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Information on EC 2.5.1.55 - 3-deoxy-8-phosphooctulonate synthase and Organism(s) Aquifex aeolicus and UniProt Accession O66496
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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
-
metal-dependent
- dah7ps
- d-erythrose
-
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: Aquifex aeolicus
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, atkdsa2, 
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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-
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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
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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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-
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KDO-8-P synthetase
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-
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KDO8-P
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Kdo8P synthase
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KDO8PS
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KDOPS
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KDPO synthetase
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-
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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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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
condensation
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-
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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
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
phosphoenolpyruvate + D-arabinose 5-phosphate + H2O
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
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
the enzyme catalyzes the first commited step in the production of 2-dehydro-3-deoxy-D-octonate, an integral part of the inner core region of the lipopolysaccharide layer in Gram-negative bacteria
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-
?
phosphoenolpyruvate + erythrose 4-phosphate
3-deoxy-D-ribo-heptulosonate 7-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
His185 is necessary for the correct binding of phosphoenolpyruvate and of a catalytic water molecule
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?
phosphoenolpyruvate + D-arabinose 5-phosphate + H2O
2-dehydro-3-deoxy-D-octonate 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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-
-
-
?
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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-
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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
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
-
-
-
?
phosphoenolpyruvate + D-arabinose-5-phosphate + H2O
2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate
the enzyme catalyzes the first commited step in the production of 2-dehydro-3-deoxy-D-octonate, an integral part of the inner core region of the lipopolysaccharide layer in Gram-negative bacteria
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-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Cd2+
Cu2+
third in enzyme activity, octahedral or distorted tetrahedral delocalized electronic structure computed with quantum mechanics/molecular mechanics geometry optimization, product is bound in its linear conformation in the crystal structure of the enzyme with Cu2+, greenish color of enzyme, new absorption peak at 380 nm instead of 505 nm
Fe2+
Zn2+
Cd2+
Fe2+
-
contains 0.2-0.3 equivalents of iron per enzyme subunit. FeSO4 stimulates
Zn2+
-
enzyme contains approximately 0.4 equivalents of zinc per enzyme subunit. Maximal activation below 0.1 mM Zn2+
additional information
Cd2+
the enzyme is most active when the endogenous metal is removed by incubation with EDTA and replaced with Cd2+
Cd2+
second in enzyme activity, square pyramidal delocalized electronic structure computed with quantum mechanics/molecular mechanics geometry optimization
Fe2+
wild-type enzyme contains Zn2+ and Fe2+ with the ratio Zn2+/Fe2+ ranging from 1 to 2 in different preparations. Mutation H185G decreases the ability of the enzyme to bind Fe2+, but not Zn2+. Maximal activity, about 8-10% of the wild-type activity is obtained when the native metal is replaced with Cd2+
Zn2+
wild-type enzyme contains Zn2+ and Fe2+ with the ratio Zn2+/Fe2+ ranging from 1 to 2 in different preparations
Zn2+
highest enzyme activity, square pyramidal delocalized electronic structure computed with quantum mechanics/molecular mechanics geometry optimization
Cd2+
-
in the presence of the metal, the enzyme is asymmetric and appears to alternate catalysis between the active sites located on the other face. In the absence of metal, the asymmetry is lost
additional information
the type of metal bound in the active site affects the behavior of the enzyme in vivo and the rate of product release in the crystal environment
additional information
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the type of metal bound in the active site affects the behavior of the enzyme in vivo and the rate of product release in the crystal environment
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2-dehydro-3-deoxy-D-octonate 8-phosphate
mutant enzyme R106G is more severely inhibited than wild-type enzyme
D-arabinose 5-phosphate
mutant enzyme R106G is less severely inhibited than wild-type enzyme
phosphate
mutant enzyme R106G is more severely inhibited than wild-type enzyme
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0005
D-arabinose 5-phosphate
same enzyme preparation as following, substitution with 50 microM Zn2+, 100 mM Tris-acetate, pH 7.5, 40°C
0.00123
D-arabinose 5-phosphate
recombinant enzyme produced in Escherichia coli, native Zn2+ and Fe2+ not substituted, 100 mM Tris-acetate, pH 7.5, 40°C
0.00156
D-arabinose 5-phosphate
same enzyme preparation as following, substitution with 5 microM Cu2+, 100 mM Tris-acetate, pH 7.5, 40°C
0.002
D-arabinose 5-phosphate
