EzCatDB: D00867
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DB codeD00867
RLCP classification3.1177.220080.38 : Transfer
5.115.129300.66 : Elimination
3.1197.15020.136 : Transfer
CATH domainDomain 13.40.47.10 : Peroxisomal Thiolase; Chain A, domain 1Catalytic domain
Domain 23.40.47.10 : Peroxisomal Thiolase; Chain A, domain 1Catalytic domain
E.C.2.3.1.180

CATH domainRelated DB codes (homologues)
3.40.47.10 : Peroxisomal Thiolase; Chain A, domain 1D00090,D00411,D00509,D00825,D00826,D00871

Enzyme Name
UniProtKBKEGG

O67185Q820T1
Protein name3-oxoacyl-[acyl-carrier-protein] synthase 33-oxoacyl-[acyl-carrier-protein] synthase 3Beta-ketoacyl-acyl-carrier-protein synthase III
3-Oxoacyl:ACP synthase III
3-Ketoacyl-acyl carrier protein synthase III
KASIII
KAS III
FabH
Beta-ketoacyl-acyl carrier protein synthase III
Beta-ketoacyl-ACP synthase III
Beta-ketoacyl (acyl carrier protein) synthase III
Beta-ketoacyl-[acyl-carrier-protein] synthase III
Acetyl-CoA:malonyl-[acyl-carrier-protein] C-acyltransferase
SynonymsEC 2.3.1.180
3-oxoacyl-[acyl-carrier-protein] synthase III
Beta-ketoacyl-ACP synthase III
KAS III
EC 2.3.1.180
3-oxoacyl-[acyl-carrier-protein] synthase III
Beta-ketoacyl-ACP synthase III
KAS III
RefSeqNP_213748.1 (Protein)
NC_000918.1 (DNA/RNA sequence)
NP_816505.1 (Protein)
NC_004668.1 (DNA/RNA sequence)
PfamPF08545 (ACP_syn_III)
PF08541 (ACP_syn_III_C)
[Graphical view]
PF08545 (ACP_syn_III)
PF08541 (ACP_syn_III_C)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00061Fatty acid biosynthesis

UniProtKB:Accession NumberO67185Q820T1
Entry nameFABH_AQUAEFABH_ENTFA
ActivityAcetyl-CoA + malonyl-[acyl-carrier-protein] = acetoacyl-[acyl-carrier-protein] + CoA + CO2.Acetyl-CoA + malonyl-[acyl-carrier-protein] = acetoacyl-[acyl-carrier-protein] + CoA + CO2.
SubunitHomodimer (By similarity).Homodimer (By similarity).
Subcellular locationCytoplasm (Probable).Cytoplasm (Probable).
Cofactor


Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00024C01209C05744C00010C00011I00132I00133I00134I00135
Compoundacetyl-CoAmalonyl-[acyl-carrier protein]acetoacetyl-[acyl-carrier protein]CoACO2Peptidyl-Cys-tetrahedral-acetyl-CoAPeptidyl-Cys-S-acetyl[Acyl-carrier protein]-decarboxylated malonyl group (Peptidyl-Ser-phosphopantetheine-S-enolate)Peptidyl-Cys-tetrahedral-acetyl-keto-[acyl-carrier protein]
Typeamine group,carbohydrate,nucleotide,peptide/protein,sulfide groupcarbohydrate,carboxyl group,peptide/protein,phosphate group/phosphate ion,sulfide groupcarbohydrate,peptide/protein,phosphate group/phosphate ion,sulfide groupamine group,carbohydrate,nucleotide,peptide/protein,sulfhydryl groupothers



ChEBI15351


15346
16526




PubChem6302
444493


87642
6816
280




                 
2ebdA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2ebdB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il4A01Bound:ACOUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il4B01Bound:ACOUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il4C01Bound:ACOUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il4D01Bound:ACOUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il5A01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il5B01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il5C01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il5D01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il6A01UnboundUnboundUnboundUnboundUnboundUnboundIntermediate-bound:SCYUnboundUnbound
2ebdA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
2ebdB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il4A02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il4B02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il4C02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il4D02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il5A02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il5B02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il5C02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il5D02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
3il6A02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [2], [3], [5], [9], [10], [13], [14], [15], [18], [21] & Swiss-prot;O67185, P0A6R0, P43711, Q6GIA4, Q820T1, Q8NXE2
pdbCatalytic residuesModified residuesMain-chain involved in catalysiscomment
            
