EzCatDB: S00244
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeS00244
CATH domainDomain 13.20.20.70 : TIM BarrelCatalytic domain
E.C.2.5.1.55
CSA1q3n

CATH domainRelated DB codes (homologues)
3.20.20.70 : TIM BarrelS00215,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

Enzyme Name
UniProtKBKEGG

P0A715
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_415733.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_489482.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF00793 (DAHP_synth_1)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00540Lipopolysaccharide biosynthesis

UniProtKB:Accession NumberP0A715
Entry nameKDSA_ECOLI
ActivityPhosphoenolpyruvate + D-arabinose 5-phosphate + H(2)O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate.
SubunitHomotrimer.
Subcellular locationCytoplasm.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00074C01112C00001C04478C00009

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

ChEBI44897
16241
15377
18069
26078


PubChem59658623
58114173
1005
230
188324
962
22247451
15942880
22486802
1004


               
1d9eAUnboundUnbound UnboundAnalogue:SO4 1999UnboundUnbound
1d9eBUnboundUnbound UnboundAnalogue:SO4 2999UnboundUnbound
1d9eCUnboundUnbound UnboundAnalogue:SO4 3999UnboundUnbound
1d9eDUnboundUnbound UnboundAnalogue:SO4 4999UnboundUnbound
1g7uABound:PEPUnboundUnboundUnboundUnboundUnboundUnbound
1g7vAUnboundUnboundUnboundUnboundUnboundTransition-state-analogue:PAIUnbound
1gg0AUnboundUnbound UnboundBound:PO4 290UnboundUnbound
1phqAAnalogue:FPEUnbound UnboundUnboundUnboundUnbound
1phwAAnalogue:ROBUnbound UnboundUnboundUnboundUnbound
1pl9AAnalogue:FPEUnbound UnboundUnboundUnboundUnbound
1q3nABound:PEPUnbound UnboundUnboundUnboundUnbound
1x6uAUnboundUnbound Bound:DO8UnboundUnboundUnbound
1x8fAUnboundUnbound UnboundUnboundUnboundUnbound

Active-site residues
resource
literature [9], [17]
pdbCatalytic residuescomment
          
1d9eAASN 1026;LYS 1060;ASP 1095;HIS 1097;LYS 1138;HIS 1202;GLU 1239;        
invisible 1246-1251
1d9eBASN 2026;LYS 2060;ASP 2095;HIS 2097;LYS 2138;HIS 2202;GLU 2239;        
invisible 2246-2251
1d9eCASN 3026;LYS 3060;ASP 3095;HIS 3097;LYS 3138;HIS 3202;GLU 3239;        
invisible 3246-3251
1d9eDASN 4026;LYS 4060;ASP 4095;HIS 4097;LYS 4138;HIS 4202;GLU 4239;        
invisible 4245-4252
1g7uAASN   26;LYS   60;ASP   95;HIS   97;LYS  138;HIS  202;GLU  239;ASP  250
 
