EzCatDB: M00189
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DB codeM00189
RLCP classification3.1177.805.79 : Transfer
CATH domainDomain 12.40.50.100 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Domain 22.40.50.100 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Domain 32.40.50.100 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Domain 4-.-.-.-
Domain 54.10.320.10 : Dihydrolipoamide Transferase
Domain 63.30.559.10 : Chloramphenicol AcetyltransferaseCatalytic domain
E.C.2.3.1.12

CATH domainRelated DB codes (homologues)
2.40.50.100 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)M00163,M00222,M00145,M00188,T00223,M00190,M00191,M00208
3.30.559.10 : Chloramphenicol AcetyltransferaseM00188,T00223,M00190,M00191
4.10.320.10 : Dihydrolipoamide TransferaseM00188,T00223,M00190,M00191

Enzyme Name
UniProtKBKEGG

P10802
Protein nameDihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complexdihydrolipoyllysine-residue acetyltransferase
acetyl-CoA:dihydrolipoamide S-acetyltransferase
dihydrolipoamide S-acetyltransferase
dihydrolipoate acetyltransferase
dihydrolipoic transacetylase
dihydrolipoyl acetyltransferase
lipoate acetyltransferase
lipoate transacetylase
lipoic acetyltransferase
lipoic acid acetyltransferase
lipoic transacetylase
lipoylacetyltransferase
thioltransacetylase A
transacetylase X
enzyme-dihydrolipoyllysine:acetyl-CoA S-acetyltransferase
acetyl-CoA:enzyme 6-N-(dihydrolipoyl)lysine S-acetyltransferase
SynonymsEC 2.3.1.12
E2
Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex
PfamPF00198 (2-oxoacid_dh)
PF00364 (Biotin_lipoyl)
PF02817 (E3_binding)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00010Glycolysis / Gluconeogenesis
MAP00020Citrate cycle (TCA cycle)
MAP00620Pyruvate metabolism

UniProtKB:Accession NumberP10802
Entry nameODP2_AZOVI
ActivityAcetyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-acetyldihydrolipoyl)lysine.
SubunitForms a 24-polypeptide structural core with octahedral symmetry.
Subcellular location
CofactorBinds 3 lipoyl cofactors covalently (By similarity).

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00010L00017C00024C15973
CompoundCoAEnzyme N(6)-(S-acetyldihydrolipoyl)lysineAcetyl-CoAEnzyme N(6)-(dihydrolipoyl)lysineTetrahedral intermediate
Typeamine group,carbohydrate,nucleotide,peptide/protein,sulfhydryl groupamide group,carbohydrate,lipid,peptide/protein,sulfhydryl group,sulfide groupamine group,carbohydrate,nucleotide,peptide/protein,sulfide groupamide group,lipid,peptide/protein,sulfhydryl group
ChEBI15346

15351


PubChem87642
6816

6302
444493


             
1iyuAUnboundUnboundUnboundUnboundUnbound
1iyvAUnboundUnboundUnboundUnboundUnbound
1dpbAUnboundUnboundUnboundUnboundUnbound
1dpcAUnboundUnboundUnboundUnboundUnbound
1dpdAUnboundUnboundUnboundUnboundUnbound
1eaaAUnboundUnboundUnboundUnboundUnbound
1eabABound:COAUnboundUnboundAnalogue:LPMUnbound
1eacABound:CAOUnboundUnboundAnalogue:DTTUnbound
1eadAAnalogue:CAOUnboundUnboundUnboundUnbound
1eaeAUnboundUnboundUnboundAnalogue:LPMUnbound
1eafAUnboundUnboundUnboundUnboundIntermediate-analogue:SO3

Active-site residues
resource
Swiss-prot;P10802
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
1iyuA 
LYS  39(Lipolyl binding)
 
 
1iyvA 
LYS  39(Lipolyl binding)
 
 
1dpbASER 558;       ;ASN 614
 
       
mutant H610C
1dpcASER 558;HIS 610;       
 