2ebdA01CYS  111;GLU  139
                          
CYS  111
 
2ebdB01CYS  111;GLU  139
                          
CYS  111
 
3il4A01CYS  117;GLU  145
                          
CYS  117
 
3il4B01CYS  117;GLU  145
                          
CYS  117
 
3il4C01CYS  117;GLU  145
                          
CYS  117
 
3il4D01CYS  117;GLU  145
                          
CYS  117
 
3il5A01CYS  117;GLU  145
                          
CYS  117
 
3il5B01CYS  117;GLU  145
                          
CYS  117
 
3il5C01CYS  117;GLU  145
                          
CYS  117
 
3il5D01CYS  117;GLU  145
                          
CYS  117
 
3il6A01        ;GLU  145
SCY 117(S-acetyl-cysteine)
SCY  117
 
2ebdA02HIS  236;ASN  266;SER  268
 
GLY  298
 
2ebdB02HIS  236;ASN  266;SER  268
 
GLY  298
 
3il4A02HIS  250;ASN  280;SER  282
 
GLY  314
mutant A192T, N253S, invisible 211-212
3il4B02HIS  250;ASN  280;SER  282
 
GLY  314
mutant A192T, N253S, invisible 211-212
3il4C02HIS  250;ASN  280;SER  282
 
GLY  314
mutant A192T, N253S, invisible 211-212
3il4D02HIS  250;ASN  280;SER  282
 
GLY  314
mutant A192T, N253S, invisible 211-212
3il5A02HIS  250;ASN  280;SER  282
 
GLY  314
 
3il5B02HIS  250;ASN  280;SER  282
 
GLY  314
 
3il5C02HIS  250;ASN  280;SER  282
 
GLY  314
 
3il5D02HIS  250;ASN  280;SER  282
 
GLY  314
 
3il6A02HIS  250;ASN  280;SER  282
 
GLY  314
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig.6A, p.36467-36470
[3]Scheme 1, p.158-160
[5]Fig.7b, 3p.190-192
[9]p.349-352
[10]p.1561-1565
[13]Fig.6b, p.806-809
[14]Fig.6, p.32544-32547
[15]Fig.1
[18]Fig.1B
[21]Fig.5, p.696-697

