EzCatDB: S00532
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DB codeS00532
RLCP classification4.151.774000.401 : Addition
4.16.66400.4 : Addition
5.41.2776000.400 : Elimination
CATH domainDomain 13.20.20.70 : TIM BarrelCatalytic domain
E.C.2.5.1.55

CATH domainRelated DB codes (homologues)
3.20.20.70 : TIM BarrelS00215,S00217,S00218,S00219,S00198,S00220,S00745,S00537,S00538,S00539,S00826,S00841,S00235,S00239,S00240,S00243,S00244,S00199,S00200,S00201,S00221,S00222,S00847,S00224,S00225,S00226,D00014,D00029,M00141,T00015,T00239,D00664,D00665,D00804,D00863,T00089

Enzyme Name
UniProtKBKEGG

O66496
Protein name2-dehydro-3-deoxyphosphooctonate aldolase3-deoxy-8-phosphooctulonate synthase
2-dehydro-3-deoxy-D-octonate-8-phosphateD-arabinose-5-phosphate-lyase (pyruvate-phosphorylating)
2-dehydro-3-deoxy-phosphooctonate aldolase
2-keto-3-deoxy-8-phosphooctonic synthetase
3-deoxy-D-manno-octulosonate-8-phosphate synthase
3-deoxy-D-mannooctulosonate-8-phosphate synthetase
3-deoxyoctulosonic 8-phosphate synthetase
KDOP synthase
phospho-2-keto-3-deoxyoctonate aldolase
SynonymsEC 2.5.1.55
Phospho-2-dehydro-3-deoxyoctonate aldolase
3-deoxy-D-manno-octulosonic acid 8-phosphate synthetase
KDO-8-phosphate synthetase
KDO 8-P synthase
KDOPS
RefSeqNP_213056.1 (Protein)
NC_000918.1 (DNA/RNA sequence)
PfamPF00793 (DAHP_synth_1)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00540Lipopolysaccharide biosynthesis

UniProtKB:Accession NumberO66496
Entry nameKDSA_AQUAE
ActivityPhosphoenolpyruvate + D-arabinose 5-phosphate + H(2)O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate.
SubunitOligomer.
Subcellular locationCytoplasm (By similarity).
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00038C00074C01112C00001C04478C00009

CompoundZincPhosphoenolpyruvateD-Arabinose 5-phosphateH2O2-Dehydro-3-deoxy-D-octonate 8-phosphateOrthophosphateTransition-state with an oxocarbenium ionA linear tetrahedral intermediate
Typeheavy metalcarboxyl group,phosphate group/phosphate ioncarbohydrate,phosphate group/phosphate ionH2Ocarbohydrate,carboxyl group,phosphate group/phosphate ionphosphate group/phosphate ion

ChEBI29105
44897
16241
15377
18069
26078


PubChem32051
59658623
58114173
1005
230
188324
962
22247451
15942880
22486802
1004