HIS 610
mutant N614D
1dpdA       ;HIS 610;ASN 614
 
HIS 610
mutant S558A
1eaaASER 558;HIS 610;ASN 614
 
HIS 610
 
1eabASER 558;HIS 610;ASN 614
 
HIS 610
 
1eacASER 558;HIS 610;ASN 614
 
HIS 610
 
1eadASER 558;HIS 610;ASN 614
 
HIS 610
 
1eaeASER 558;HIS 610;ASN 614
 
HIS 610
 
1eafASER 558;HIS 610;ASN 614
 
HIS 610
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[13]p.1547
[14]Scheme I, p.3899-3901
[17]p.1194-1195
[20]Fig.1, p.4292-4295
[32]Fig.6

references
[1]
PubMed ID389239
JournalBiochem Biophys Res Commun
Year1979
Volume90
Pages431-8
AuthorsFuller CC, Reed LJ, Oliver RM, Hackert ML
TitleCrystallization of a dihydrolipoyl transacetylase--dihydrolipoyl dehydrogenase subcomplex and its implications regarding the subunit structure of the pyruvate dehydrogenase complex from Escherichia coli.
[2]
PubMed ID6376124
JournalEur J Biochem
Year1984
Volume141
Pages361-74
AuthorsSpencer ME, Darlison MG, Stephens PE, Duckenfield IK, Guest JR
TitleNucleotide sequence of the sucB gene encoding the dihydrolipoamide succinyltransferase of Escherichia coli K12 and homology with the corresponding acetyltransferase.
[3]
PubMed ID3101735
JournalBiochemistry
Year1986
Volume25
Pages8173-8
AuthorsYang YS, Frey PA
TitleDihydrolipoyl transacetylase of Escherichia coli. Formation of 8-S-acetyldihydrolipoamide.
[4]
CommentsLIPOYL DOMAIN CONFORMATION.
Medline ID89052887
PubMed ID3191993
JournalFEBS Lett
Year1988
Volume240
Pages205-10
AuthorsHanemaaijer R, Vervoort J, Westphal AH, de Kok A, Veeger C
TitleMobile sequences in the pyruvate dehydrogenase complex, the E2 component, the catalytic domain and the 2-oxoglutarate dehydrogenase complex of Azotobacter vinelandii, as detected by 600 MHz 1H-NMR spectroscopy.
Related UniProtKBP10802
[5]
PubMed ID2271545
JournalBiochemistry
Year1990
Volume29
Pages8614-9
AuthorsNiu XD, Stoops JK, Reed LJ
TitleOverexpression and mutagenesis of the catalytic domain of dihydrolipoamide acetyltransferase from Saccharomyces cerevisiae.
[6]
PubMed ID2192914
JournalFEBS Lett
Year1990
Volume264
Pages206-10
AuthorsDardel F, Packman LC, Perham RN
TitleExpression in Escherichia coli of a sub-gene encoding the lipoyl domain of the pyruvate dehydrogenase complex of Bacillus stearothermophilus.
[7]
PubMed ID1908777
JournalEur J Biochem
Year1991
Volume200
Pages29-34
AuthorsSchulze E, Benen JA, Westphal AH, de Kok A
TitleInteraction of lipoamide dehydrogenase with the dihydrolipoyl transacetylase component of the pyruvate dehydrogenase complex from Azotobacter vinelandii.
[8]
PubMed ID1935951
JournalEur J Biochem
Year1991
Volume201
Pages561-8
AuthorsSchulze E, Westphal AH, Obmolova G, Mattevi A, Hol WG, de Kok A
TitleThe catalytic domain of the dihydrolipoyl transacetylase component of the pyruvate dehydrogenase complex from Azotobacter vinelandii and Escherichia coli. Expression, purification, properties and preliminary X-ray analysis.
[9]
PubMed ID1590756
JournalBiochem J
Year1992
Volume283
Pages665-71
AuthorsHipps DS, Perham RN
TitleExpression in Escherichia coli of a sub-gene encoding the lipoyl and peripheral subunit-binding domains of the dihydrolipoamide acetyltransferase component of the pyruvate dehydrogenase complex of Bacillus stearothermophilus.
[10]
PubMed ID1730230
JournalEur J Biochem
Year1992
Volume203
Pages245-50
AuthorsSnoep JL, Westphal AH, Benen JA, Teixeira de Mattos MJ, Neijssel OM, de Kok A
TitleIsolation and characterisation of the pyruvate dehydrogenase complex of anaerobically grown Enterococcus faecalis NCTC 775.
[11]
PubMed ID1429691
JournalJ Biol Chem
Year1992
Volume267
Pages23484-8
AuthorsGreen JD, Perham RN, Ullrich SJ, Appella E
TitleConformational studies of the interdomain linker peptides in the dihydrolipoyl acetyltransferase component of the pyruvate dehydrogenase multienzyme complex of Escherichia coli.
[12]
PubMed ID1589018
JournalNature
Year1992
Volume357
Pages196-7
AuthorsDeRosier DJ
TitleEnzyme complexes. A farewell to arms.
[13]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 381-637.
Medline ID92196586
PubMed ID1549782
JournalScience
Year1992
Volume255
Pages1544-50
AuthorsMattevi A, Obmolova G, Schulze E, Kalk KH, Westphal AH, de Kok A, Hol WG
TitleAtomic structure of the cubic core of the pyruvate dehydrogenase multienzyme complex.
Related PDB1eaa,1eab,1eac,1ead,1eae,1eaf
Related UniProtKBP10802
[14]
PubMed ID8471601
JournalBiochemistry
Year1993
Volume32
Pages3887-901
AuthorsMattevi A, Obmolova G, Kalk KH, Teplyakov A, Hol WG
TitleCrystallographic analysis of substrate binding and catalysis in dihydrolipoyl transacetylase (E2p).
[15]
PubMed ID8436118
JournalEur J Biochem
Year1993
Volume211
Pages591-9
AuthorsSchulze E, Westphal AH, Hanemaaijer R, de Kok A
TitleStructure/function relationships in the pyruvate dehydrogenase complex from Azotobacter vinelandii. Role of the linker region between the binding and catalytic domain of the dihydrolipoyl transacetylase component.
[16]
PubMed ID8500617
JournalFEBS Lett
Year1993
Volume323
Pages243-6