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
PubMed ID10571059
JournalFEBS Lett
Year1999
Volume460
Pages46-52
AuthorsOlsen JG, Kadziola A, von Wettstein-Knowles P, Siggaard-Andersen M, Lindquist Y, Larsen S
TitleThe X-ray crystal structure of beta-ketoacyl [acyl carrier protein] synthase I.
Related PDB1dd8
Related UniProtKBP0A953
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
PubMed ID10593943
JournalJ Biol Chem
Year1999
Volume274
Pages36465-71
AuthorsQiu X, Janson CA, Konstantinidis AK, Nwagwu S, Silverman C, Smith WW, Khandekar S, Lonsdale J, Abdel-Meguid SS
TitleCrystal structure of beta-ketoacyl-acyl carrier protein synthase III. A key condensing enzyme in bacterial fatty acid biosynthesis.
Related PDB1d9b,1hn9
Related UniProtKBP0A6R0
[3]
PubMed ID10600651
JournalBiochem J
Year2000
Volume345 Pt 1
Pages153-60
AuthorsAbbadi A, Brummel M, Schutt BS, Slabaugh MB, Schuch R, Spener F
TitleReaction mechanism of recombinant 3-oxoacyl-(acyl-carrier-protein) synthase III from Cuphea wrightii embryo, a fatty acid synthase type II condensing enzyme.
[4]
PubMed ID11006298
JournalJ Biol Chem
Year2000
Volume275
Pages39640-6
AuthorsJez JM, Noel JP
TitleMechanism of chalcone synthase. pKa of the catalytic cysteine and the role of the conserved histidine in a plant polyketide synthase.
[5]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
PubMed ID10673437
JournalStructure
Year2000
Volume8
Pages185-95
AuthorsDavies C, Heath RJ, White SW, Rock CO
TitleThe 1.8 A crystal structure and active-site architecture of beta-ketoacyl-acyl carrier protein synthase III (FabH) from escherichia coli.
Related PDB1ebl
Related UniProtKBP0A6R0
[6]
PubMed ID11502177
JournalBiochemistry
Year2001
Volume40
Pages9836-45
AuthorsMcGuire KA, Siggaard-Andersen M, Bangera MG, Olsen JG, von Wettstein-Knowles P
Titlebeta-Ketoacyl-[acyl carrier protein] synthase I of Escherichia coli: aspects of the condensation mechanism revealed by analyses of mutations in the active site pocket.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
PubMed ID11278743
JournalJ Biol Chem
Year2001
Volume276
Pages20516-22
AuthorsScarsdale JN, Kazanina G, He X, Reynolds KA, Wright HT
TitleCrystal structure of the Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein synthase III.
Related PDB1hzp
Related UniProtKBP0A574
[8]
PubMed ID11078736
JournalJ Biol Chem
Year2001
Volume276
Pages8231-8
AuthorsZhang YM, Rao MS, Heath RJ, Price AC, Olson AJ, Rock CO, White SW
TitleIdentification and analysis of the acyl carrier protein (ACP) docking site on beta-ketoacyl-ACP synthase III.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
PubMed ID11243824
JournalJ Mol Biol
Year2001
Volume307
Pages341-56
AuthorsQiu X, Janson CA, Smith WW, Head M, Lonsdale J, Konstantinidis AK
TitleRefined structures of beta-ketoacyl-acyl carrier protein synthase III.
Related PDB1hnd,1hnh,1hnj,1hnk
Related UniProtKBP0A6R0
[10]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
PubMed ID12429097
JournalStructure
Year2002
Volume10
Pages1559-68
AuthorsPan H, Tsai S, Meadows ES, Miercke LJ, Keatinge-Clay AT, O'Connell J, Khosla C, Stroud RM
TitleCrystal structure of the priming beta-ketosynthase from the R1128 polyketide biosynthetic pathway.
Related PDB1mzj
Related UniProtKBQ9F6D4
[11]
PubMed ID12502353
JournalJ Med Chem
Year2003
Volume46
Pages5-8
AuthorsDaines RA, Pendrak I, Sham K, Van Aller GS, Konstantinidis AK, Lonsdale JT, Janson CA, Qiu X, Brandt M, Khandekar SS, Silverman C, Head MS
TitleFirst X-ray cocrystal structure of a bacterial FabH condensing enzyme and a small molecule inhibitor achieved using rational design and homology modeling.
Related PDB1mzs
[12]
PubMed ID12866053
JournalProteins
Year2003
Volume52
Pages427-35
AuthorsDawe JH, Porter CT, Thornton JM, Tabor AB
TitleA template search reveals mechanistic similarities and differences in beta-ketoacyl synthases (KAS) and related enzymes.
[13]
PubMed ID15952903
JournalAnnu Rev Biochem
Year2005
Volume74
Pages791-831
AuthorsWhite SW, Zheng J, Zhang YM, Rock
TitleThe structural biology of type II fatty acid biosynthesis.
[14]
PubMed ID16040614
JournalJ Biol Chem
Year2005
Volume280
Pages32539-47
AuthorsBrown AK, Sridharan S, Kremer L, Lindenberg S, Dover LG, Sacchettini JC, Besra GS
TitleProbing the mechanism of the Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein synthase III mtFabH: factors influencing catalysis and substrate specificity.
Related PDB1m1m,2ahb,2aj9
[15]
PubMed ID15713483
JournalJ Mol Biol
Year2005
Volume346
Pages1313-21
AuthorsMusayev F, Sachdeva S, Scarsdale JN, Reynolds KA, Wright HT
TitleCrystal structure of a substrate complex of Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein synthase III (FabH) with lauroyl-coenzyme A.
Related PDB1u6e,1u6s
[16]
PubMed ID15987898
JournalProtein Sci
Year2005
Volume14
Pages2087-94
AuthorsQiu X, Choudhry AE, Janson CA, Grooms M, Daines RA, Lonsdale JT, Khandekar SS
TitleCrystal structure and substrate specificity of the beta-ketoacyl-acyl carrier protein synthase III (FabH) from Staphylococcus aureus.
Related PDB1zow
[17]
PubMed ID16356722
JournalTrends Biochem Sci
Year2005
Volume31
Pages64-71
AuthorsHaapalainen AM, Merilainen G, Wierenga RK
TitleThe thiolase superfamily: condensing enzymes with diverse reaction specificities.
[18]
PubMed ID17524982
JournalChem Biol
Year2007
Volume14
Pages513-24
AuthorsAlhamadsheh MM, Musayev F, Komissarov AA, Sachdeva S, Wright HT, Scarsdale N, Florova G, Reynolds KA
TitleAlkyl-CoA disulfides as inhibitors and mechanistic probes for FabH enzymes.
Related PDB2eft,2gyo
[19]
PubMed ID18096200
JournalBioorg Chem
Year2008
Volume36
Pages85-90
AuthorsSachdeva S, Musayev F, Alhamadsheh MM, Neel Scarsdale J, Tonie Wright H, Reynolds KA
TitleProbing reactivity and substrate specificity of both subunits of the dimeric Mycobacterium tuberculosis FabH using alkyl-CoA disulfide inhibitors and acyl-CoA substrates.
[20]
PubMed ID18420147
JournalChem Biol
Year2008
Volume15
Pages402-12
AuthorsSachdeva S, Musayev FN, Alhamadsheh MM, Scarsdale JN, Wright HT, Reynolds KA
TitleSeparate entrance and exit portals for ligand traffic in Mycobacterium tuberculosis FabH.
Related PDB2qnz,2qny,2qnx,2qo0,2qo1
[21]
PubMed ID18824113
JournalMol Phylogenet Evol
Year2008
Volume49
Pages691-701
AuthorsJiang C, Kim SY, Suh DY
TitleDivergent evolution of the thiolase superfamily and chalcone synthase family.
[22]
PubMed ID19665020
JournalFEBS Lett
Year2009
Volume583
Pages2939-46
AuthorsGajiwala KS, Margosiak S, Lu J, Cortez J, Su Y, Nie Z, Appelt K
TitleCrystal structures of bacterial FabH suggest a molecular basis for the substrate specificity of the enzyme.
Related PDB3il3,3il4,3il5,3il6,3il7,3il9

