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Information on EC 4.1.1.85 - 3-dehydro-L-gulonate-6-phosphate decarboxylase and Organism(s) Escherichia coli and UniProt Accession P39304

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EC Tree
     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.1 Carboxy-lyases
                4.1.1.85 3-dehydro-L-gulonate-6-phosphate decarboxylase
IUBMB Comments
Requires Mg2+. Along with EC 5.1.3.22, L-ribulose-5-phosphate 3-epimerase, this enzyme is involved in a pathway for the utilization of L-ascorbate by Escherichia coli.
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Escherichia coli
UNIPROT: P39304
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
kgpdc, 3-keto-l-gulonate 6-phosphate decarboxylase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3-keto-L-gulonate 6-phosphate decarboxylase
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3-keto-L-gulonate 6-phosphate decarboxylase
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-
additional information
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
show the reaction diagram
SYSTEMATIC NAME
IUBMB Comments
3-dehydro-L-gulonate-6-phosphate carboxy-lyase (L-xylulose-5-phosphate-forming)
Requires Mg2+. Along with EC 5.1.3.22, L-ribulose-5-phosphate 3-epimerase, this enzyme is involved in a pathway for the utilization of L-ascorbate by Escherichia coli.
CAS REGISTRY NUMBER
COMMENTARY hide
406722-60-9
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
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-
-
-
?
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
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
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-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
L-gulonate 6-phosphate
binding structure involving Glu33 and Asp62 and Mg2+
L-xylitol 5-phosphate
binding structure
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
(beta/alpha)8-barrel enzyme, the active site is located at the dimer interface
dimer
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x-ray crystallography
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme complexed with L-gulonate 6-phosphate, L-threonohydroxamate 4-phosphate, and L-xylitol 5-phosphate, analogues of the substrate, enediolate intermediate, and product, as well as with the product L-xylulose 5-phosphate, 15 mg/ml protein in 50 mM HEPES, pH 7.5, 5 mM MgCl2, 100 mM NaCl, micro-batch method, 0.01 ml protein solution mixed with equal volume of crystallization solution containing 16% monomethyl PEG 5000, 100 mM Bis-Tris propane, pH 7.0, and 5 mM MgCl2, with 25 mM ligand, X-ray diffraction structure determination and analysis at 1.2, 1.8, 1.7, and 1.8 A resolution, respectively
purified recombinant mutant enzymes K64A, H136A, E112Q, and E112Q/H136A, in complex with reaction intermediate analogue L-threonohydroxamate 4-phosphate, 15 mg/ml protein in 50 mM HEPES, pH 7.5, 5 mM MgCl2, 100 mM NaCl, 0.01 ml protein solution mixed with equal volume of crystallization solution containing 16% monomethyl PEG 5000, 100 mM Bis-Tris propane, pH 7.0, 5 mM MgCl2, and 25 mM L-threonohydroxamate 4-phosphate, X-ray diffraction structure determination and analysis at 1.7, 1.9, 1.8, and 1.9 A resolution, respectively
purified recombinant wild-type and selenomethionine-labeled enzymes, free or complexed with inhibitor L-gulonate 6-phosphate, 15 mg/ml protein in 50 mM HEPES, pH 7.5, 5 mM MgCl2, 100 mM NaCl, room temperature, micro-batch method, 0.01 ml protein solution mixed with equal volume of crystallization solution containing 18% monomethyl PEG 5000, 50 mM NaH2PO4, 50 mM K2HPO4, and 50 mM Bis-Tris propane, pH 7.0, with or without 20 mM inhibitor L-gulonate 6-phosphate, crystals appear a few days after microseeding, growing for 1 week, X-ray diffraction structure determination and analysis at 2.0 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E112Q
site-directed mutagenesis, crystal structure determination and analysis, the mutant enzyme shows altered reaction intermediate binding at the active site, reaction mechanism, and stereochemistry
E112Q/H136A
site-directed mutagenesis, crystal structure determination and analysis, the mutant enzyme shows altered reaction intermediate binding at the active site, reaction mechanism, and stereochemistry
H136A
site-directed mutagenesis, crystal structure determination and analysis, the mutant enzyme shows altered reaction intermediate binding at the active site, reaction mechanism, and stereochemistry
K64A
site-directed mutagenesis, crystal structure determination and analysis, the mutant enzyme shows altered reaction intermediate binding at the active site, reaction mechanism, and stereochemistry
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged UlaD from strain BL21(DE3), the His-tag is removed by thrombin
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of mutant enzymes in strain BLR(DE3)recA-strain
gene ulaD, expression as His-tagged protein in strain BL21(DE3), and as selenomethionine-labeled enzyme
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Wise, E.; Yew, W.S.; Babbitt, P.C.; Gerlt, J.A.; Rayment, I.
Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase
Biochemistry
41
3861-3869
2002
Escherichia coli (P39304), Escherichia coli
Manually annotated by BRENDA team
Wise, E.L.; Yew, W.S.; Gerlt, J.A.; Rayment, I.
Structural evidence for a 1,2-enediolate intermediate in the reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylase, a member of the orotidine 5'-monophosphate decarboxylase suprafamily
Biochemistry
42
12133-12142
2003
Escherichia coli (P39304)
Manually annotated by BRENDA team
Wise, E.L.; Yew, W.S.; Gerlt, J.A.; Rayment, I.
Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: crystallographic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylase
Biochemistry
43
6438-6446
2004
Escherichia coli (P39304)
Manually annotated by BRENDA team
Akana, J.; Fedorov, A.A.; Fedorov, E.; Novak, W.R.; Babbitt, P.C.; Almo, S.C.; Gerlt, J.A.
D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily
Biochemistry
45
2493-2503
2006
Escherichia coli
Manually annotated by BRENDA team