DB code: S00532

RLCP classification 4.151.774000.401 : Addition
4.16.66400.4 : Addition
5.41.2776000.400 : Elimination
CATH domain 3.20.20.70 : TIM Barrel Catalytic domain
E.C. 2.5.1.55
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.20.20.70 : TIM Barrel S00215 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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
O66496 2-dehydro-3-deoxyphosphooctonate aldolase
EC 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
NP_213056.1 (Protein)
NC_000918.1 (DNA/RNA sequence)
PF00793 (DAHP_synth_1)
[Graphical View]

KEGG enzyme name
3-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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
O66496 KDSA_AQUAE Phosphoenolpyruvate + D-arabinose 5-phosphate + H(2)O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate. Oligomer. Cytoplasm (By similarity).

KEGG Pathways
Map code Pathways E.C.
MAP00540 Lipopolysaccharide biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00074 C01112 C00001 C04478 C00009
E.C.
Compound Zinc Phosphoenolpyruvate D-Arabinose 5-phosphate H2O 2-Dehydro-3-deoxy-D-octonate 8-phosphate Orthophosphate Transition-state with an oxocarbenium ion A linear tetrahedral intermediate
Type heavy metal carboxyl group,phosphate group/phosphate ion carbohydrate,phosphate group/phosphate ion H2O carbohydrate,carboxyl group,phosphate group/phosphate ion phosphate group/phosphate ion
ChEBI 29105
 29105
 		44897
 44897
 		16241
 16241
 		15377
 15377
 		18069
 18069
 		26078
 26078
PubChem 32051
 32051
 		1005
 58114173
 59658623
 1005
 58114173
 59658623
 		188324
 230
 188324
 230
 		22247451
 962
 22247451
 962
 		15942880
 15942880
 		1004
 22486802
 1004
 22486802
1fwnA Unbound Bound:PEP Unbound Unbound Unbound Unbound Unbound
1fwnB Unbound Bound:PEP Unbound Unbound Unbound Unbound Unbound
1fwsA Analogue:_CD Bound:PEP Unbound Unbound Unbound Unbound Unbound
1fwsB Analogue:_CD Bound:PEP Unbound Unbound Unbound Unbound Unbound
1fwtA Analogue:_CD Bound:PEP Unbound Unbound Unbound Unbound Unbound
1fwtB Analogue:_CD Bound:PEP Analogue:E4P Unbound Unbound Unbound Unbound
1fwwA Analogue:_CD Bound:PEP Bound:A5P Bound:HOH_3026 Unbound Unbound Unbound Unbound
1fwwB Analogue:_CD Bound:PEP Unbound Bound:HOH_3060 Unbound Unbound Unbound Unbound
1fx6A Unbound Unbound Unbound Unbound Bound:PO4 Unbound Unbound
1fx6B Unbound Unbound Unbound Unbound Bound:PO4 Unbound Unbound
1fxpA Analogue:_CD Unbound Unbound Unbound Bound:PO4 Unbound Unbound
1fxpB Analogue:_CD Unbound Unbound Unbound Bound:PO4 Unbound Unbound
1fxqA Unbound Bound:PEP Bound:A5P Unbound Unbound Unbound Unbound
1fxqB Unbound Bound:PEP Bound:A5P Unbound Unbound Unbound Unbound
1fy6A Analogue:_CD Unbound Bound:A5P Unbound Bound:PO4 Unbound Unbound
1fy6B Analogue:_CD Unbound Unbound Unbound Bound:PO4 Unbound Unbound
1jcxA Analogue:_CD Unbound Unbound Bound:HOH_3056 Unbound Unbound Transition-state-analogue:PAI Unbound
1jcxB Analogue:_CD Unbound Unbound Bound:HOH_3105 Unbound Unbound Transition-state-analogue:PAI Unbound
1jcyA Analogue:_CD Bound:PEP Analogue:R5P Unbound Unbound Unbound Unbound
1jcyB Analogue:_CD Bound:PEP Unbound Unbound Unbound Unbound Unbound
1lrnA Analogue:_CD Unbound Unbound Unbound Bound:PO4 Unbound Unbound
1lrnB Analogue:_CD Unbound Unbound Unbound Bound:PO4 Unbound Unbound
1lroA Analogue:_CD Bound:PEP Unbound Unbound Unbound Unbound Unbound
1lroB Analogue:_CD Bound:PEP Unbound Unbound Unbound Unbound Unbound
1lrqA Analogue:_CD Bound:PEP Bound:A5P Unbound Unbound Unbound Unbound
1lrqB Analogue:_CD Unbound Unbound Unbound Bound:PO4 Unbound Unbound
1pckA Analogue:_CD Analogue:PEZ Unbound Unbound Unbound Unbound Unbound
1pckB Analogue:_CD Analogue:PEZ Unbound Unbound Unbound Unbound Unbound
