18407-12
Authors Shenoy BC, Xie Y, Park VL, Kumar GK, Beegen H, Wood HG, Samols D
Title The importance of methionine residues for the catalysis of the biotin enzyme, transcarboxylase. Analysis by site-directed mutagenesis
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8346913
Journal Arch Biochem Biophys
Year 1993
Volume 304
Pages 359-66
Authors Shenoy BC, Samols D, Kumar GK
Title The conserved methionines of the 1.3 S biotinyl subunit of transcarboxylase: effect of mutations on conformation and activity
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8420991
Journal J Biol Chem
Year 1993
Volume 268
Pages 2232-8
Authors Shenoy BC, Kumar GK, Samols D
Title Dissection of the biotinyl subunit of transcarboxylase into regions essential for activity and assembly
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9398186
Journal Biochemistry
Year 1997
Volume 36
Pages 14676-82
Authors Reddy DV, Shenoy BC, Carey PR, Sonnichsen FD
Title Absence of observable biotin-protein interactions in the 1.3S subunit of transcarboxylase: an NMR study
Related PDB 1dcz 1dd2
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9720239
Journal Carbohydr Res
Year 1998
Volume 309
Pages 89-94
Authors Paramonov NA, Parolis LA, Parolis H, Boan IF, Anton J, Rodriguez-Valera F
Title The structure of the exocellular polysaccharide produced by the Archaeon Haloferax gibbonsii (ATCC 33959)
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9792103
Journal Protein Sci
Year 1998
Volume 7
Pages 2156-63
Authors Reddy DV, Rothemund S, Shenoy BC, Carey PR, Sonnichsen FD
Title Structural characterization of the entire 1.3S subunit of transcarboxylase from Propionibacterium shermanii
Related PDB 1dcz 1dd2
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10542197
Journal J Biol Chem
Year 1999
Volume 274
Pages 31767-9
Authors Blanchard CZ, Chapman-Smith A, Wallace JC, Waldrop GL
Title The biotin domain peptide from the biotin carboxyl carrier protein of Escherichia coli acetyl-CoA carboxylase causes a marked increase in the catalytic efficiency of biotin carboxylase and carboxyltransferase relative to free biotin
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 10704200
Journal Biochemistry
Year 2000
Volume 39
Pages 2509-16
Authors Reddy DV, Shenoy BC, Carey PR, Sonnichsen FD
Title High resolution solution structure of the 1.3S subunit of transcarboxylase from Propionibacterium shermanii
Related PDB 1dcz 1dd2
Related UniProtKB
[12]
Resource
Comments Homologous enzyme
Medline ID
PubMed ID 10769118
Journal Biochemistry
Year 2000
Volume 39
Pages 4630-9
Authors Benning MM, Haller T, Gerlt JA, Holden HM
Title New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 11173475
Journal Acta Crystallogr D Biol Crystallogr
Year 2001
Volume 57
Pages 266-8
Authors Wang YF, Hyatt DC, Rivera RE, Carey PR, Yee VC
Title Crystallization and preliminary X-ray analysis of the 12S central subunit of transcarboxylase from Propionibacterium shermanii
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11841210
Journal Biochemistry
Year 2002
Volume 41
Pages 2191-7
Authors Rivera-Hainaj RE, Pusztai-Carey M, Venkat Reddy D, Choowongkomon K, Sonnichsen FD, Carey PR
Title Characterization of the carboxylate delivery module of transcarboxylase: following spontaneous decarboxylation of the 1.3S-CO2- subunit by NMR and FTIR spectroscopies
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 12196011
Journal Biochemistry
Year 2002
Volume 41
Pages 10741-6
Authors Zheng X, Rivera-Hainaj RE, Zheng Y, Pusztai-Carey M, Hall PR, Yee VC, Carey PR
Title Substrate binding induces a cooperative conformational change in the 12S subunit of transcarboxylase: Raman crystallographic evidence
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 12743028
Journal EMBO J
Year 2003
Volume 22
Pages 2334-47
Authors Hall PR, Wang YF, Rivera-Hainaj RE, Zheng X, Pustai-Carey M, Carey PR, Yee VC
Title Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core.
Related PDB
Related UniProtKB

Comments
As annotated in Swiss-prot (P02904), this enzyme is a multienzyme, which is composed of three subunits, 1.3S, 5S, and 12S. The 1.3S subunit (PDB;1dcz, 1dd2) serves as a carrier of carboxyl group from the 12S subunit (PDB; 1on3, 1on9) to the 5S one (see [11]).
The 12 subunit transfers a carboxyl group from the terminal of methyl-malonyl-CoA to the 1.3S subunit, whilst the 5S subunit transfers the carboxyl group from the carrier protein to pyruvate, producing oxalacetate (see [11]).

Created Updated
2004-03-19 2009-02-26