same enzyme preparation as following, substitution with 50 microM Cd2+, 100 mM Tris-acetate, pH 7.5, 40°C
0.00227
D-arabinose 5-phosphate
independently prepared enzyme, substitution with 50 microM Cd2+, pH 5.0, 40°C
0.00318
D-arabinose 5-phosphate
independently prepared enzyme, substitution with 50 microM Cd2+, 100 mM Tris-acetate, pH 7.5, 40°C
0.01926
D-arabinose 5-phosphate
same enzyme preparation as before, substitution with 5 microM Cu2+, pH 5.0, 40°C
0.0000066
phosphoenolpyruvate
same enzyme preparation as before, substitution with 5 microM Cu2+, pH 5.0, 40°C
0.00004
phosphoenolpyruvate
independently prepared enzyme, substitution with 50 microM Cd2+, pH 5.0, 40°C
0.00014
phosphoenolpyruvate
same enzyme preparation as following, substitution with 50 microM Cd2+, 100 mM Tris-acetate, pH 7.5, 40°C
0.00015
phosphoenolpyruvate
same enzyme preparation as following, substitution with 5 microM Cu2+, 100 mM Tris-acetate, pH 7.5, 40°C
0.00016
phosphoenolpyruvate
independently prepared enzyme, substitution with 50 microM Cd2+, 100 mM Tris-acetate, pH 7.5, 40°C
0.00016
phosphoenolpyruvate
recombinant enzyme produced in Escherichia coli, native Zn2+ and Fe2+ not substituted, 100 mM Tris-acetate, pH 7.5, 40°C
0.00028
phosphoenolpyruvate
same enzyme preparation as following, substitution with 50 microM Zn2+, 100 mM Tris-acetate, pH 7.5, 40°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.31
phosphoenolpyruvate
recombinant enzyme produced in Escherichia coli, native Zn2+ and Fe2+ not substituted, 100 mM Tris-acetate, pH 7.5, 40°C
0.34
phosphoenolpyruvate
enzyme preparation 1, substitution with 5 microM Cu2+, 100 mM Tris-acetate, pH 7.5, 40°C
0.36
phosphoenolpyruvate
enzyme preparation 1, substitution with 5 microM Cu2+, pH 5.0, 40°C
0.41
phosphoenolpyruvate
enzyme preparation 1, substitution with 50 microM Cd2+, 100 mM Tris-acetate, pH 7.5, 40°C
0.46
phosphoenolpyruvate
independent enzyme preparation 2, substitution with 50 microM Cd2+, pH 5.0, 40°C
0.47
phosphoenolpyruvate
enzyme preparation 1, substitution with 50 microM Zn2+, 100 mM Tris-acetate, pH 7.5, 40°C
0.48
phosphoenolpyruvate
independent preparation 2 enzyme, substitution with 50 microM Cd2+, 100 mM Tris-acetate, pH 7.5, 40°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
catalyzes the formation of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P), a key precursor in the biosynthesis of the endotoxin of Gram-negative bacteria
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
X-ray structure of wild-type enzyme shows that when both phosphoenolpyruvate and D-arabinose 5-phosphate bind, the active site becomes isolated from the environment due to a conformational change of the L7 loop. The structures of the R106G mutant, without substrates, and with phosphoenolpyruvate and phosphoenolpyruvate plus D-arabinose 5-phosphate bound reveal that in R106G closure of the L7 loop is impaired
structure of the metal-free and Cd2+ forms of the enzyme are determined in the uncomplexed state and in complex with various combinations of phosphoenolpyruvate, arabinose 5-phosphate and erythrose 4-phosphate
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C11N
mutant is not capable of binding metal and lacks the structural asymmetry among subunits with regard to substrate binding and conformation of the L7 loop, shows decreased thermal stability
C11N/S235P/Q237A
mutant is not capable of binding metal and lacks the structural asymmetry among subunits with regard to substrate binding and conformation of the L7 loop, shows decreased thermal stability
H185G
mutation decreases the affinity of the enzyme to bind Fe2+, but not Zn2+. Maximal activity, about 8-10% of the wild-type activity is obtained when the native metal is replaced with Cd2+
P10M/C11N
mutant is not capable of binding metal and lacks the structural asymmetry among subunits with regard to substrate binding and conformation of the L7 loop, shows decreased thermal stability
P10M/C11N/S235P/Q237A
mutant is not capable of binding metal and lacks the structural asymmetry among subunits with regard to substrate binding and conformation of the L7 loop, shows decreased thermal stability
R106G
the closure of the L7 loop is impaired. The mutant enzyme shows a smaller KM-value for phosphoenolpyruvate, larger Ki-value and KM-value for D-arabinose 5-phosphate and smaller Ki-values for phosphate and 2-dehydro-3-deoxy-D-octonate 8-phosphate compared ti wild-type enzyme
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
enzyme purification followed by incubation with 50 microM Cd2+, Zn2+, or Cu2+ in 20 mM Tris-HCl buffer, pH 7.5, to substitute the metal ions Fe2+ or Co2+
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Duewel, H.S.; Radaev, S.; Wang, J.; Woodard, R.W.; Gatti, D.L.
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
J. Biol. Chem.
276
8393-8402
2001
Aquifex aeolicus
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
Wang, J.; Duewel, H.S.; Stuckey, J.A.; Woodard, R.W.; Gatti, D.L.
Function of His185 in Aquifex aeolicus 3-deoxy-D-manno-octulosonate 8-phosphate synthase
J. Mol. Biol.
324
205-214
2002
Aquifex aeolicus (O66496), Aquifex aeolicus
Duewel, H.S.; Sheflyan, G.Y.; Woodard, R.W.
Functional and biochemical characterization of a recombinant 3-deoxy-D-manno-octulosonic acid 8-phosphate synthase from the hyperthermophilic bacterium Aquifex aeolicus
Biochem. Biophys. Res. Commun.
263
346-351
1999
Aquifex aeolicus
Duewel, H.S.; Woodard, R.W.
A metal bridge between two enzyme families. 3-Deoxy-D-manno-octulosonate-8-phosphate synthase from Aquifex aeolicus requires a divalent metal for activity
J. Biol. Chem.
275
22824-22831
2000
Aquifex aeolicus
Xu, X.; Kona, F.; Wang, J.; Lu, J.; Stemmler, T.; Gatti, D.L.
The catalytic and conformational cycle of Aquifex aeolicus KDO8P synthase: role of the L7 loop
Biochemistry
44
12434-12444
2005
Aquifex aeolicus (O66496), Aquifex aeolicus
Kona, F.; Xu, X.; Martin, P.; Kuzmic, P.; Gatti, D.L.
Structural and mechanistic changes along an engineered path from metallo to nonmetallo 3-deoxy-D-manno-octulosonate 8-phosphate synthases
Biochemistry
46
4532-4544
2007
Aquifex aeolicus (O66496), Aquifex aeolicus
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