                
1fwnAUnboundBound:PEPUnbound UnboundUnboundUnboundUnbound
1fwnBUnboundBound:PEPUnbound UnboundUnboundUnboundUnbound
1fwsAAnalogue:_CDBound:PEPUnbound UnboundUnboundUnboundUnbound
1fwsBAnalogue:_CDBound:PEPUnbound UnboundUnboundUnboundUnbound
1fwtAAnalogue:_CDBound:PEPUnbound UnboundUnboundUnboundUnbound
1fwtBAnalogue:_CDBound:PEPAnalogue:E4P UnboundUnboundUnboundUnbound
1fwwAAnalogue:_CDBound:PEPBound:A5PBound:HOH 3026UnboundUnboundUnboundUnbound
1fwwBAnalogue:_CDBound:PEPUnboundBound:HOH 3060UnboundUnboundUnboundUnbound
1fx6AUnboundUnboundUnbound UnboundBound:PO4UnboundUnbound
1fx6BUnboundUnboundUnbound UnboundBound:PO4UnboundUnbound
1fxpAAnalogue:_CDUnboundUnbound UnboundBound:PO4UnboundUnbound
1fxpBAnalogue:_CDUnboundUnbound UnboundBound:PO4UnboundUnbound
1fxqAUnboundBound:PEPBound:A5P UnboundUnboundUnboundUnbound
1fxqBUnboundBound:PEPBound:A5P UnboundUnboundUnboundUnbound
1fy6AAnalogue:_CDUnboundBound:A5P UnboundBound:PO4UnboundUnbound
1fy6BAnalogue:_CDUnboundUnbound UnboundBound:PO4UnboundUnbound
1jcxAAnalogue:_CDUnboundUnboundBound:HOH 3056UnboundUnboundTransition-state-analogue:PAIUnbound
1jcxBAnalogue:_CDUnboundUnboundBound:HOH 3105UnboundUnboundTransition-state-analogue:PAIUnbound
1jcyAAnalogue:_CDBound:PEPAnalogue:R5P UnboundUnboundUnboundUnbound
1jcyBAnalogue:_CDBound:PEPUnbound UnboundUnboundUnboundUnbound
1lrnAAnalogue:_CDUnboundUnbound UnboundBound:PO4UnboundUnbound
1lrnBAnalogue:_CDUnboundUnbound UnboundBound:PO4UnboundUnbound
1lroAAnalogue:_CDBound:PEPUnbound UnboundUnboundUnboundUnbound
1lroBAnalogue:_CDBound:PEPUnbound UnboundUnboundUnboundUnbound
1lrqAAnalogue:_CDBound:PEPBound:A5P UnboundUnboundUnboundUnbound
1lrqBAnalogue:_CDUnboundUnbound UnboundBound:PO4UnboundUnbound
1pckAAnalogue:_CDAnalogue:PEZUnbound UnboundUnboundUnboundUnbound
1pckBAnalogue:_CDAnalogue:PEZUnbound UnboundUnboundUnboundUnbound
1pcwAAnalogue:_CDUnboundUnboundBound:HOH 31UnboundUnboundTransition-state-analogue:H4PUnbound
1pcwBAnalogue:_CDUnboundUnboundBound:HOH 93UnboundUnboundTransition-state-analogue:H4PUnbound
1pe1AAnalogue:_CDAnalogue:2PGUnboundUnboundUnboundUnboundUnboundUnbound
1pe1BAnalogue:_CDAnalogue:2PGUnboundUnboundUnboundUnboundUnboundUnbound
1t8xAAnalogue:_CDBound:PEPBound:A5P UnboundUnboundUnboundUnbound
1t8xBAnalogue:_CDBound:PEPUnbound UnboundUnboundUnboundUnbound
1t96AAnalogue:_CDBound:PEPUnbound UnboundUnboundUnboundUnbound
1t96BAnalogue:_CDBound:PEPUnbound UnboundUnboundUnboundUnbound
1t99AAnalogue:_CDUnboundUnbound UnboundBound:PO4UnboundUnbound
1t99BAnalogue:_CDUnboundUnbound UnboundBound:PO4UnboundUnbound
1zhaAAnalogue:_CDBound:PEPAnalogue:R5P UnboundUnboundUnboundUnbound
1zhaBAnalogue:_CDBound:PEPUnbound UnboundUnboundUnboundUnbound
1zjiAAnalogue:_CDAnalogue:2PGAnalogue:R5PUnboundUnboundUnboundUnboundUnbound
1zjiBAnalogue:_CDAnalogue:2PGUnboundUnboundUnboundUnboundUnboundUnbound
2a21ABound:_ZNBound:PEPUnbound UnboundUnboundUnboundUnbound
2a21BBound:_ZNBound:PEPUnbound UnboundUnboundUnboundUnbound
2a2iABound:_ZNBound:PEPBound:A5PBound:HOH 3088UnboundUnboundUnboundUnbound
2a2iBBound:_ZNBound:PEPBound:A5PBound:HOH 3093UnboundUnboundUnboundUnbound

Active-site residues
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
1fwnALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1fwnBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1fwsALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1fwsBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1fwtALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1fwtBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1fwwALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1fwwBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1fx6ALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1fx6BLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1fxpALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1fxpBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1fxqALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1fxqBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1fy6ALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1fy6BLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1jcxALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1jcxBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1jcyALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1jcyBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1lrnALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;        ;GLU 1222;ASP 1233(metal-binding)
ALA 1102
mutant H1185G
1lrnBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;        ;GLU 2222;ASP 2233(metal-binding)
ALA 2102
mutant H2185G
1lroALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;        ;GLU 1222;ASP 1233(metal-binding)
ALA 1102
mutant H1185G
1lroBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;        ;GLU 2222;ASP 2233(metal-binding)
ALA 2102
mutant H2185G
1lrqALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;        ;GLU 1222;ASP 1233(metal-binding)
ALA 1102
mutant H1185G
1lrqBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;        ;GLU 2222;ASP 2233(metal-binding)
ALA 2102
mutant H2185G
1pckALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1pckBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1pcwALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1pcwBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1pe1ALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
1pe1BLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
1t8xALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
mutant R1106G
1t8xBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
mutant R2106G
1t96ALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
mutant R1106G
1t96BLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
mutant R2106G
1t99ALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
mutant R1106G
1t99BLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
mutant R2106G
1zhaALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
mutant R1106G
1zhaBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
mutant R2106G
1zjiALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
mutant R1106G
1zjiBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
mutant R2106G
2a21ALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
2a21BLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 
2a2iALYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154
CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding)
ALA 1102
 