1pcwA Analogue:_CD Unbound Unbound Bound:HOH_31 Unbound Unbound Transition-state-analogue:H4P Unbound
1pcwB Analogue:_CD Unbound Unbound Bound:HOH_93 Unbound Unbound Transition-state-analogue:H4P Unbound
1pe1A Analogue:_CD Analogue:2PG Unbound Unbound Unbound Unbound Unbound Unbound
1pe1B Analogue:_CD Analogue:2PG Unbound Unbound Unbound Unbound Unbound Unbound
1t8xA Analogue:_CD Bound:PEP Bound:A5P Unbound Unbound Unbound Unbound
1t8xB Analogue:_CD Bound:PEP Unbound Unbound Unbound Unbound Unbound
1t96A Analogue:_CD Bound:PEP Unbound Unbound Unbound Unbound Unbound
1t96B Analogue:_CD Bound:PEP Unbound Unbound Unbound Unbound Unbound
1t99A Analogue:_CD Unbound Unbound Unbound Bound:PO4 Unbound Unbound
1t99B Analogue:_CD Unbound Unbound Unbound Bound:PO4 Unbound Unbound
1zhaA Analogue:_CD Bound:PEP Analogue:R5P Unbound Unbound Unbound Unbound
1zhaB Analogue:_CD Bound:PEP Unbound Unbound Unbound Unbound Unbound
1zjiA Analogue:_CD Analogue:2PG Analogue:R5P Unbound Unbound Unbound Unbound Unbound
1zjiB Analogue:_CD Analogue:2PG Unbound Unbound Unbound Unbound Unbound Unbound
2a21A Bound:_ZN Bound:PEP Unbound Unbound Unbound Unbound Unbound
2a21B Bound:_ZN Bound:PEP Unbound Unbound Unbound Unbound Unbound
2a2iA Bound:_ZN Bound:PEP Bound:A5P Bound:HOH_3088 Unbound Unbound Unbound Unbound
2a2iB Bound:_ZN Bound:PEP Bound:A5P Bound:HOH_3093 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
1fwnA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1fwnB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1fwsA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1fwsB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1fwtA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1fwtB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1fwwA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1fwwB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1fx6A LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1fx6B LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1fxpA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1fxpB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1fxqA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1fxqB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1fy6A LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1fy6B LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1jcxA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1jcxB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1jcyA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1jcyB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1lrnA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011; ;GLU 1222;ASP 1233(metal-binding) ALA 1102 mutant H1185G
1lrnB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011; ;GLU 2222;ASP 2233(metal-binding) ALA 2102 mutant H2185G
1lroA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011; ;GLU 1222;ASP 1233(metal-binding) ALA 1102 mutant H1185G
1lroB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011; ;GLU 2222;ASP 2233(metal-binding) ALA 2102 mutant H2185G
1lrqA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011; ;GLU 1222;ASP 1233(metal-binding) ALA 1102 mutant H1185G
1lrqB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011; ;GLU 2222;ASP 2233(metal-binding) ALA 2102 mutant H2185G
1pckA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1pckB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1pcwA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1pcwB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1pe1A LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
1pe1B LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
1t8xA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102 mutant R1106G