comments
This enzyme belongs to chalcone synthase family in thiolase superfamily (see [21]). This enzyme is homologous to the counterpart enzymes from different bacteria (D00825 and D00826 in EzCatDB), with a slightly different catalytic site. Moreover, these enzymes are categorized in type III of beta-ketoacyl-acyl-carrier protein synthases (KAS).
According to the literature, the catalysis proceeds through the Ping-Pong reaction mechanism.
According to the literature [2], [3], [5], [9], [10], [14], [15] and [21], this enzyme catalyzes the following reactions:
(A) Transfer of acyl group from sulfur atom of acetyl-CoA to catalytic cysteine (see [9]):
(A0) Asn266 (of 2ebd) modulate the pKa of His236, whereas His236 may lower the pKa of the sidechain of Cys111.
(A1) Glu139 acts as a general base to deprotonate the nucleophile, Cys111, through the sidechain of Ser268. (Helix dipole moment may also activate the cysteine sidechain.)
(A2) The activated thiol group of Cys111 makes a nucleophilic attack on the acetyl group of acetyl-CoA, leading to a transition-state (I00132). The oxyanion hole, composed of the mainchain amide groups of Cys111 and Gly298, stabilizes the negative charge of the oxyanion on the tetrahedral transition-state (I00132).
(A3) His236 acts as a general acid to protonate the leaving sulfur atom of CoA, generating an acetyl group on Cys111 (I00133).
(B) Decarboxylation of malonyl-ACP (Elimination of carboxylate group from malonyl group) forming carbanion/enolate transition-state (I00134):
(B0) Asn266 and His236 interact with the carbonyl oxygen of the second substrate, malonyl-ACP, and stabilize it.
(B1) His236 may act as a general base to deprotonate the carboxylic group of malonyl-ACP, to facilitate the decarboxylation. This reaction generates a carbanion/enolate transition-state (I00134). The enolate is stabilized by Asn266 and His236.
(C) Transfer of acetyl group from catalytic cysteine to carbanion on the transition-state (I00134):
(C0) Asn266 and His236 stabilize the enol group of the transition-state (I00134).
(C1) The carbanion makes a nucleophilic attack on the acetyl group of the acetyl intermediate (I00133), forming a tetrahedral transition-state (I00135). The oxyanion of the tetrahedral transition-state (I00135) is stabilized by the oxyanion hole composed of the mainchain amide groups of Cys111 and Gly298.
(C2) Glu139 may act as a general acid to protonate the leaving catalytic residue, Cys111, through the sidechain of Ser268.

createdupdated
2009-11-262012-07-06


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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