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Information on EC 5.3.1.13 - arabinose-5-phosphate isomerase and Organism(s) Escherichia coli and UniProt Accession P45395
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5.3.1.13 arabinose-5-phosphate isomeraseIUBMB Comments
The enzyme is involved in the pathway for synthesis of 3-deoxy-D-manno-octulosonate (Kdo), a component of bacterial lipopolysaccharides and plant call walls.
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Word Map
- 5.3.1.13
- kdo
- 3-deoxy-d-manno-octulosonate
- lipopolysaccharide
- lps
- d-ribulose
-
isomerization
- isomerases
- d-ribulose-5-phosphate
-
cmp-kdo
- beta-synthase
-
mime
- cystathionine
-
8-phosphate
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uropathogenic
-
enediol
-
3-deoxy-d-manno-oct-2-ulosonic
- d-glucitol
-
single-domain
- fragilis
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k-antigen
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
d-arabinose 5-phosphate isomerase, arabinose 5-phosphate isomerase, arabinose-5-phosphate isomerase, k-api, d-arabinose-5-phosphate isomerase, c3406 protein, a5p isomerase, d-arabinose-5p isomerase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Arabinose phosphate isomerase
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Arabinose phosphate isomerase, arabinose phosphate
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-
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D-Arabinose 5-phosphate isomerase
D-arabinose-5-phosphate ketol-isomerase
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Isomerase, arabinose phosphate
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-
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Phosphoarabinoisomerase
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D-Arabinose 5-phosphate isomerase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
D-Arabinose 5-phosphate = D-ribulose 5-phosphate
mechanism is envisioned to involve an enediol intermediate
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
isomerization
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intramolecular oxidoreduction
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-
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SYSTEMATIC NAME
IUBMB Comments
D-arabinose-5-phosphate aldose-ketose-isomerase
The enzyme is involved in the pathway for synthesis of 3-deoxy-D-manno-octulosonate (Kdo), a component of bacterial lipopolysaccharides and plant call walls.
CAS REGISTRY NUMBER
COMMENTARY
9023-86-3
-
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
3-deoxy-D-threo-pentofuranose 5-phosphate
3-deoxy-D-glycero-pentulose 5-phosphate
the catalysis proceeds 10fold slower than for the natural substrate isomerization
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-
?
4-deoxy-D-threo-arabinose 5-phosphate
4-deoxy-D-glycero-pentulose 5-phosphate
the isomerization rate for this compound is 2fold higher than that of the natural substrate
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-
?
3-deoxy-D-arabinose 5-phosphate
3-deoxy-D-glycero-pentulose 5-phosphate
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KdsD converts 3-deoxy-A5P to 3-deoxy-Ru5P, but the catalysis proceeds tenfold slower than for the natural substrate isomerization
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-
?
4-deoxy-D-arabinose 5-phosphate
4-deoxy-D-glycero-pentulose 5-phosphate
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KdsD converts 4-deoxy-A5P to 4-deoxy-Ru5P, but the catalysis proceeds slower than for the natural substrate isomerization
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-
?
D-Ribulose 5-phosphate
?
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the product arabinose 5-phosphate is the precursor for 2-keto-3-deoxyoctonate, a constituent of a cell wall lipopolysaccharide
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-
?
D-Arabinose 5-phosphate
D-Ribulose 5-phosphate
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no activity with D-ribose-5-phosphate, D-arabinose, D-glucose-6-phosphate, D-mannose-6-phosphate, alpha-D-glucose-1-phosphate and D-glucosamine-6-phosphate, Ru5P, no activity with D-ribose-5-phosphate, D-arabinose, D-glucose-6-phosphate, D-mannose-6-phosphate, alpha-D-glucose-1-phosphate and D-glucosamine-6-phosphate
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r
D-Arabinose 5-phosphate
D-Ribulose 5-phosphate
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Ru5P, no activity with D-ribose-5-phosphate, D-arabinose, D-glucose-6-phosphate, D-mannose-6-phosphate, alpha-D-glucose-1-phosphate and D-glucosamine-6-phosphate
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r
D-Arabinose 5-phosphate
D-Ribulose 5-phosphate
A5P
Ru5P, no activity with D-ribose-5-phosphate, D-arabinose, D-glucose-6-phosphate, D-mannose-6-phosphate, alpha-D-glucose-1-phosphate and D-glucosamine-6-phosphate
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r
D-Arabinose 5-phosphate
D-Ribulose 5-phosphate
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the gut operon is inducible. GutQ is not directly involved in D-glucitol catabolism. The conditional mutant TCM15(DELTAgutQDELTAkdsD) is dependent on exogenous D-arabinose 5-phosphate both for lipopolysaccharide synthesis/growth and for upregulation of the gut operon
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-
?
D-ribulose 5-phosphate
D-arabinose 5-phosphate
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first enzyme in the biosynthesis of 3-deoxy-D-manno-octulosonate
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r
additional information
?
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the enzyme does not isomerize D-xylulose-5-phosphate, D-arabinose, D-ribose, and D-ribulose
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?
additional information
?
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DL-glyceraldehyde 3-phosphate and D-erythrose 4-phosphate do not serve as alternate substrates
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?
additional information
?
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key enzyme in synthesis of lipopolysaccharides
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?
additional information
?
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D-ribose 5-phosphate, D-arabinose, D-glucose-6-phosphate, D-mannose 6-phosphate, and D-glucosamine 6-phosphate are no substrates
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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
D-Ribulose 5-phosphate
?
