DB code: S00244

CATH domain 3.20.20.70 : TIM Barrel Catalytic domain
E.C. 2.5.1.55
CSA 1q3n
M-CSA 1q3n
MACiE

CATH domain Related DB codes (homologues)
3.20.20.70 : TIM Barrel S00215 S00217 S00218 S00219 S00532 S00198 S00220 S00745 S00537 S00538 S00539 S00826 S00841 S00235 S00239 S00240 S00243 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
P0A715 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_415733.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489482.1 (Protein)
NC_007779.1 (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
P0A715 KDSA_ECOLI Phosphoenolpyruvate + D-arabinose 5-phosphate + H(2)O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate. Homotrimer. Cytoplasm.

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

Compound table
Substrates Products Intermediates
KEGG-id C00074 C01112 C00001 C04478 C00009
E.C.
Compound 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 carboxyl group,phosphate group/phosphate ion carbohydrate,phosphate group/phosphate ion H2O carbohydrate,carboxyl group,phosphate group/phosphate ion phosphate group/phosphate ion
ChEBI 44897
16241
15377
18069
26078
PubChem 1005
58114173
59658623
188324
230
22247451
962
15942880
1004
22486802
1d9eA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:SO4_1999 Unbound Unbound
1d9eB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:SO4_2999 Unbound Unbound
1d9eC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:SO4_3999 Unbound Unbound
1d9eD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:SO4_4999 Unbound Unbound
1g7uA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PEP Unbound Unbound Unbound Unbound Unbound Unbound
1g7vA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Transition-state-analogue:PAI Unbound
1gg0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:PO4_290 Unbound Unbound
1phqA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:FPE Unbound Unbound Unbound Unbound Unbound
1phwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:ROB Unbound Unbound Unbound Unbound Unbound
1pl9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:FPE Unbound Unbound Unbound Unbound Unbound
1q3nA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:PEP Unbound Unbound Unbound Unbound Unbound
1x6uA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:DO8 Unbound Unbound Unbound
1x8fA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [9], [17]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1d9eA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 1026;LYS 1060;ASP 1095;HIS 1097;LYS 1138;HIS 1202;GLU 1239; invisible 1246-1251
1d9eB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 2026;LYS 2060;ASP 2095;HIS 2097;LYS 2138;HIS 2202;GLU 2239; invisible 2246-2251
1d9eC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 3026;LYS 3060;ASP 3095;HIS 3097;LYS 3138;HIS 3202;GLU 3239; invisible 3246-3251
1d9eD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 4026;LYS 4060;ASP 4095;HIS 4097;LYS 4138;HIS 4202;GLU 4239; invisible 4245-4252
1g7uA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 26;LYS 60;ASP 95;HIS 97;LYS 138;HIS 202;GLU 239;ASP 250
1g7vA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 26;LYS 60;ASP 95;HIS 97;LYS 138;HIS 202;GLU 239;ASP 250
1gg0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 26;LYS 60;ASP 95;HIS 97;LYS 138;HIS 202;GLU 239;ASP 250
1phqA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 26;LYS 60;ASP 95;HIS 97;LYS 138;HIS 202;GLU 239;ASP 250
1phwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 1138;LYS 1060;ASP 1095;HIS 1097;ASN 1026;HIS 1202;GLU 1239;ASP 1250
1pl9A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 26;LYS 60;ASP 95;HIS 97;LYS 138;HIS 202;GLU 239;ASP 250
1q3nA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 26;LYS 60;ASP 95;HIS 97;LYS 138;HIS 202;GLU 239;ASP 250
1x6uA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 26;LYS 60;ASP 95;HIS 97;LYS 138;HIS 202;GLU 239;ASP 250
1x8fA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 26;LYS 60;ASP 95;HIS 97;LYS 138;HIS 202;GLU 239;ASP 250

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Scheme 1
[2]
Fig.5, p.12396
[3]
Scheme 1, Scheme 2, p.13702-13704
[6]
Scheme 1, p.2676-2677
[7]
Scheme 1, Scheme 2, p.14875
[9]
Fig.8, p.9480-9483
[10]
Fig.2
[12]
Scheme 1, Fig.5, p.6329-6332
[13]
Fig.1, Fig.8, Fig.9, p.4852
[14]
Scheme 1, p.308
[16]
Scheme 1, Scheme 2, p.45118-45120
[17]
Fig.6, p.462-464
[18]
Chart 1
[19]
Scheme 1