2a2iBLYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154
CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding)
ALA 2102
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.8, p.8398-8401
[2]Scheme 1, Fig.4, p.15680-15683
[3]Fig.1, p.210-212
[6]Scheme 1, Scheme 2, p.45118-45120
[7]Scgene 1, p.7334
[8]Fig.1

references
[1]
PubMed ID11115499
JournalJ Biol Chem
Year2001
Volume276
Pages8393-402
AuthorsDuewel HS, Radaev S, Wang J, Woodard RW, Gatti DL
TitleSubstrate and metal complexes of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Aquifex aeolicus at 1.9-A resolution. Implications for the condensation mechanism.
Related PDB1fwn,1fws,1fwt,1fww,1fx6,1fxp,1fxq,1fy6
[2]
PubMed ID11747443
JournalBiochemistry
Year2001
Volume40
Pages15676-83
AuthorsWang J, Duewel HS, Woodard RW, Gatti DL
TitleStructures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis.
Related PDB1jcx,1jcy
[3]
PubMed ID12441100
JournalJ Mol Biol
Year2002
Volume324
Pages205-14
AuthorsWang J, Duewel HS, Stuckey JA, Woodard RW, Gatti DL
TitleFunction of His185 in Aquifex aeolicus 3-deoxy-D-manno-octulosonate 8-phosphate synthase.
Related PDB1lrn,1lro,1lrq
Related UniProtKBO66496
[4]
PubMed ID14675946
JournalDrug Des Discov
Year2003
Volume18
Pages91-9
AuthorsXu X, Wang J, Grison C, Petek S, Coutrot P, Birck MR, Woodard RW, Gatti DL
TitleStructure-based design of novel inhibitors of 3-deoxy-D-manno-octulosonate 8-phosphate synthase.
Related PDB1pck,1pcw,1pe1
[5]
PubMed ID14701842
JournalJ Biol Chem
Year2004
Volume279
Pages15787-94
AuthorsSau AK, Li Z, Anderson KS
TitleProbing the role of metal ions in the catalysis of Helicobacter pylori 3-deoxy-D-manno-octulosonate-8-phosphate synthase using a transient kinetic analysis.
[6]
PubMed ID15308670
JournalJ Biol Chem
Year2004
Volume279
Pages45110-20
AuthorsShulami S, Furdui C, Adir N, Shoham Y, Anderson KS, Baasov T
TitleA reciprocal single mutation affects the metal requirement of 3-deoxy-D-manno-2-octulosonate-8-phosphate (KDO8P) synthases from Aquifex pyrophilus and Escherichia coli.
[7]
PubMed ID15882071
JournalBiochemistry
Year2005
Volume44
Pages7326-35
AuthorsFurdui CM, Sau AK, Yaniv O, Belakhov V, Woodard RW, Baasov T, Anderson KS
TitleThe use of (E)- and (Z)-phosphoenol-3-fluoropyruvate as mechanistic probes reveals significant differences between the active sites of KDO8P and DAHP synthases.
[8]
PubMed ID16156656
JournalBiochemistry
Year2005
Volume44
Pages12434-44
AuthorsXu X, Kona F, Wang J, Lu J, Stemmler T, Gatti DL
TitleThe catalytic and conformational cycle of Aquifex aeolicus KDO8P synthase: role of the L7 loop.
Related PDB1zha,1zji,1t8x,1t96,1t99

comments
This enzyme was transferred from E.C. 4.1.2.16 to E.C. 2.5.1.55.
While its counterpart enzyme from E. coli is metal-independent (class I; S00244), this enzyme, from Aquifex pyrophilus, is metal-dependent (class II).
Although the catalytic residues are completely conserved, compared with those of the homologous enzymes (S00243, S00244 in EzCatDB), which are metal-dependent and metal-independent, respectively, the catalytic mechanism of this enzyme can be different from those enzymes, utilizing different catalytic residues. However, more recent studies suggested that the metal ion is not directly involved in catalysis, and that the mechanism can be similar to each other (see [6], [7]).
Although the detailed mechanism has not been elucidated yet, this enzyme catalyzes the following three reactions successively (see [6], [7]).
(A) Addition of the double-bonded carbon of PEP (si face) to the carbonyl group of another substrate, A5P (re face), leading to the formation of oxocarbenium ion and hydroxyl oxygen from carbonyl oxygen (see S00243):
(A1) The pi-electrons on the C3=C2 double-bond of PEP make a nucleophilic attack from the si-face onto the re-face of the metal-activated aldehyde group of A5P, to form a covalent bond.
(A2) Lys46 acts as a general acid, which protonates the C1-carbonyl oxygen of A5P, converting the carbonyl oxygen to hydroxyl one.
(B) Addition of water to the oxocarbenium-ion intermediate, created by the condensation of PEP and A5P:
(B1) Asp81 acts as a general base, activating a water molecule positioned on the re-side (opposite to si-face) of PEP. Here, His83 act as a second general base, accepting the proton of Asp81, left over by the attacking water.
(B2) The activated water, the hydroxide ion, makes a nucleophilic attack on the oxocarbenium ion (C2 atom of originarily PEP), leading to the a linear intermediate.
(C) Elimination of phosphate oxygen leading to formation of carbonyl group:
(C1) Sidechains of Arg154, and mainchain amide of Ala102 stabilize the negative charge on the eliminated phosphate group.
(C2) Lys124 acts as a general acid, which donates a proton to the eliminated phosphate group, leading to the cleavage of the C-O bond.
(C3) Lys124 acts as a general base to deprotonate the hydroxyl group (created by the attacking water), leading to the formation of the carbonyl group.
During these reactions, metal ions, such as zinc, assisted the reactions by orienting the substrates/intermediates.

createdupdated
2004-04-072009-02-26


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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© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.