Information on EC 4.1.1.85 - 3-dehydro-L-gulonate-6-phosphate decarboxylase:

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The expected taxonomic range for this enzyme is: Bacteria


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EC NUMBERCOMMENTARY
4.1.1.85-

RECOMMENDED NAMEGeneOntology No.
3-dehydro-L-gulonate-6-phosphate decarboxylaseGO:0033982

REACTIONREACTION DIAGRAMCOMMENTARYORGANISM UNIPROT ACCESSION NO.LITERATURE
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
formation and stabilization of an enediolate anion intermediate is part of reaction mechanism, mechanism overview, the active site is located at the dimer interface, structure-function relationship, overviewEscherichia coliP39304650143
3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
show the reaction diagram
active site structure, substrate binding structure, formation of a cis-1,2-enediolate anion intermediate, intermediate structure and reaction mechanism involving residues Lys64, Asp67, and His136, overviewEscherichia coli-657958
3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
show the reaction diagram
catalytic mechanism, formation and Mg2+-stabilization of an cis-1,2-enediolate anion intermediate, important residues for the stereospecific exchange of the pro-1S hydrogen are Lys64, Asp67, Glu112, Arg139, and Lys64, the latter stabilizes the intermediate via hydrogen bonds to O1 and O2 of the intermediate involving conserved active site residue Asp67, His136 takes part in hydrogen exchange with solvent of the 1-hydroxymethylene group of the product, overviewEscherichia coli K-12-658079
3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
show the reaction diagram
formation and stabilization of an 1,2-enediolate anion intermediate, protonation of the intermediate involving residues Glu112, His136, and Arg139, active site structure-function relationship, overviewEscherichia coli-658080
3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
show the reaction diagram
active site structure, substrate binding structure, structure-function relationship, overviewEscherichia coli K-12P39304658107
3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
show the reaction diagram
-Escherichia coli K-12-659013

REACTION TYPEORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
No entries in this field

PATHWAYKEGG LinkMetaCyc Link
Ascorbate and aldarate metabolism00053 -
L-ascorbate degradation I (bacterial, anaerobic)-PWY0-301
L-ascorbate degradation II (bacterial, aerobic)-PWY-6961
Metabolic pathways01100 -
Microbial metabolism in diverse environments01120 -
Pentose and glucuronate interconversions00040 -

SYSTEMATIC NAMEIUBMB 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.

SYNONYMSORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
3-keto-L-gulonate 6-phosphate decarboxylaseMethylomonas aminofaciens--658106
3-keto-L-gulonate 6-phosphate decarboxylaseEscherichia coli K-12--658079, 658106, 658107, 659013
3-keto-L-gulonate 6-phosphate decarboxylaseEscherichia coli--650143, 657958, 658080, 672127
3-keto-L-gulonate 6-phosphate decarboxylaseStreptococcus mutans--702041
3-keto-L-gulonate 6-phosphate decarboxylaseStreptococcus mutans UA159---
KGPDCMethylomonas aminofaciens--658106
KGPDCEscherichia coli K-12--658079, 658106, 658107
KGPDCEscherichia coli--650143, 657958, 658080, 672127
KGPDCStreptococcus mutans--702041
SgaHEscherichia coli K-12--659013
SgbHEscherichia coli K-12--659013
UlaDEscherichia coli K-12--659013
KGPDCStreptococcus mutans UA159---
additional informationEscherichia coli-the enzyme belongs to the orotidine 5'-monophosphate decarboxylase OMPDC suprafamily, overview650143, 657958
additional informationEscherichia coli-the enzyme belongs to the orotidine 5'-monophosphate decarboxylase OMPDC suprafamily658080
additional informationMethylomonas aminofaciens-the enzyme belongs to the orotidine 5'-monophosphate decarboxylase OMPDC suprafamily658106
additional informationEscherichia coli K-12-the enzyme belongs to the orotidine 5'-monophosphate decarboxylase OMPDC suprafamily658079, 658106, 658107

