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Information on EC 2.5.1.55 - 3-deoxy-8-phosphooctulonate synthase and Organism(s) Helicobacter pylori and UniProt Accession P56060
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EC Tree
2.5.1.55 3-deoxy-8-phosphooctulonate synthaseSpecify your search results
Word Map
- 2.5.1.55
- aquifex
- aeolicus
- 7-phosphate
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3-deoxy-d-arabino-heptulosonate
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metal-dependent
- dah7ps
- d-erythrose
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aldol-type
- pyrophilus
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3-deoxy-d-arabino-heptulosonate-7-phosphate
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oxocarbenium
- medicine
The taxonomic range for the selected organisms is: Helicobacter pylori
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
kdo8ps, kdo8p synthase, kdo 8-p synthase, kdo-8-p synthase, kdops, 3-deoxy-d-manno-octulosonate 8-phosphate synthase, kdo-8-phosphate synthetase, 3-deoxy-d-manno-octulosonate-8-phosphate synthase, atkdsa1, 3-deoxy-d-manno-2-octulosonate-8-phosphate synthase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
2-dehydro-3-deoxy-D-octonate-8-phosphate D-arabinose-5-phosphate-lyase (pyruvate-phosphorylating)
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2-dehydro-3-deoxyphosphooctonate aldolase
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2-keto-3-deoxy-8-phosphooctonic acid synthetase
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2-keto-3-deoxy-8-phosphooctonic synthetase
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3-deoxy-D-manno-octulosonate 8-phosphate synthetase
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3-deoxy-D-manno-octulosonate-8-phosphate synthase
3-deoxy-D-manno-octulosonic acid 8-phosphate synthase
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3-deoxy-D-mannooctulosonate-8-phosphate synthetase
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3-deoxyoctulosonic 8-phosphate synthetase
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8-phospho-2-dehydro-3-deoxy-D-octonate D-arabinose-5-phosphate-lyase (pyruvate-phosphorylating)
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aldolase, phospho-2-keto-3-deoxyoctonate
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KDO-8-P synthase
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KDO-8-P synthetase
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KDO8-P
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Kdo8P synthase
KDO8PS
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KDOPS
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KDPO synthetase
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KdsA
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Phospho-2-dehydro-3-deoxyoctonate aldolase
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phospho-2-keto-3-deoxyoctonate aldolase
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3-deoxy-D-manno-octulosonate-8-phosphate synthase
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Kdo8P synthase
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
condensation
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SYSTEMATIC NAME
IUBMB Comments
phosphoenolpyruvate:D-arabinose-5-phosphate C-(1-carboxyvinyl)transferase (phosphate-hydrolysing, 2-carboxy-2-oxoethyl-forming)
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CAS REGISTRY NUMBER
COMMENTARY
9026-96-4
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
phosphoenolpyruvate + D-arabinose 5-phosphate + H2O
3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
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?
phosphoenolpyruvate + D-arabinose 5-phosphate
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
phosphoenolpyruvate + D-arabinose 5-phosphate + H2O
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
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?
phosphoenolpyruvate + D-arabinose 5-phosphate
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
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?
phosphoenolpyruvate + D-arabinose 5-phosphate
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
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?
phosphoenolpyruvate + D-arabinose 5-phosphate
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
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?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
phosphoenolpyruvate + D-arabinose 5-phosphate + H2O
3-deoxy-D-manno-octulosonate 8-phosphate + phosphate
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?
phosphoenolpyruvate + D-arabinose 5-phosphate + H2O
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Cd2+
activates, stabilizes, active site bound by Cys18, His204, Glu241, and Asp252
Cd2+
Co2+
Cu2+
Zn2+
additional information
Cd2+
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the Zn2+ in the enzyme can be quantitatively replaced by Cd2+ which increases the observed turnover number and decreases the apparent Km-value for D-arabinose-5-phosphate by 6.5fold
Cd2+
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4 Cd2+ are bound in native tetrameric enzyme, 2 in dimer, 1 in monomer, Cd2+ reconstituted enzyme is less stable than that of Zn2+, Co2+ and Cu2+ enzymes
Co2+
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monomer and dimer are each bound with 1 metal ion, tetramer with 2
Cu2+
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4 Cu2+ are bound in native tetrameric enzyme, 2 in dimer, 1 in monomer
Zn2+
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the enzyme contains one mol of Zn per monomer, apoenzyme is catalytically inactive
Zn2+
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4 Zn2+ are bound in native tetrameric enzyme, 2 in dimer, 1 in monomer
additional information
the enzyme is specifically coordinated with Cd2+ or Zn2+ ions, and isothermal titration calorimetry and differential scanning fluorimetry reveal that Cd2+ thermally stabilizes the protein structure more efficiently than Zn2
additional information
