EzCatDB: M00145

DB codeM00145
CATH domainDomain 12.40.50.100
Domain 23.90.226.10Catalytic domain
Domain 33.90.226.10
Domain 43.20.20.-
E.C.2.1.3.1

CATH domainRelated DB codes (homologues)
2.40.50.100M00163,M00222,M00188,M00189,T00223,M00190,M00191,M00208
3.90.226.10M00122,S00849,D00254

Enzyme Name
Swiss-protKEGG

P02904Q8GBW6
Protein nameMethylmalonyl-CoA carboxyltransferase 1.3S subunitMethylmalonyl-CoA carboxyltransferase 12S subunitmethylmalonyl-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]
SynonymsEC 2.1.3.1
Biotin carboxyl carrier protein of transcarboxylase
Transcarboxylase, 1.3S subunit
EC 2.1.3.1
Transcarboxylase 12S subunit

KEGG pathways
MAP codePathways
MAP00640Propanoate metabolism

Swiss-prot:Accession NumberP02904Q8GBW6
Entry nameBCCP_PROFR12S_PROFR
Activity(S)-methylmalonyl-CoA + pyruvate = propanoyl- CoA + oxaloacetate.(S)-methylmalonyl-CoA + pyruvate = propanoyl- CoA + oxaloacetate.
SubunitTranscarboxylase 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).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).
Subcellular location

Cofactor



CofactorsSubstratesProducts
KEGG-idC00120C00175C00038C00683C00022C00100C00036
CompoundBiotinCobaltZinc(S)-2-Methyl-3-oxopropanoyl-CoAPyruvatePropanoyl-CoAOxaloacetate
Typeamide group,amine group,fatty acid,sulfide groupheavy metalheavy metalamine group,carbohydrate,carboxyl group,nucleotide,peptide/protein,sulfide groupcarbohydrate,carboxyl groupamine group,carbohydrate,nucleotide,peptide/protein,sulfide groupcarbohydrate,carboxyl group
1dczAUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1dd2AUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1on3A01UnboundUnboundUnboundBound:MCAAnalogue:DXXUnboundUnbound
1on3B01UnboundUnboundUnboundBound:MCAAnalogue:DXXUnboundUnbound
1on3C01UnboundUnboundUnboundBound:MCAAnalogue:DXXUnboundUnbound
1on3D01UnboundUnboundUnboundBound:MCAAnalogue:DXXUnboundUnbound
1on3E01UnboundUnboundUnboundBound:MCAAnalogue:DXXUnboundUnbound
1on3F01UnboundUnboundUnboundBound:MCAAnalogue:DXXUnboundUnbound
1on9A01UnboundUnboundUnboundAnalogue:MCAUnboundUnboundUnbound
1on9B01UnboundUnboundUnboundAnalogue:MCAUnboundUnboundUnbound
1on9C01UnboundUnboundUnboundAnalogue:MCAUnboundUnboundUnbound
1on9D01UnboundUnboundUnboundAnalogue:MCAUnboundUnboundUnbound
1on9E01UnboundUnboundUnboundAnalogue:MCAUnboundUnboundUnbound
1on9F01UnboundUnboundUnboundAnalogue:MCAUnboundUnboundUnbound
1on3A02UnboundAnalogue:_CDUnboundUnboundUnboundUnboundUnbound
1on3B02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1on3C02UnboundAnalogue:_CDUnboundUnboundUnboundUnboundUnbound
1on3D02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1on3E02UnboundAnalogue:_CDUnboundUnboundUnboundUnboundUnbound
1on3F02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1on9A02UnboundAnalogue:_CDUnboundUnboundUnboundUnboundUnbound
1on9B02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1on9C02UnboundAnalogue:_CDUnboundUnboundUnboundUnboundUnbound
1on9D02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1on9E02UnboundAnalogue:_CDUnboundUnboundUnboundUnboundUnbound
1on9F02UnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
1dczA


1dd2A


1on3A01TYR 185

ALA 143;ALA 180;GLY 182;ALA 183
1on3B01TYR 185

ALA 143;ALA 180;GLY 182;ALA 183
1on3C01TYR 185

ALA 143;ALA 180;GLY 182;ALA 183
1on3D01TYR 185

ALA 143;ALA 180;GLY 182;ALA 183
1on3E01TYR 185

ALA 143;ALA 180;GLY 182;ALA 183
1on3F01TYR 185

ALA 143;ALA 180;GLY 182;ALA 183
1on9A01TYR 185

ALA 143;ALA 180;GLY 182;ALA 183
1on9B01TYR 185

ALA 143;ALA 180;GLY 182;ALA 183
1on9C01TYR 185

ALA 143;ALA 180;GLY 182;ALA 183
1on9D01TYR 185

ALA 143;ALA 180;GLY 182;ALA 183
1on9E01TYR 185

ALA 143;ALA 180;GLY 182;ALA 183
1on9F01TYR 185

ALA 143;ALA 180;GLY 182;ALA 183
1on3A02
HIS 388(metal binding)
GLY 414
1on3B02
HIS 388(metal binding)
GLY 414
1on3C02
HIS 388(metal binding)
GLY 414
1on3D02
HIS 388(metal binding)
GLY 414
1on3E02
HIS 388(metal binding)
GLY 414
1on3F02
HIS 388(metal binding)
GLY 414
1on9A02
HIS 388(metal binding)
GLY 414
1on9B02
HIS 388(metal binding)
GLY 414
1on9C02
HIS 388(metal binding)
GLY 414
1on9D02
HIS 388(metal binding)
GLY 414
1on9E02
HIS 388(metal binding)
GLY 414
1on9F02
HIS 388(metal binding)
GLY 414