CAS REGISTRY NUMBERCOMMENTARY
406722-60-9-

ORGANISMCOMMENTARYLITERATURESEQUENCE CODESEQUENCE DB SOURCE
Escherichia coli-650143, 657958, 658080P39304UniprotManually annotated by BRENDA team
Escherichia coli-672127--Manually annotated by BRENDA team
Escherichia coli K-12-658079, 658106--Manually annotated by BRENDA team
Escherichia coli K-12-658107P39304UniprotManually annotated by BRENDA team
Escherichia coli K-12-659013--Manually annotated by BRENDA team
Methylomonas aminofaciens-658106--Manually annotated by BRENDA team
Streptococcus mutans-702041--Manually annotated by BRENDA team
Streptococcus mutans UA159-702041--Manually annotated by BRENDA team

GENERAL INFORMATIONORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
No entries in this field

SUBSTRATEPRODUCT                      REACTION DIAGRAMORGANISM UNIPROT ACCESSION NO. COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
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
Escherichia coliP39304-650143, 657958--?
3-dehydro-L-gulonate 6-phosphate + H+L-xylulose 5-phosphate + CO2
show the reaction diagram
Escherichia coli--658080, 672127--?
3-dehydro-L-gulonate 6-phosphate + H+L-xylulose 5-phosphate + CO2
show the reaction diagram
Escherichia coli K-12P39304-658107--?
3-dehydro-L-gulonate 6-phosphate + H+L-xylulose 5-phosphate + CO2
show the reaction diagram
Methylomonas aminofaciens--658106--?
3-dehydro-L-gulonate 6-phosphate + H+L-xylulose 5-phosphate + CO2
show the reaction diagram
Escherichia coli K-12-stereochemistry658079, 658106--?
3-dehydro-L-gulonate 6-phosphate + H+L-xylulose 5-phosphate + CO2
show the reaction diagram
Escherichia coliP39304substrate binding structure657958--?
3-dehydro-L-gulonate 6-phosphate + H+L-xylulose 5-phosphate + CO2
show the reaction diagram
Escherichia coli K-12-SgaH/UlaD and SgbH659013--?
3-dehydro-L-gulonate 6-phosphate + H+L-xylulose 5-phosphate + CO2
show the reaction diagram
Escherichia coli K-12-step in the catabolic pathway of L-ascorbate utilization658079, 658106--?
additional information?-Escherichia coli K-12-enzyme catalyzes one step in the L-ascorbate utilization pathway, L-ascorbate is converted to L-xylulose, overview, enzymes SgaH/UlaD and SgbH are not active with 3-dehydro-L-gulonate659013---
additional information?-Methylomonas aminofaciens-the D-arabino-hex-3-ulose 6-phosphate synthase of Methylomonas aminofaciens also performs the 3-keto-L-gulonate 6-phosphate decarboxylase reaction with lower activity than for the preferred reaction catalyzing Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate, proton exchange reaction rates, overview658106---
additional information?-Escherichia coli K-12P39304the enzyme also performs the Methylomonas aminofaciens D-arabino-hex-3-ulose 6-phosphate synthase reaction with low activity catalyzing Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate, while the Methylomonas aminofaciens enzyme also performs the 3-keto-L-gulonate 6-phosphate decarboxylase reaction, overview658107---
additional information?-Escherichia coli K-12-the enzyme also performs the Methylomonas aminofaciens D-arabino-hex-3-ulose 6-phosphate synthase reaction with low activity catalyzing Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate, while the Methylomonas aminofaciens enzyme also performs the 3-keto-L-gulonate 6-phosphate decarboxylase reaction, proton exchange reaction rates, overview658106---

NATURAL SUBSTRATESNATURAL PRODUCTSREACTION DIAGRAMORGANISM UNIPROT ACCESSION NO.COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
No entries in this field

COFACTORORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATUREIMAGE
No entries in this field

METALS and IONS ORGANISM UNIPROT ACCESSION NO.COMMENTARY LITERATURE
Mg2+Escherichia coliP39304dependent on, binding structure involving Glu33 and Asp62, overview650143
Mg2+Escherichia coliP39304dependent on657958, 658080
Mg2+Escherichia coli K-12-dependent on658079, 658106
Mg2+Escherichia coli K-12--659013
Mg2+Escherichia coli--672127
Mg2+Streptococcus mutans-Mg2+ dependent decarboxylation702041

INHIBITORSORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
L-gulonate 6-phosphateEscherichia coliP39304binding structure involving Glu33 and Asp62 and Mg2+650143 2D-image
L-xylitol 5-phosphateEscherichia coli-binding structure657958 2D-image

ACTIVATING COMPOUNDORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
No entries in this field

KM VALUE [mM]KM VALUE [mM] MaximumSUBSTRATEORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
0.15-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112Q/H136A658079 2D-image
0.22-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112Q/H136A/R139V658079 2D-image
0.27-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant D67A/H136A658079 2D-image
0.3-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutants K64R and D67N/H136A658079 2D-image
0.31-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112Q658079 2D-image
0.34-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112A658079 2D-image
0.36-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant R139V658079 2D-image
0.37-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant H136N658079 2D-image
0.41-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant D67N658079 2D-image
0.44-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant K64R/H136A658079 2D-image
0.5-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant D67A658079 2D-image
0.51-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant K64A658079 2D-image
0.52-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant H136Q658079 2D-image
0.55-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant K64A/E112Q/H136A658079 2D-image
0.58-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant K64A/H136A658079 2D-image
0.65-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112A/H136A658079 2D-image
0.67-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant wild-type enzyme658079, 658106 2D-image
0.7-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant H136A658079 2D-image
0.77-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112A/H136A/R139V658079 2D-image
0.9-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant K64A/R139V658079 2D-image
0.91-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112D/R139V/T169A658106 2D-image
1.4-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutants H136A/R139V and K64A/E112A/H136A/R139V658079 2D-image
5.4-3-dehydro-L-gulonate 6-phosphateMethylomonas aminofaciens-pH 7.5, 25C, recombinant enzyme658106 2D-image
additional information-additional informationEscherichia coli K-12-analysis of kinetics and activity of the mutant enzymes, overview658079-

TURNOVER NUMBER [1/s] TURNOVER NUMBER MAXIMUM[1/s] SUBSTRATEORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
0.19-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant D67A/H136A658079 2D-image
0.2-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112Q/H136A/R139V658079 2D-image
0.21-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112A/H136A/R139V658079 2D-image
0.23-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112Q/H136A658079 2D-image
0.26-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant K64A/E112A/H136A/R139V658079 2D-image
0.3-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112A658079 2D-image
0.45-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112A/H136A658079 2D-image
0.75-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant K64A/H136A658079 2D-image
1.1-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant D67N658079 2D-image
1.2-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant K64A/R139V658079 2D-image
1.3-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant D67N/H136A658079 2D-image
1.4-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant H136Q658079 2D-image
2.4-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutants D67A and H136A658079 2D-image
2.4-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112D/R139V/T169A658106 2D-image
2.9-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant K64A/E112Q/H136A658079 2D-image
4-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant E112Q658079 2D-image
4.2-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant K64R/H136A658079 2D-image
4.3-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant H136N658079 2D-image
8.3-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant K64A658079 2D-image
8.9-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant R139V658079 2D-image
9.2-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant H136A/R139V658079 2D-image
15-3-dehydro-L-gulonate 6-phosphateMethylomonas aminofaciens-pH 7.5, 25C, recombinant enzyme658106 2D-image
17-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant mutant K64R658079 2D-image
51-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-pH 7.5, 25C, recombinant wild-type enzyme658079, 658106 2D-image
51-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-SgaH, pH 7.5, 25C659013 2D-image
64-3-dehydro-L-gulonate 6-phosphateEscherichia coli K-12-SgbH, pH 7.5, 25C659013 2D-image

kcat/KM VALUE [1/mMs-1]kcat/KM VALUE [1/mMs-1] MaximumSUBSTRATEORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
No entries in this field

Ki VALUE [mM]Ki VALUE [mM] MaximumINHIBITORORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
No entries in this field

