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Information on EC 2.5.1.55 - 3-deoxy-8-phosphooctulonate synthase and Organism(s) Escherichia coli and UniProt Accession P0A715

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Escherichia coli
UNIPROT: P0A715 not found.
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The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
Synonyms
kdo8ps, kdo8p synthase, kdo 8-p synthase, kdops, 3-deoxy-d-manno-octulosonate 8-phosphate synthase, kdo-8-p synthase, kdo-8-phosphate synthetase, atkdsa1, 3-deoxy-d-manno-octulosonate-8-phosphate synthase, atkdsa2, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3-deoxy-D-manno-2-octulosonate-8-phosphate synthase
-
3-deoxy-D-manno-octulosonate 8-phosphate synthase
-
2-dehydro-3-deoxy-D-octonate-8-phosphate D-arabinose-5-phosphate-lyase (pyruvate-phosphorylating)
-
-
-
-
2-dehydro-3-deoxyphosphooctonate aldolase
-
-
-
-
2-keto-3-deoxy-8-phosphooctonic acid synthetase
-
-
-
-
2-keto-3-deoxy-8-phosphooctonic synthetase
-
-
-
-
3-deoxy-D-manno-octulosonate 8-phosphate synthase
-
-
3-deoxy-D-manno-octulosonate 8-phosphate synthetase
-
-
-
-
3-deoxy-D-manno-octulosonate-8-phosphate synthase
-
-
-
-
3-deoxy-D-manno-octulosonic acid 8-phosphate synthase
-
-
-
-
3-deoxy-D-mannooctulosonate-8-phosphate synthetase
-
-
-
-
3-deoxyoctulosonic 8-phosphate synthetase
-
-
-
-
8-phospho-2-dehydro-3-deoxy-D-octonate D-arabinose-5-phosphate-lyase (pyruvate-phosphorylating)
-
-
-
-
aldolase, phospho-2-keto-3-deoxyoctonate
-
-
-
-
KDO 8-phosphate synthetase
-
-
KDO-8-P synthase
KDO-8-P synthetase
-
-
-
-
Kdo-8-phosphate synthase
-
-
KDO8-P
-
-
-
-
Kdo8P synthase
KDO8PS
-
-
-
-
KDOPS
KDPO synthetase
-
-
-
-
Phospho-2-dehydro-3-deoxyoctonate aldolase
-
-
-
-
phospho-2-keto-3-deoxyoctonate aldolase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
phosphoenolpyruvate + D-arabinose 5-phosphate + H2O = 3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
show the reaction diagram
the synthesis of 2-dehydro-3-deoxy-D-octonate 8-phosphate proceeds through the formation of a linear rather than a cyclic intermediate
phosphoenolpyruvate + D-arabinose 5-phosphate + H2O = 3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
condensation
-
-
-
-
PATHWAY SOURCE
PATHWAYS
-
-, -
SYSTEMATIC NAME
IUBMB Comments
phosphoenolpyruvate:D-arabinose-5-phosphate C-(1-carboxyvinyl)transferase (phosphate-hydrolysing, 2-carboxy-2-oxoethyl-forming)
-
CAS REGISTRY NUMBER
COMMENTARY hide
9026-96-4
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
phosphoenolpyruvate + D-arabinose 5-phosphate
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
show the reaction diagram
phosphoenolpyruvate + D-arabinose 5-phosphate + H2O
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
show the reaction diagram
-
-
-
?
phosphoenolpyruvate + D-arabinose-5-phosphate + H2O
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
show the reaction diagram
2-dehydro-3-deoxy-D-octonate 8-phosphate is the phosphorylated precursor of 3-deoxy-D-manno-octulosonate, an essential sugar of the liposaccharide of gram-negative bacteria
-
-
?
phosphoenolpyruvate + 2-deoxyribose 5-phosphate
?
show the reaction diagram
-
-
-
-
?
phosphoenolpyruvate + D-arabinose 5-phosphate
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
show the reaction diagram
phosphoenolpyruvate + D-arabinose 5-phosphate + H2O
3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
show the reaction diagram
-
-
-
-
?
phosphoenolpyruvate + D-arabinose-5-phosphate + H2O
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
show the reaction diagram
phosphoenolpyruvate + erythrose 4-phosphate
3-deoxy-D-ribo-heptulosonate 7-phosphate
show the reaction diagram
-
the enzyme does not catalyze the condensation of D-erythrose 4-phosphate and phosphoenolpyruvate to form 3-deoxy-D-ribo-heptulosonate 7-phosphate
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
phosphoenolpyruvate + D-arabinose 5-phosphate + H2O
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
show the reaction diagram
-
-
-
?