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[12]Fig.7, p.4638-46392
[16]Fig.6, p.2340-2341

references
[1]
PubMed ID3910092
JournalBiochemistry
Year1985
Volume24
Pages6163-9
AuthorsHoving H, Crysell B, Leadlay PF
TitleFluorine NMR studies on stereochemical aspects of reactions catalyzed by transcarboxylase, pyruvate kinase, and enzyme I
[2]
PubMed ID3735431
JournalJ Mol Biol
Year1986
Volume188
Pages495-8
AuthorsSkrzypczak-Jankun E, Tulinsky A, Fillers JP, Kumar KG, Wood HG
TitlePreliminary crystallographic data and quaternary structural implications of the central subunit of the multi-subunit complex transcarboxylase
[3]
PubMed ID2269346
JournalFEBS Lett
Year1990
Volume277
Pages156-8
AuthorsBendrat K, Berger S, Buckel W, Etzel WA, Rohm KH
TitleCarbon-13 labelled biotin--a new probe for the study of enzyme catalyzed carboxylation and decarboxylation reactions
[4]
PubMed ID1526981
JournalJ Biol Chem
Year1992
Volume267
Pages18407-12
AuthorsShenoy BC, Xie Y, Park VL, Kumar GK, Beegen H, Wood HG, Samols D
TitleThe importance of methionine residues for the catalysis of the biotin enzyme, transcarboxylase. Analysis by site-directed mutagenesis
[5]
PubMed ID8346913
JournalArch Biochem Biophys
Year1993
Volume304
Pages359-66
AuthorsShenoy BC, Samols D, Kumar GK
TitleThe conserved methionines of the 1.3 S biotinyl subunit of transcarboxylase: effect of mutations on conformation and activity
[6]
PubMed ID8420991
JournalJ Biol Chem
Year1993
Volume268
Pages2232-8
AuthorsShenoy BC, Kumar GK, Samols D
TitleDissection of the biotinyl subunit of transcarboxylase into regions essential for activity and assembly
[7]
PubMed ID9398186
JournalBiochemistry
Year1997
Volume36
Pages14676-82
AuthorsReddy DV, Shenoy BC, Carey PR, Sonnichsen FD
TitleAbsence of observable biotin-protein interactions in the 1.3S subunit of transcarboxylase: an NMR study
Related PDB1dcz,1dd2
[8]
PubMed ID9720239
JournalCarbohydr Res
Year1998
Volume309
Pages89-94
AuthorsParamonov NA, Parolis LA, Parolis H, Boan IF, Anton J, Rodriguez-Valera F
TitleThe structure of the exocellular polysaccharide produced by the Archaeon Haloferax gibbonsii (ATCC 33959)
[9]
PubMed ID9792103
JournalProtein Sci
Year1998
Volume7
Pages2156-63
AuthorsReddy DV, Rothemund S, Shenoy BC, Carey PR, Sonnichsen FD
TitleStructural characterization of the entire 1.3S subunit of transcarboxylase from Propionibacterium shermanii
Related PDB1dcz,1dd2
[10]
PubMed ID10542197
JournalJ Biol Chem
Year1999
Volume274
Pages31767-9
AuthorsBlanchard CZ, Chapman-Smith A, Wallace JC, Waldrop GL
TitleThe 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
[11]
PubMed ID10704200
JournalBiochemistry
Year2000
Volume39
Pages2509-16
AuthorsReddy DV, Shenoy BC, Carey PR, Sonnichsen FD
TitleHigh resolution solution structure of the 1.3S subunit of transcarboxylase from Propionibacterium shermanii
Related PDB1dcz,1dd2
[12]
CommentsHomologous enzyme
PubMed ID10769118
JournalBiochemistry
Year2000
Volume39
Pages4630-9
AuthorsBenning MM, Haller T, Gerlt JA, Holden HM
TitleNew reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli.
[13]
PubMed ID11173475
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages266-8
AuthorsWang YF, Hyatt DC, Rivera RE, Carey PR, Yee VC
TitleCrystallization and preliminary X-ray analysis of the 12S central subunit of transcarboxylase from Propionibacterium shermanii
[14]
PubMed ID11841210
JournalBiochemistry
Year2002
Volume41
Pages2191-7
AuthorsRivera-Hainaj RE, Pusztai-Carey M, Venkat Reddy D, Choowongkomon K, Sonnichsen FD, Carey PR
TitleCharacterization of the carboxylate delivery module of transcarboxylase: following spontaneous decarboxylation of the 1.3S-CO2- subunit by NMR and FTIR spectroscopies
[15]
PubMed ID12196011
JournalBiochemistry
Year2002
Volume41
Pages10741-6
AuthorsZheng X, Rivera-Hainaj RE, Zheng Y, Pusztai-Carey M, Hall PR, Yee VC, Carey PR
TitleSubstrate binding induces a cooperative conformational change in the 12S subunit of transcarboxylase: Raman crystallographic evidence
[16]
PubMed ID12743028
JournalEMBO J
Year2003
Volume22
Pages2334-47
AuthorsHall PR, Wang YF, Rivera-Hainaj RE, Zheng X, Pustai-Carey M, Carey PR, Yee VC
TitleTranscarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core.

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]).

createdupdated
2004-03-192009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.