References
[1]
Resource
Comments
Medline ID
PubMed ID 1521535
Journal Eur J Biochem
Year 1992
Volume 208
Pages 443-9
Authors Kohen A, Jakob A, Baasov T
Title Mechanistic studies of 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase from Escherichia coli.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8241128
Journal Biochemistry
Year 1993
Volume 32
Pages 12392-7
Authors Dotson GD, Nanjappan P, Reily MD, Woodard RW
Title Stereochemistry of 3-deoxyoctulosonate 8-phosphate synthase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7775423
Journal J Biol Chem
Year 1995
Volume 270
Pages 13698-705
Authors Dotson GD, Dua RK, Clemens JC, Wooten EW, Woodard RW
Title Overproduction and one-step purification of Escherichia coli 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase and oxygen transfer studies during catalysis using isotopic-shifted heteronuclear NMR.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8778790
Journal Proteins
Year 1996
Volume 24
Pages 407-8
Authors Tolbert WD, Moll JR, Bauerle R, Kretsinger RH
Title Crystallization and preliminary crystallographic studies of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 10572007
Journal Biochemistry
Year 1999
Volume 38
Pages 14320-9
Authors Sheflyan GY, Duewel HS, Chen G, Woodard RW
Title Identification of essential histidine residues in 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase: analysis by chemical modification with diethyl pyrocarbonate and site-directed mutagenesis.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 10658571
Journal Bioorg Med Chem
Year 1999
Volume 7
Pages 2671-82
Authors Du S, Faiger H, Belakhov V, Baasov T
Title Towards the development of novel antibiotics: synthesis and evaluation of a mechanism-based inhibitor of Kdo8P synthase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 11101302
Journal Biochemistry
Year 2000
Volume 39
Pages 14865-76
Authors Kaustov L, Kababya S, Du S, Baasov T, Gropper S, Shoham Y, Schmidt A
Title Structural and mechanistic investigation of 3-deoxy-D-manno-octulosonate-8-phosphate synthase by solid-state REDOR NMR.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 10988284
Journal J Biol Chem
Year 2000
Volume 275
Pages 40258-65
Authors Howe DL, Duewel HS, Woodard RW
Title Histidine 268 in 3-deoxy-D-arabino-heptulosonic acid 7-phosphate synthase plays the same role as histidine 202 in 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase.
Related PDB
Related UniProtKB
[9]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10734095
Journal J Biol Chem
Year 2000
Volume 275
Pages 9476-84
Authors Radaev S, Dastidar P, Patel M, Woodard RW, Gatti DL
Title Structure and mechanism of 3-deoxy-D-manno-octulosonate 8-phosphate synthase.
Related PDB 1d9e
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10913123
Journal J Biol Chem
Year 2000
Volume 275
Pages 32141-6
Authors Taylor WP, Sheflyan GY, Woodard RW
Title A single point mutation in 3-deoxy-D-manno-octulosonate-8-phosphate synthase is responsible for temperature sensitivity in a mutant strain of Salmonella typhimurium.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
Medline ID 20384849
PubMed ID 10926505
Journal J Mol Biol
Year 2000
Volume 301
Pages 233-8
Authors Wagner T, Kretsinger RH, Bauerle R, Tolbert WD
Title 3-Deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli. Model of binding of phosphoenolpyruvate and D-arabinose-5-phosphate.
Related PDB 1gg0
Related UniProtKB P0A715
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
Medline ID 21264114
PubMed ID 11371194
Journal Biochemistry
Year 2001
Volume 40
Pages 6326-34
Authors Asojo O, Friedman J, Adir N, Belakhov V, Shoham Y, Baasov T
Title Crystal structures of KDOP synthase in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor.
Related PDB 1g7u 1g7v
Related UniProtKB P0A715
[13]
Resource
Comments
Medline ID
PubMed ID 12718525
Journal Biochemistry
Year 2003
Volume 42
Pages 4843-54
Authors Howe DL, Sundaram AK, Wu J, Gatti DL, Woodard RW
Title Mechanistic insight into 3-deoxy-D-manno-octulosonate-8-phosphate synthase and 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase utilizing phosphorylated monosaccharide analogues.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 12877880
Journal Bioorg Chem
Year 2003
Volume 31
Pages 306-21
Authors Kaustov L, Baasov T, Schmidt A
Title Binding of the natural substrates and products to KDO8P synthase: 31P and 13C solution NMR characterization.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 12683839
Journal J Am Chem Soc
Year 2003
Volume 125
Pages 4662-9
Authors Kaustov L, Kababya S, Belakhov V, Baasov T, Shoham Y, Schmidt A
Title Inhibition mode of a bisubstrate inhibitor of KDO8P synthase: a frequency-selective REDOR solid-state and solution NMR characterization.
Related PDB
Related UniProtKB
[16]
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
[17]
Resource
Comments
Medline ID
PubMed ID 15276836
Journal J Mol Biol
Year 2004
Volume 341
Pages 455-66
Authors Shumilin IA, Bauerle R, Wu J, Woodard RW, Kretsinger RH
Title Crystal structure of the reaction complex of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Thermotoga maritima refines the catalytic mechanism and indicates a new mechanism of allosteric regulation.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 15721322
Journal Carbohydr Res
Year 2005
Volume 340
Pages 529-37
Authors Grison C, Petek S, Finance C, Coutrot P
Title Synthesis and antibacterial activity of mechanism-based inhibitors of KDO8P synthase and DAH7P synthase.
Related PDB
Related UniProtKB
[19]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 16023668
Journal J Mol Biol
Year 2005
Volume 351
Pages 641-52
Authors Vainer R, Belakhov V, Rabkin E, Baasov T, Adir N
Title Crystal Structures of Escherichia coli KDO8P Synthase Complexes Reveal the Source of Catalytic Irreversibility.
Related PDB 1phw 1q3n 1x6u 1x8f
Related UniProtKB

Comments
This enzyme was transferred from E.C. 4.1.2.16 to E.C. 2.5.1.55.
This enzyme from E. coli is metal-independent (class I), whilst its counterpart enzyme from Aquifex pyrophilus is metal-dependent (class II; S00532 in EzCatDB) (see [16]).
Although the catalytic residues are completely conserved, compared with those of the homologous enzymes (S00243, S00532 in EzCatDB), which are metal-dependent enzymes, 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] of S00532).
On the other hand, comparing the structures of their complexes with ligand molecules, the relative positions of ligand molecules in this metal-independent enzyme are quite different from those in the metal-dependent enzymes.
Although the detailed mechanism has not been elucidated yet, this enzyme catalyzes the following three reactions successively (see [9], [16], [19]).
(A) Addition of the double-bonded carbon of PEP (si face) to the carbonyl group of another substrate, A5P (re face), changing the carbonyl oxygen to hydroxyl oxygen:
(B) Addition of water to the intermediate, created by the condensation of PEP and A5P:
(C) Elimination of phosphate leading to formation of aldehyde carbonyl group:

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