phosphoenolpyruvate + D-arabinose-5-phosphate + H2O
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
show the reaction diagram
2-dehydro-3-deoxy-D-octonate 8-phosphate is the phosphorylated precursor of 3-deoxy-D-manno-octulosonate, an essential sugar of the liposaccharide of gram-negative bacteria
-
-
?
phosphoenolpyruvate + D-arabinose 5-phosphate + H2O
3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
show the reaction diagram
-
-
-
-
?
phosphoenolpyruvate + D-arabinose-5-phosphate + H2O
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Magnesium
wild-type enzyme contains 0.05 mol of magnesium per mol of enzyme, mutant enzyme N26C contains 0.4 mol of magnesium per mol of enzyme
Zinc
wild-type enzyme contains 0.05 mol of zinc per mol of enzyme, mutant enzyme N26C contains 0.2 mol of zinc per mol of enzyme
Ba2+
-
1 mM, 5-10% stimulation
Fe3+
-
1 mM, 5-10% stimulation
Li+
-
1 mM, 5-10% stimulation
Mg2+
-
1 mM, 5-10% stimulation
Mn2+
-
1 mM, 5-10% stimulation
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,10-phenanthroline
-
-
2,6-Anhydro-3-deoxy-2beta-phosphonylmethyl-8-phosphate-D-glycero-D-talo-octonate
-
most potent inhibitor
2-Deoxy-2-fluoro-D-arabinoate-5-phosphate
-
-
6H-6-Imino-(2,3,4,5-tetrahydropyrimido)[1,2-c]-[1,3]benzothiazine
-
PD404,182,displays strong inhibition in vitro, but is ineffective in vivo against Gram-negative bacteria due to an inability to cross the bacterial plasma membran
Bromopyruvate
-
phosphoenolpyruvate, but not arabinose-5-phosphate protects
D-ribose 5-phosphate
phosphate
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
EDTA
-
1 mM, 40% stimulation
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.02 - 0.11
D-arabinose 5-phosphate
0.0058 - 0.032
phosphoenolpyruvate
0.05
2-deoxyribose 5-phosphate
-
pH 7.6, 37°C
0.00773 - 0.026
D-arabinose 5-phosphate
0.00443 - 0.006
phosphoenolpyruvate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.36 - 6.1
D-arabinose 5-phosphate
0.36 - 6.1
phosphoenolpyruvate
0.12
2-deoxyribose 5-phosphate
-
pH 7.6, 37°C
5.31 - 6.8
D-arabinose 5-phosphate
5.31 - 100
phosphoenolpyruvate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.6
2,6-Anhydro-3-deoxy-2beta-phosphonylmethyl-8-phosphate-D-glycero-D-talo-octonate
-
pH 7.3, 37°C
0.000026
6H-6-Imino-(2,3,4,5-tetrahydropyrimido)[1,2-c]-[1,3]benzothiazine
-
pH and temperature not specified in the publication
1
D-ribose 5-phosphate
-
pH 7.3, 37°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4 - 6
-
and a second optimum at pH 9.0
9
-
and a second optimum at pH 4.0-6.0
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
-
the enzyme synthesizes 3-deoxy-D-manno-octulosonic acid, that is an important component of the nonrepeating core oligosaccharide part of bacterial lipopolysaccharides and in capsular polysaccharides of many bacteria
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
123400
tetramer, ESI-MS
30845
30850
monomer, ESI-MS
62680
dimer, ESI-MS
30842
-
x * 30842, electrospray mass spectrometry
32000
-
3 * 32000, SDS-PAGE
90000
-
gel filtration, non-denaturing PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
2 * 30845, ESI-MS, predominant in unbound enzyme in complex with substrate D-arabinose 5-phosphate or product 3-deoxy-D-manno-octulosonate 8-phosphate, phosphoenolpyruvate-bound and unbound enzyme exists as dimer
monomer
1 * 30845, ESI-MS, unbound enzyme with substrate phosphoenolpyruvate or product phosphate favors the formation of monomers, phosphoenolpyruvate-bound and unbound enzyme exists as monomer
tetramer
?