IC50 VALUE [mM]IC50 VALUE [mM] MaximumINHIBITORORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE IMAGE
No entries in this field

SPECIFIC ACTIVITY [µmol/min/mg] SPECIFIC ACTIVITY MAXIMUM ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
additional information-Escherichia coli K-12--659013

pH OPTIMUMpH MAXIMUMORGANISM UNIPROT ACCESSION NO. COMMENTARYLITERATURE
7.5-Escherichia coli K-12-assay at658079, 658106
7.5-Methylomonas aminofaciens-assay at658106
7.5-Escherichia coli K-12-assay at659013

pH RANGEpH RANGE MAXIMUMORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
No entries in this field

TEMPERATURE OPTIMUMTEMPERATURE OPTIMUM MAXIMUMORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
25-Escherichia coli K-12-assay at658079, 658106
25-Methylomonas aminofaciens-assay at658106
25-Escherichia coli K-12-assay at659013

TEMPERATURE RANGE TEMPERATURE MAXIMUM ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
No entries in this field

pI VALUEpI VALUE MAXIMUMORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
No entries in this field

SOURCE TISSUE ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE SOURCE
No entries in this field

LOCALIZATION ORGANISM UNIPROT ACCESSION NO. COMMENTARY GeneOntology No. LITERATURE SOURCE
No entries in this field

PDBSCOPCATHORGANISM
3exr, downloadSCOP (3exr)CATH (3exr)Streptococcus mutans
3exs, downloadSCOP (3exs)CATH (3exs)Streptococcus mutans
3ext, downloadSCOP (3ext)CATH (3ext)Streptococcus mutans

MOLECULAR WEIGHT MOLECULAR WEIGHT MAXIMUM ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
No entries in this field

SUBUNITS ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
dimerEscherichia coliP39304(beta/alpha)8-barrel enzyme, the active site is located at the dimer interface650143
dimerEscherichia coli K-12-(beta/alpha)8-barrel enzyme658079, 658106
dimerEscherichia coli-x-ray crystallography672127
homodimerStreptococcus mutans-gel filtration702041
homodimerStreptococcus mutans UA159-gel filtration-
additional informationMethylomonas aminofaciens-(beta/alpha)8-barrel enzyme658106

POSTTRANSLATIONAL MODIFICATION ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
No entries in this field

Crystallization/COMMENTARY ORGANISM UNIPROT ACCESSION NO. LITERATURE
-Escherichia coli-672127
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, respectivelyEscherichia coli-657958
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, respectivelyEscherichia coli-658080
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 resolutionEscherichia coliP39304650143
purified recombinant wild-type and mutant enzymes E112D/R139V, E112D/T169A, and E112D/R139V/T169A, 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, 5 mM MgCl2, and 25 mM L-xylulose 5-phosphate or D-ribulose 5-phosphate, cryoprotection of crystals in 15% monomethylPEG 5000, 100 mM PIPES, pH 7.0, 15% ethylene glycol, 200 mM NaCl, and 50 mM L-threonohydroxamate 4-phosphate or 50 mM D-ribulose 5-phosphate, X-ray diffraction structure determination and analysis at 1.6-1.8 A resolution, molecular replacementEscherichia coli K-12P39304658107
at 289 K using the hanging-drop vapor-diffusion technique. Apoenzyme obtained in two different space groups P212121 (without Mg2+) and I422 (in complex with Mg2+) and in the absence and presence of the product analog D-ribulose 5-phosphate. An 8 A alphaB-helix movement and other structural rearrangements around the active site between the apostructures and product analog bound structure. Conformational flexibility around the active site for substrate/product binding. Especially the alphaB-helix (residues 144-149) and the side chains of the conserved Arg144 and Arg197 exhibit openclosed conformational changes between the apo-structure and complex structure with ligand bound at the active siteStreptococcus mutans-702041

pH STABILITYpH STABILITY MAXIMUM ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
No entries in this field

TEMPERATURE STABILITYTEMPERATURE STABILITY MAXIMUM ORGANISM UNIPROT ACCESSION NO. COMMENTARYLITERATURE
No entries in this field