-
the product arabinose 5-phosphate is the precursor for 2-keto-3-deoxyoctonate, a constituent of a cell wall lipopolysaccharide
-
-
?
D-ribulose 5-phosphate
D-arabinose 5-phosphate
-
first enzyme in the biosynthesis of 3-deoxy-D-manno-octulosonate
-
r
additional information
?
-
-
key enzyme in synthesis of lipopolysaccharides
-
-
?
D-Arabinose 5-phosphate
D-Ribulose 5-phosphate
-
the gut operon is inducible. GutQ is not directly involved in D-glucitol catabolism. The conditional mutant TCM15(DELTAgutQDELTAkdsD) is dependent on exogenous D-arabinose 5-phosphate both for lipopolysaccharide synthesis/growth and for upregulation of the gut operon
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-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Zn2+
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Phosphorylated sugars
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in a series of nonphosphorylated sugars, the order of decreasing inhibitory activity is as follows: aldonic acids, alditols, aldoses
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
EDTA
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EDTA treatment increases the activity of c3406 protein by approximately 2.5fold
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5 - 7.5
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only trace A5P isomerase activity observed below pH 5.5 or above pH 7.5
7 - 10
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pH 7.0: about 70% of maximal activity, pH 10.0: about 70% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
API is a key enzyme in the biosynthesis of lipopolysaccharide, it catalyzes the first reaction of 3-deoxy-d-manno-octulosonate biosynthesis
malfunction
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a c3406 deletion mutant is still able to compete with wild type CFT073 in a transurethral cochallenge in mice and cannot colonize the mouse kidney
physiological function
-
the presence of c3406 is not essential for a pathogenic phenotype
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
tetramer
tetramer
trimer or tetramer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
mutant enzyme K59A, sitting drop vapor diffusion method, using 20% PEG 8K and 0.1 M HEPES, pH 7.5
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
H88A
the enzyme site-specific mutant is able to catalyze the isomerization of A5P to R5P in vitro with 9.5% of the wild type protein activity
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
of the recombinant protein by Q-Sepharose fast flow column chromatography
recombinant His-tagged KdsD from Escherichia coli strain Bl21(DE3) by nickel affinity chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
GutQ. GutQ is a second copy of D-arabinose 5-phosphate isomerase (API) from the genome of Escherichia coli K-12, with biochemical properties similar to those of KdsD
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kdsD and gutQ, API is encoded by the two paralogous genes, which may substitute for each other, expression of His-tagged KdsD in Escherichia coli strain BL21(DE3), subcloning in strain DH5alpha
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Noltmann, E.A.
Aldose-ketose isomerases
The Enzymes, 3rd Ed. (Boyer, P. D. , ed. )
6
271-354
1972
Acidipropionibacterium acidipropionici, Escherichia coli
-
Bigham, E.C.; Gragg, Ch.E.; Hall, W.R.; Kelsey, J.E.; Mallory, W.R.; Richardson, C.B.; Benedict, C.; Ray, P.H.
Inhibition of arabinose 5-phosphate isomerase. An approach to the inhibition of bacterial lipopolysaccharide biosynthesis
J. Med. Chem.
27
717-726
1984
Escherichia coli
Meredith, T.C.; Woodard, R.W.
Escherichia coli YrbH is a D-arabinose 5-phosphate isomerase
J. Biol. Chem.
278
32771-32777
2003
Escherichia coli
D'Aniello, S.; Spinelli, P.; Ferrandino, G.; Peterson, K.; Tsesarskia, M.; Fisher, G.; D'Aniello, A.
Cephalopod vision involves dicarboxylic amino acids: D-aspartate, L-aspartate and L-glutamate
Biochem. J.
386
331-340
2005
Escherichia coli, Escherichia coli CFT073
Meredith, T.C.; Woodard, R.W.
Identification of GutQ from Escherichia coli as a D-arabinose 5-phosphate isomerase
J. Bacteriol.
187
6936-6942
2005
Escherichia coli
Meredith, T.C.; Woodard, R.W.
Characterization of Escherichia coli D-arabinose 5-phosphate isomerase encoded by kpsF: implications for group 2 capsule biosynthesis
Biochem. J.
395
427-432
2006
Escherichia coli (P45395), Escherichia coli, Escherichia coli CFT073 (P45395)
Yeom, S.J.; Kim, N.H.; Park, C.S.; Oh, D.K.
L-ribose production from L-arabinose by using purified L-arabinose isomerase and mannose-6-phosphate isomerase from Geobacillus thermodenitrificans
Appl. Environ. Microbiol.
75
6941-6943
2009
Escherichia coli
Airoldi, C.; Sommaruga, S.; Merlo, S.; Sperandeo, P.; Cipolla, L.; Polissi, A.; Nicotra, F.
Targeting bacterial membranes: NMR spectroscopy characterization of substrate recognition and binding requirements of D-arabinose-5-phosphate isomerase
Chemistry
16
1897-1902
2010
Escherichia coli (P45395)
Mosberg, J.A.; Yep, A.; Meredith, T.C.; Smith, S.; Wang, P.F.; Holler, T.P.; Mobley, H.L.; Woodard, R.W.
A unique arabinose 5-phosphate isomerase found within a genomic island associated with the uropathogenicity of Escherichia coli CFT073
J. Bacteriol.
193
2981-2988
2011
Escherichia coli, Escherichia coli CFT073
Gourlay, L.J.; Sommaruga, S.; Nardini, M.; Sperandeo, P.; Deho, G.; Polissi, A.; Bolognesi, M.
Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography
Protein Sci.
19
2430-2439
2010
Escherichia coli (P45395), Escherichia coli
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