-
x * 30842, electrospray mass spectrometry
tetramer
-
tetrameric quaternary structure with an active site in each monomer, by NMR study and crystal structure analysis
trimer
-
3 * 32000, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallization is performed by vapor diffusion in hanging drops
crystals are grown at 23°C by vapor diffusion in hanging drops, crystal structures of the enzyme in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor
structures of apo-enzyme and of binary complexes with the substrates phosphoenolpyruvate, the product 2-dehydro-3-deoxy-D-octonate 8-phosphate and the catalytically inactive 1-deoxy analog of arabinose 5-phosphate
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
N26C
activity of the wild-type enzyme is independent of metal ions, the activity of mutant enzyme is decreased by EDTA and increased by Mn2+ and Cd2+
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
-
15 min, 30% loss of activity
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
dialysis against 10 mM EDTA in 50 mM Tris-HCl buffer, pH 7.3, inactivates
-
repeated freezing and thawing causes loss of activity
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 50% loss of activity after 14 days
-
-90°C, 0.1 M potassium phosphate buffer, pH 7.2, stable for up to 1 year
-
4°C, in 20 mM ammonium acetate (pH 7.8), overnight, remains stable in the phosphoenol-bound state
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
overnight dialysis against 50 mM ammonium acetate, pH 7.8, 4°C, reconstitution with substrates and products
one-step purification
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Salmonella typhimurium
-
localization of the kdsA gene with the aid of the physical map of the Escherichia coli chromosome
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ray, P.
Purification and characterization of 3-deoxy-D-manno-octulosonate 8-phosphate synthetase from Escherichia coli
J. Bacteriol.
141
635-644
1980
Escherichia coli, Escherichia coli B / ATCC 11303
Manually annotated by BRENDA team
Ray, P.H.
3-Deoxy-D-manno-octulosonate-8-phosphate (KDO-8-P) synthase
Methods Enzymol.
83
525-530
1982
Escherichia coli, Escherichia coli B / ATCC 11303
Manually annotated by BRENDA team
Woisetschlger, M.; Hgenauer, G.
Cloning and characterization of the gene encoding 3-deoxy-D-manno-octulosonate 8-phosphate synthetase from Escherichia coli
J. Bacteriol.
168
437-439
1986
Escherichia coli
Manually annotated by BRENDA team
Woisetschlaeger, M.; Hoedl-Neuhofer, A.; Hoegenauer, G.
Localization of the kdsA gene with the aid of the physical map of the Escherichia coli chromosome
J. Bacteriol.
170
5382-5384
1988
Escherichia coli
Manually annotated by BRENDA team
Dotson, G.D.; Nanjappan, P.; Reily, M.D.; Woodward, R.W.
Stereochemistry of 3-deoxyoctulosonate 8-phosphate synthase
Biochemistry
32
12392-12397
1993
Escherichia coli
Manually annotated by BRENDA team
Liang, P.H.; Lewis, J.; Anderson, K.S.
Catalytic mechanism of Kdo8P synthase: transient kinetic studies and evaluation of a putative reaction intermediate
Biochemistry
37
1639-16399
1998
Escherichia coli
-
Manually annotated by BRENDA team
Hedstrom, L.; Abeles, R.
3-Deoxy-D-manno-octulosonate-8-phosphate synthase catalyzes the C-O bond cleavage of phosphoenolpyruvate
Biochem. Biophys. Res. Commun.
157
816-820
1988
Escherichia coli
Manually annotated by BRENDA team
Tolbert, W.D.; Moll, J.R.; Bauerle, R.; Kretsinger, R.H.
Crystallization and preliminary crystallographic studies of 3-deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli
Proteins Struct. Funct. Genet.
24
407-408
1996
Escherichia coli
Manually annotated by BRENDA team
Dotson, G.D.; Dua, R.K.; Clemens, J.C.; Wooten, E.W.; Woodard, R.W.
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
J. Biol. Chem.
270
13698-13705
1995
Escherichia coli
Manually annotated by BRENDA team
Kohen, A.; Jakob, A.; Baasov, T.
Mechanistic studies of 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase from Escherichia coli
Eur. J. Biochem.
208
443-449
1992
Escherichia coli
Manually annotated by BRENDA team
Baasov, T.; Sheffer-Dee-Noor, S.; Kohen, A.; Jakob, A.; Belakhov, V.
Catalytic mechanism of 3-deoxy-D-manno-octulosonate-8-phosphate synthase. The use of synthetic analogues to probe the structure of the putative reaction intermediate
Eur. J. Biochem.
217
991-999
1993
Escherichia coli
Manually annotated by BRENDA team
Radaev, S.; Dastidar, P.; Patel, M.; Woodard, R.W.; Gatti, D.L.
Structure and mechanism of 3-deoxy-D-manno-octulosonate 8-phosphate synthase
J. Biol. Chem.
275
9476-9484
2000
Escherichia coli (P0A715), Escherichia coli
Manually annotated by BRENDA team
Birck, M.R.; Woodard, R.W.
Aquifex aeolicus 3-Deoxy-D-manno-2-octulosonic acid 8-phosphate synthase: A new class of KDO 8-P synthase?