AuthorsMachado RS, Guest JR, Williamson MP
TitleMobility in pyruvate dehydrogenase complexes with multiple lipoyl domains.
[17]
CommentsX-ray crystallography
PubMed ID8487300
JournalJ Mol Biol
Year1993
Volume230
Pages1183-99
AuthorsMattevi A, Obmolova G, Kalk KH, Westphal AH, de Kok A, Hol WG
TitleRefined crystal structure of the catalytic domain of dihydrolipoyl transacetylase (E2p) from Azotobacter vinelandii at 2.6 A resolution.
Related PDB1dpb,1dpc,1dpd
[18]
PubMed ID8433963
JournalProtein Eng
Year1993
Volume6
Pages101-8
AuthorsTurner SL, Russell GC, Williamson MP, Guest JR
TitleRestructuring an interdomain linker in the dihydrolipoamide acetyltransferase component of the pyruvate dehydrogenase complex of Escherichia coli.
[19]
CommentsSTRUCTURE BY NMR OF 1-78.
Medline ID94222112
PubMed ID8068086
JournalEur J Biochem
Year1994
Volume221
Pages87-100
AuthorsBerg A, de Kok A, Vervoort J
TitleSequential 1H and 15N nuclear magnetic resonance assignments and secondary structure of the N-terminal lipoyl domain of the dihydrolipoyl transacetylase component of the pyruvate dehydrogenase complex from Azotobacter vinelandii.
Related UniProtKBP10802
[20]
PubMed ID7703242
JournalBiochemistry
Year1995
Volume34
Pages4287-98
AuthorsHendle J, Mattevi A, Westphal AH, Spee J, de Kok A, Teplyakov A, Hol WG
TitleCrystallographic and enzymatic investigations on the role of Ser558, His610, and Asn614 in the catalytic mechanism of Azotobacter vinelandii dihydrolipoamide acetyltransferase (E2p).
[21]
PubMed ID8918601
JournalJ Mol Biol
Year1996
Volume263
Pages463-74
AuthorsWallis NG, Allen MD, Broadhurst RW, Lessard IA, Perham RN
TitleRecognition of a surface loop of the lipoyl domain underlies substrate channelling in the pyruvate dehydrogenase multienzyme complex.
[22]
CommentsSTRUCTURE BY NMR OF 1-78.
Medline ID97234563
PubMed ID9119000
JournalEur J Biochem
Year1997
Volume244
Pages352-60
AuthorsBerg A, Vervoort J, de Kok A
TitleThree-dimensional structure in solution of the N-terminal lipoyl domain of the pyruvate dehydrogenase complex from Azotobacter vinelandii.
Related PDB1iyu,1iyv
Related UniProtKBP10802
[23]
PubMed ID9280309
JournalFEBS Lett
Year1997
Volume413
Pages339-43
AuthorsAllen MD, Perham RN
TitleThe catalytic domain of dihydrolipoyl acetyltransferase from the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. Expression, purification and reversible denaturation.
[24]
PubMed ID9729480
JournalBiochem J
Year1998
Volume334
Pages703-11
AuthorsJackson JC, Vinluan CC, Dragland CJ, Sundararajan V, Yan B, Gounarides JS, Nirmala NR, Topiol S, Ramage P, Blume JE, Aicher TD, Bell PA, Mann WR
TitleHeterologously expressed inner lipoyl domain of dihydrolipoyl acetyltransferase inhibits ATP-dependent inactivation of pyruvate dehydrogenase complex. Identification of important amino acid residues.
[25]
PubMed ID10419491
JournalJ Biol Chem
Year1999
Volume274
Pages21769-75
AuthorsThelen JJ, Muszynski MG, David NR, Luethy MH, Elthon TE, Miernyk JA, Randall DD
TitleThe dihydrolipoamide S-acetyltransferase subunit of the mitochondrial pyruvate dehydrogenase complex from maize contains a single lipoyl domain.
[26]
PubMed ID10653630
JournalBiochemistry
Year2000
Volume39
Pages872-9
AuthorsSpector S, Wang M, Carp SA, Robblee J, Hendsch ZS, Fairman R, Tidor B, Raleigh DP
TitleRational modification of protein stability by the mutation of charged surface residues.
[27]
PubMed ID10735853
JournalJ Bacteriol
Year2000
Volume182
Pages2119-24
AuthorsStein A, Firshein W
TitleProbable identification of a membrane-associated repressor of Bacillus subtilis DNA replication as the E2 subunit of the pyruvate dehydrogenase complex.
[28]
PubMed ID10913250
JournalBiochemistry
Year2000
Volume39
Pages8448-59
AuthorsJones DD, Stott KM, Howard MJ, Perham RN
TitleRestricted motion of the lipoyl-lysine swinging arm in the pyruvate dehydrogenase complex of Escherichia coli.
Related PDB1qjo
[29]
PubMed ID11368334
JournalArch Biochem Biophys
Year2001
Volume386
Pages123-35
AuthorsLiu S, Gong X, Yan X, Peng T, Baker JC, Li L, Robben PM, Ravindran S, Andersson LA, Cole AB, Roche TE
TitleReaction mechanism for mammalian pyruvate dehydrogenase using natural lipoyl domain substrates.
[30]
PubMed ID11114246
JournalJ Mol Biol
Year2001
Volume305
Pages49-60
AuthorsJones DD, Stott KM, Reche PA, Perham RN
TitleRecognition of the lipoyl domain is the ultimate determinant of substrate channelling in the pyruvate dehydrogenase multienzyme complex.
[31]
PubMed ID12173931
JournalBiochemistry
Year2002
Volume41
Pages10446-53
AuthorsJung HI, Cooper A, Perham RN
TitleIdentification of key amino acid residues in the assembly of enzymes into the pyruvate dehydrogenase complex of Bacillus stearothermophilus: a kinetic and thermodynamic analysis.
[32]
PubMed ID12526798
JournalCell
Year2003
Volume112
Pages113-22
AuthorsJogl G, Tong L
TitleCrystal structure of carnitine acetyltransferase and implications for the catalytic mechanism and fatty acid transport.