GENERAL STABILITYORGANISM UNIPROT ACCESSION NO.LITERATURE
No entries in this field

ORGANIC SOLVENT ORGANISM UNIPROT ACCESSION NO. COMMENTARY LITERATURE
No entries in this field

OXIDATION STABILITY ORGANISM UNIPROT ACCESSION NO. LITERATURE
No entries in this field

STORAGE STABILITY ORGANISM UNIPROT ACCESSION NO. LITERATURE
No entries in this field

Purification/COMMENTARY ORGANISM UNIPROT ACCESSION NO. LITERATURE
recombinant His-tagged UlaD from strain BL21(DE3), the His-tag is removed by thrombinEscherichia coliP39304650143
recombinant N-terminally His10-tagged SgbH from strain BL21(DE3) to homogeneity, the His-tag is removed by thrombinEscherichia coli K-12-659013
on Ni2+-chelating affinity column and by gel filtrationStreptococcus mutans-702041

Cloned/COMMENTARY ORGANISM UNIPROT ACCESSION NO. LITERATURE
expression of mutant enzymes in strain BLR(DE3)recA-strainEscherichia coli-658080
gene ulaD, expression as His-tagged protein in strain BL21(DE3), and as selenomethionine-labeled enzymeEscherichia coliP39304650143
expression of N-terminally His10-tagged wild-type and mutant enzymes in enzyme-deficient strain BLR(DE3)Escherichia coli K-12-658079, 658106, 658107
gene sgbH, expression in strain BL21(DE3) as N-terminally His10-tagged proteinEscherichia coli K-12-659013
expression of N-terminally His10-tagged wild-type and mutant enzymes in enzyme-deficient strain BLR(DE3)Methylomonas aminofaciens-658106
into pET-28a vector containing an N-terminal His6-tag and expressed in Escherichia coli strain BL21 (DE3) cellsStreptococcus mutans-702041

EXPRESSION ORGANISM UNIPROT ACCESSION NO. LITERATURE
No entries in this field

ENGINEERINGORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
E112QEscherichia coli-site-directed mutagenesis, crystal structure determination and analysis, the mutant enzyme shows altered reaction intermediate binding at the active site, reaction mechanism, and stereochemistry658080
E112Q/H136AEscherichia coli-site-directed mutagenesis, crystal structure determination and analysis, the mutant enzyme shows altered reaction intermediate binding at the active site, reaction mechanism, and stereochemistry658080
H136AEscherichia coli-site-directed mutagenesis, crystal structure determination and analysis, the mutant enzyme shows altered reaction intermediate binding at the active site, reaction mechanism, and stereochemistry658080
K64AEscherichia coli-site-directed mutagenesis, crystal structure determination and analysis, the mutant enzyme shows altered reaction intermediate binding at the active site, reaction mechanism, and stereochemistry658080
D67AEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
D67A/H136AEscherichia coli K-12-site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme658079
D67NEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
D67N/H136AEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
E112AEscherichia coli K-12-site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme658079
E112A/H136AEscherichia coli K-12-site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme658079
E112A/H136A/R139VEscherichia coli K-12-site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme658079
E112D/R139VEscherichia coli K-12P39304site-directed mutagenesis, mutations alter the Escherichia coli residues to those of Methylomonas aminofaciens D-arabino-hex-3-ulose 6-phosphate synthase, a homologous enzyme, also altering the enzyme activity of the 3-keto-L-gulonate 6-phosphate decarboxylase performing th Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate with highly increased activity compared to the wild-type enzyme658107
E112D/R139V/T169AEscherichia coli K-12-site-directed mutagenesis, mutations alter the Escherichia coli residues to those of Methylomonas aminofaciens D-arabino-hex-3-ulose 6-phosphate synthase, a homologous enzyme, also altering the enzyme activity of the 3-keto-L-gulonate 6-phosphate decarboxylase performing th Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate with highly increased activity compared to the wild-type enzyme658106, 658107
E112D/R139V/T169A/R192AEscherichia coli K-12-site-directed mutagenesis, mutations alter the Escherichia coli residues to those of Methylomonas aminofaciens D-arabino-hex-3-ulose 6-phosphate synthase, a homologous enzyme, also altering the enzyme activity of the 3-keto-L-gulonate 6-phosphate decarboxylase performing th Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate with highly increased activity compared to the wild-type enzyme658106
E112D/T169AEscherichia coli K-12P39304site-directed mutagenesis, mutations alter the Escherichia coli residues to those of Methylomonas aminofaciens D-arabino-hex-3-ulose 6-phosphate synthase, a homologous enzyme, also altering the enzyme activity of the 3-keto-L-gulonate 6-phosphate decarboxylase performing th Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate with highly increased activity compared to the wild-type enzyme658107
E112QEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
E112Q/H136AEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
E112Q/H136A/R139VEscherichia coli K-12-site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme658079
E33KEscherichia coli K-12-site-directed mutagenesis, inactive mutant658079
H136AEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
H136A/R139VEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
H136NEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
H136QEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
K64AEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
K64A/E112A/H136A/R139VEscherichia coli K-12-site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme658079
K64A/E112Q/H136AEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
K64A/H136AEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
K64A/R139VEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
K64REscherichia coli K-12-site-directed mutagenesis, slightly reduced activity compared to the wild-type enzyme658079
K64R/H136AEscherichia coli K-12-site-directed mutagenesis, reduced activity compared to the wild-type enzyme658079
R139VEscherichia coli K-12-site-directed mutagenesis, slightly reduced activity compared to the wild-type enzyme658079