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the enzyme is specifically coordinated with Cd2+ or Zn2+ ions, and isothermal titration calorimetry and differential scanning fluorimetry reveal that Cd2+ thermally stabilizes the protein structure more efficiently than Zn2
additional information
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divalent metal ions play an important role in the quaternary structure of the protein
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3-[[(1R,2R,3S,4S,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]oxy]-4H-chromen-4-one
i.e. hyperin, structure analysis, and enzyme interaction study, binding structure, overview
N-[3-(furan-2-yl)phenyl]-1-(3-phenylpropyl)piperidine-4-carboxamide
i.e. MC181, structure analysis, and enzyme interaction study, binding structure, overview
Cu2+
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activity is enhanced below 0.001 mM, inhibitory at higher concentrations
additional information
21 inhibitor compounds synthesis and screening based on the API inhibitor structure, docking study and molecular modelling, overview
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additional information
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21 inhibitor compounds synthesis and screening based on the API inhibitor structure, docking study and molecular modelling, overview
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
in the substrate-bound structure, water molecules play a key role in fixing residues in the proper configuration to achieve a compact structure. The active site is formed by residues the active site Lys52, Asn54, Arg55, Gln133, Asp252, and Asn255
additional information
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in the substrate-bound structure, water molecules play a key role in fixing residues in the proper configuration to achieve a compact structure. The active site is formed by residues the active site Lys52, Asn54, Arg55, Gln133, Asp252, and Asn255
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
121500
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tetramer with 2 Co2+, ESI-MS, 50 mM ammonium acetate solution, pH 7.5
121600
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tetramer with 4 Zn2+ or 4 Cu2+, ESI-MS, 50 mM ammonium acetate solution, pH 7.5
121800
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tetramer with 4 Cd2+, ESI-MS, 50 mM ammonium acetate solution, pH 7.5
30400
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monomer with 1 Co2+, ESI-MS, 50 mM ammonium acetate solution, pH 7.5
30440
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monomer with 1 Zn2+ or 1 Cu2+, ESI-MS, 50 mM ammonium acetate solution, pH 7.5
30480
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monomer with 1 Cd2+, ESI-MS, 50 mM ammonium acetate solution, pH 7.5
60690
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dimer with 1 Cd2+, ESI-MS, 50 mM ammonium acetate solution, pH 7.5
60760
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dimer with 1 Co2+, ESI-MS, 50 mM ammonium acetate solution, pH 7.5
60840
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dimer with 2 Zn2+ or 2 Cu2+, ESI-MS, 50 mM ammonium acetate solution, pH 7.5
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
2 * 30300, SDS-PAGE, two monomers in each asymmetric unit. The monomers adopt the (beta/alpha)8 barrel topology
tetramer
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4 * 30440 (with 2 Co2+), 4 * 30440 (with 4 Zn2+ or Cu2+), 4 * 30480 (with 4 Cd2+), tetramer formed by 2 dimers each, ESI-MS
additional information
additional information
in the substrate-bound structure, water molecules play a key role in fixing residues in the proper configuration to achieve a compact structure
additional information
-
in the substrate-bound structure, water molecules play a key role in fixing residues in the proper configuration to achieve a compact structure
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant His-tagged wild-type and mutant H204A enzymes in apoform, or wild-type enzyme complexed with Zn2+ or Cd2+, hanging drop vapor diffusion method, mixing of 0.001 ml of protein solution, containing inhibitor in a 1:2 ratio, with 0.001 ml of reservoir solution, containing 18% PEG 3350, 0.1 M HEPES, pH 7.5, and 0.25 M magnesium chloride hexahydrate, equilibration against reservoir solution, 20°C, 14 days, X-ray diffraction structure determination and analysis at 2.0 A resolution, molecular replacement and modelling
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
Cd2+ thermally stabilizes the protein structure more efficiently than Zn2+
additional information
-
Cd2+ thermally stabilizes the protein structure more efficiently than Zn2+
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme in Escherichia coli strain pTf16/BL21 by nickel affinity chromatography, dialysis, and ultrafiltration
apoenzyme + 200 microM metal ion salt + 50 mM Tris-HCl buffer, pH 7.5 dialyzed against 50 mM ammonium acetate buffer, pH 7.5, 4°C
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene kdsA, recombinant expression of His-tagged enzyme in Escherichia coli strain pTf16/BL21
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
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enzyme absent in mammals, therefore potential target for the development of new antibiotics
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
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
Sau, A.K.; Li, Z.; Anderson, K.S.
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
J. Biol. Chem.
279
15787-15794
2004
Helicobacter pylori
Li, Z.; Sau, A.K.
Structural studies on Helicobacter pylori 3-deoxy-D-manno-2-octulosonate-8-phosphate synthase using electrospray ionization mass spectrometry: a tetrameric complex composed of dimeric dimers
Rapid Commun. Mass Spectrom.
23
1573-1578
2009
Helicobacter pylori
Cho, S.; Im, H.; Lee, K.Y.; Chen, J.; Kang, H.J.; Yoon, H.J.; Min, K.H.; Lee, K.R.; Park, H.J.; Lee, B.J.
Identification of novel scaffolds for potential anti-Helicobacter pylori agents based on the crystal structure of H. pylori 3-deoxy-D-manno-octulosonate 8-phosphate synthase (HpKDO8PS)
Eur. J. Med. Chem.
108
188-202
2016
Helicobacter pylori (P56060), Helicobacter pylori
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