comments
This enzyme is Dihydrolipoyllysine-residue acetyltransferase, E2 component of pyruvate dehydrogenase complex.
The pyruvate dehydrogenase complex is composed of pyruvate dehydrogenaes (E1 component; E.C. 1.2.4.1), dihydrolipoyllysine S-acetyltransferase (E2 component; E.C. 2.3.1.12), and lipoamide dehydrogenase (E3 component; E.C. 1.8.1.4). (The E3 component corresponds to the entry T00017 in EzCatDB.)
This enzyme is composed of three N-terminal lipoyl-binding domains, E1/E3-binding domain, and the C-terminal catalytic domain. Although this enzyme has the same domain composition as that of its homologue (M00191 in EzCatDB), the catalytic residues are slightly different from those of the homologue. (The structure of the catalytic domain of this enzyme has not been solved yet.)
This enzyme catalyzes transfer of acetyl group from lypoyllysine of the lipoyl-binding domain to thiol group of CoA.
According to the literature [20], the reaction proceeds as follows:
(1) His610 acts as a general base to abstract a proton from the acceptor group, thiol group of CoA.
(2) Asn614 modulates the catalytic histidine, His610, along with the mainchain carbonyl oxygen of His375.
(3) The activated thiolate makes a nucleophilic attack on the transferred group, carbonyl carbon atom of the acetylated lipoamide substrate, resulting in the formation of a tetrahedral intermediate.
(4) This intermediate is stabilized by the hydroxyl group of Ser558' from the next subunit.
(5) The breakdown of this intermediate results in the transfer of the succinyl group to CoA and protonation of the leaving dithiolane group. Here, His610 acts as a general acid to protonate the leaving group.

createdupdated
2002-12-012009-02-26


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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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