1g7vAASN   26;LYS   60;ASP   95;HIS   97;LYS  138;HIS  202;GLU  239;ASP  250
 
1gg0AASN   26;LYS   60;ASP   95;HIS   97;LYS  138;HIS  202;GLU  239;ASP  250
 
1phqAASN   26;LYS   60;ASP   95;HIS   97;LYS  138;HIS  202;GLU  239;ASP  250
 
1phwALYS 1138;LYS 1060;ASP 1095;HIS 1097;ASN 1026;HIS 1202;GLU 1239;ASP 1250
 
1pl9AASN   26;LYS   60;ASP   95;HIS   97;LYS  138;HIS  202;GLU  239;ASP  250
 
1q3nAASN   26;LYS   60;ASP   95;HIS   97;LYS  138;HIS  202;GLU  239;ASP  250
 
1x6uAASN   26;LYS   60;ASP   95;HIS   97;LYS  138;HIS  202;GLU  239;ASP  250
 
1x8fAASN   26;LYS   60;ASP   95;HIS   97;LYS  138;HIS  202;GLU  239;ASP  250
 

References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID1521535
JournalEur J Biochem
Year1992
Volume208
Pages443-9
AuthorsKohen A, Jakob A, Baasov T
TitleMechanistic studies of 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase from Escherichia coli.
[2]
PubMed ID8241128
JournalBiochemistry
Year1993
Volume32
Pages12392-7
AuthorsDotson GD, Nanjappan P, Reily MD, Woodard RW
TitleStereochemistry of 3-deoxyoctulosonate 8-phosphate synthase.
[3]
PubMed ID7775423
JournalJ Biol Chem
Year1995
Volume270
Pages13698-705
AuthorsDotson GD, Dua RK, Clemens JC, Wooten EW, Woodard RW
TitleOverproduction 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.
[4]
PubMed ID8778790
JournalProteins
Year1996
Volume24
Pages407-8
AuthorsTolbert WD, Moll JR, Bauerle R, Kretsinger RH
TitleCrystallization and preliminary crystallographic studies of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli.
[5]
PubMed ID10572007
JournalBiochemistry
Year1999
Volume38
Pages14320-9
AuthorsSheflyan GY, Duewel HS, Chen G, Woodard RW
TitleIdentification 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.
[6]
PubMed ID10658571
JournalBioorg Med Chem
Year1999
Volume7
Pages2671-82
AuthorsDu S, Faiger H, Belakhov V, Baasov T
TitleTowards the development of novel antibiotics: synthesis and evaluation of a mechanism-based inhibitor of Kdo8P synthase.
[7]
PubMed ID11101302
JournalBiochemistry
Year2000
Volume39
Pages14865-76
AuthorsKaustov L, Kababya S, Du S, Baasov T, Gropper S, Shoham Y, Schmidt A
TitleStructural and mechanistic investigation of 3-deoxy-D-manno-octulosonate-8-phosphate synthase by solid-state REDOR NMR.
[8]
PubMed ID10988284
JournalJ Biol Chem
Year2000
Volume275
Pages40258-65
AuthorsHowe DL, Duewel HS, Woodard RW
TitleHistidine 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.
[9]
CommentsX-ray crystallography
PubMed ID10734095
JournalJ Biol Chem
Year2000
Volume275
Pages9476-84
AuthorsRadaev S, Dastidar P, Patel M, Woodard RW, Gatti DL
TitleStructure and mechanism of 3-deoxy-D-manno-octulosonate 8-phosphate synthase.
Related PDB1d9e
[10]
PubMed ID10913123
JournalJ Biol Chem
Year2000
Volume275
Pages32141-6
AuthorsTaylor WP, Sheflyan GY, Woodard RW
TitleA single point mutation in 3-deoxy-D-manno-octulosonate-8-phosphate synthase is responsible for temperature sensitivity in a mutant strain of Salmonella typhimurium.
[11]
CommentsX-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
Medline ID20384849
PubMed ID10926505
JournalJ Mol Biol
Year2000
Volume301
Pages233-8
AuthorsWagner T, Kretsinger RH, Bauerle R, Tolbert WD
Title3-Deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli. Model of binding of phosphoenolpyruvate and D-arabinose-5-phosphate.
Related PDB1gg0
Related UniProtKBP0A715
[12]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
Medline ID21264114
PubMed ID11371194
JournalBiochemistry
Year2001
Volume40
Pages6326-34
AuthorsAsojo O, Friedman J, Adir N, Belakhov V, Shoham Y, Baasov T
TitleCrystal structures of KDOP synthase in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor.
Related PDB1g7u,1g7v
Related UniProtKBP0A715
[13]
PubMed ID12718525
JournalBiochemistry
Year2003
Volume42
Pages4843-54
AuthorsHowe DL, Sundaram AK, Wu J, Gatti DL, Woodard RW
TitleMechanistic insight into 3-deoxy-D-manno-octulosonate-8-phosphate synthase and 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase utilizing phosphorylated monosaccharide analogues.
[14]
PubMed ID12877880
JournalBioorg Chem
Year2003
Volume31
Pages306-21
AuthorsKaustov L, Baasov T, Schmidt A
TitleBinding of the natural substrates and products to KDO8P synthase: 31P and 13C solution NMR characterization.
[15]
PubMed ID12683839
JournalJ Am Chem Soc
Year2003
Volume125
Pages4662-9
AuthorsKaustov L, Kababya S, Belakhov V, Baasov T, Shoham Y, Schmidt A
TitleInhibition mode of a bisubstrate inhibitor of KDO8P synthase: a frequency-selective REDOR solid-state and solution NMR characterization.
[16]
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.
[17]
PubMed ID15276836
JournalJ Mol Biol
Year2004
Volume341
Pages455-66
AuthorsShumilin IA, Bauerle R, Wu J, Woodard RW, Kretsinger RH
TitleCrystal 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.
[18]
PubMed ID15721322
JournalCarbohydr Res
Year2005
Volume340
Pages529-37
AuthorsGrison C, Petek S, Finance C, Coutrot P
TitleSynthesis and antibacterial activity of mechanism-based inhibitors of KDO8P synthase and DAH7P synthase.
[19]
CommentsX-ray crystallography
PubMed ID16023668
JournalJ Mol Biol
Year2005
Volume351
Pages641-52
AuthorsVainer R, Belakhov V, Rabkin E, Baasov T, Adir N
TitleCrystal Structures of Escherichia coli KDO8P Synthase Complexes Reveal the Source of Catalytic Irreversibility.
Related PDB1phw,1q3n,1x6u,1x8f

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:

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 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.