J. Mol. Evol.
52
205-214
2001
Actinobacillus pleuropneumoniae (O68662), Aggregatibacter actinomycetemcomitans, Aquifex aeolicus, Aquifex aeolicus (O66496), Arabidopsis thaliana, Bordetella bronchiseptica, Bordetella pertussis, Campylobacter jejuni, Caulobacter vibrioides, Chlamydia pneumoniae (Q9Z7I4), Chlamydia psittaci (Q46225), Chlamydia trachomatis (P0CD74), Chlorobaculum tepidum, Escherichia coli (P0A715), Escherichia coli, Haemophilus influenzae (P45251), Helicobacter pylori, Helicobacter pylori (Q9ZN55), Klebsiella pneumoniae, Mannheimia haemolytica (P95514), Neisseria gonorrhoeae (Q9XB02), Neisseria meningitidis (Q9XAZ3), Pasteurella multocida, Pisum sativum, Porphyromonas gingivalis, Pseudomonas aeruginosa (Q9ZFK4), Rickettsia prowazekii (Q9ZE84), Salmonella enterica subsp. enterica serovar Typhi, Shewanella putrefaciens, Vibrio cholerae serotype O1, Yersinia pestis
Manually annotated by BRENDA team
Asojo, O.; Friedman, J.; Adir, N.; Belokhov, V.; Shonam, Y.; Baasov, T.
Crystal structures of KDOP synthase in its binary complexes with the substrate phosphoenolpyruvate and with a mechanism-based inhibitor
Biochemistry
40
6326-6334
2001
Escherichia coli (P0A715), Escherichia coli
Manually annotated by BRENDA team
Krosky, D.J.; Alm, R.; Berg, M.; Carmel, G.; Tummino, P.J.; Xu, B.; Yang, W.
Helicobacter pylori 3-deoxy-D-manno-octulosonate-8-phosphate (KDO-8-P) synthase is a zinc-metalloenzyme
Biochim. Biophys. Acta
1594
297-306
2002
Escherichia coli, Helicobacter pylori
Manually annotated by BRENDA team
Howe, D.L.; Sundaram, A.K.; Wu, J.; Gatti, D.L.; Woodard, R.W.
Mechanistic insight into 3-deoxy-D-manno-octulosonate-8-phosphate synthase and 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase utilizing phosphorylated monosaccharide analogues
Biochemistry
42
4843-4854
2003
Escherichia coli
Manually annotated by BRENDA team
Shulami, S.; Furdui, C.; Adir, N.; Shoham, Y.; Anderson, K.S.; Baasov, T.
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
J. Biol. Chem.
279
45110-45120
2004
Escherichia coli (P0A715), Escherichia coli, Aquifex pyrophilus (Q8GLK7), Aquifex pyrophilus
Manually annotated by BRENDA team
Vainer, R.; Belakhov, V.; Rabkin, E.; Baasov, T.; Adir, N.
Crystal structures of Escherichia coli KDO8P synthase complexes reveal the source of catalytic irreversibility
J. Mol. Biol.
351
641-652
2005
Escherichia coli (P0A715), Escherichia coli
Manually annotated by BRENDA team
Li, Z.; Sau, A.K.; Furdui, C.M.; Anderson, K.S.
Probing the role of tightly bound phosphoenolpyruvate in Escherichia coli 3-deoxy-d-manno-octulosonate 8-phosphate synthase catalysis using quantitative time-resolved electrospray ionization mass spectrometry in the millisecond time range
Anal. Biochem.
343
35-47
2005
Escherichia coli
Manually annotated by BRENDA team
Li, Z.; Sau, A.
Probing the subunit-subunit interaction of the tetramer of E. coli KDO8P synthase by electrospray ionization mass spectrometry
Chin. J. Chem.
27
111-116
2009
Escherichia coli (P0A715)
-
Manually annotated by BRENDA team
Wen, L.; Zheng, Y.; Li, T.; Wang, P.G.
Enzymatic synthesis of 3-deoxy-D-manno-octulosonic acid (KDO) and its application for LPS assembly
Bioorg. Med. Chem. Lett.
26
2825-2828
2016
Escherichia coli
Manually annotated by BRENDA team
Smyth, K.M.; Marchant, A.
Conservation of the 2-keto-3-deoxymanno-octulosonic acid (Kdo) biosynthesis pathway between plants and bacteria
Carbohydr. Res.
380
70-75
2013
Escherichia coli, Arabidopsis thaliana (Q6NQL4), Arabidopsis thaliana (Q9AV97)
Manually annotated by BRENDA team