1t8xB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102 mutant R2106G
1t96A LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102 mutant R1106G
1t96B LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102 mutant R2106G
1t99A LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102 mutant R1106G
1t99B LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102 mutant R2106G
1zhaA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102 mutant R1106G
1zhaB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102 mutant R2106G
1zjiA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102 mutant R1106G
1zjiB LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102 mutant R2106G
2a21A LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
2a21B LYS 2046;ASP 2081;HIS 2083;LYS 2124;ARG 2154 CYS 2011;HIS 2185;GLU 2222;ASP 2233(metal-binding) ALA 2102
2a2iA LYS 1046;ASP 1081;HIS 1083;LYS 1124;ARG 1154 CYS 1011;HIS 1185;GLU 1222;ASP 1233(metal-binding) ALA 1102
2a2iB LYS 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
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 11115499
Journal J Biol Chem
Year 2001
Volume 276
Pages 8393-402
Authors Duewel HS, Radaev S, Wang J, Woodard RW, Gatti DL
Title Substrate 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 PDB 1fwn 1fws 1fwt 1fww 1fx6 1fxp 1fxq 1fy6
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 11747443
Journal Biochemistry
Year 2001
Volume 40
Pages 15676-83
Authors Wang J, Duewel HS, Woodard RW, Gatti DL
Title Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis.
Related PDB 1jcx 1jcy
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 12441100
Journal J Mol Biol
Year 2002
Volume 324
Pages 205-14
Authors Wang J, Duewel HS, Stuckey JA, Woodard RW, Gatti DL
Title Function of His185 in Aquifex aeolicus 3-deoxy-D-manno-octulosonate 8-phosphate synthase.
Related PDB 1lrn 1lro 1lrq
Related UniProtKB O66496
[4]
Resource
Comments
Medline ID
PubMed ID 14675946
Journal Drug Des Discov
Year 2003
Volume 18
Pages 91-9
Authors Xu X, Wang J, Grison C, Petek S, Coutrot P, Birck MR, Woodard RW, Gatti DL
Title Structure-based design of novel inhibitors of 3-deoxy-D-manno-octulosonate 8-phosphate synthase.
Related PDB 1pck 1pcw 1pe1
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 14701842
Journal J Biol Chem
Year 2004
Volume 279
Pages 15787-94
Authors Sau AK, Li Z, Anderson KS
Title Probing the role of metal ions in the catalysis of Helicobacter pylori 3-deoxy-D-manno-octulosonate-8-phosphate synthase using a transient kinetic analysis.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 15308670
Journal J Biol Chem
Year 2004
Volume 279
Pages 45110-20
Authors Shulami S, Furdui C, Adir N, Shoham Y, Anderson KS, Baasov T
Title A reciprocal single mutation affects the metal requirement of 3-deoxy-D-manno-2-octulosonate-8-phosphate (KDO8P) synthases from Aquifex pyrophilus and Escherichia coli.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 15882071
Journal Biochemistry
Year 2005
Volume 44
Pages 7326-35
Authors Furdui CM, Sau AK, Yaniv O, Belakhov V, Woodard RW, Baasov T, Anderson KS
Title The use of (E)- and (Z)-phosphoenol-3-fluoropyruvate as mechanistic probes reveals significant differences between the active sites of KDO8P and DAHP synthases.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 16156656
Journal Biochemistry
Year 2005
Volume 44
Pages 12434-44
Authors Xu X, Kona F, Wang J, Lu J, Stemmler T, Gatti DL
Title The catalytic and conformational cycle of Aquifex aeolicus KDO8P synthase: role of the L7 loop.
Related PDB 1zha 1zji 1t8x 1t96 1t99
Related UniProtKB

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.

Created Updated
2004-04-07 2009-02-26