Renatured/COMMENTARYORGANISM UNIPROT ACCESSION NO.LITERATURE
No entries in this field

APPLICATIONORGANISM UNIPROT ACCESSION NO.COMMENTARYLITERATURE
No entries in this field

REF. AUTHORS TITLE JOURNAL VOL. PAGES YEAR ORGANISM (UNIPROT ACCESSION NO.)LINK TO PUBMEDSOURCE
650143Wise, 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 decarboxylaseBiochemistry413861-38692002Escherichia coli, Escherichia coli (P39304) PubMed
657958Wise, 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 suprafamilyBiochemistry4212133-121422003Escherichia coli (P39304) PubMed
658079Yew, W.S.; Wise, E.L.; Rayment, I.; Gerlt, J.A.Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: mechanistic evidence for a proton relay system in the active site of 3-keto-L-gulonate 6-phosphate decarboxylaseBiochemistry436427-64372004Escherichia coli K-12 PubMed
658080Wise, 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 decarboxylaseBiochemistry436438-64462004Escherichia coli (P39304) PubMed
658106Yew, W.S.; Akana, J.; Wise, E.L.; Rayment, I.; Gerlt, J.A.Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: enhancing the promiscuous D-arabino-hex-3-ulose 6-phosphate synthase reaction catalyzed by 3-keto-L-gulonate 6-phosphate decarboxylaseBiochemistry441807-18152005Escherichia coli K-12, Methylomonas aminofaciens PubMed
658107Wise, E.L.; Yew, W.S.; Akana, J.; Gerlt, J.A.; Rayment, I.Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: structural basis for catalytic promiscuity in wild-type and designed mutants of 3-keto-L-gulonate 6-phosphate decarboxylaseBiochemistry441816-18232005Escherichia coli K-12 (P39304) PubMed
659013Yew, W.S.; Gerlt, J.A.Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operonsJ. Bacteriol.184302-3062002Escherichia coli K-12 PubMed
672127Akana, 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 superfamilyBiochemistry452493-25032006Escherichia coli PubMed
702041Li, G.L.; Liu, X.; Nan, J.; Brostromer, E.; Li, L.F.; Su, X.D.Open-closed conformational change revealed by the crystal structures of 3-keto-L-gulonate 6-phosphate decarboxylase from Streptococcus mutansBiochem. Biophys. Res. Commun.381429-4332009Streptococcus mutans, Streptococcus mutans UA159 PubMed

LINKS TO OTHER DATABASES (specific for EC-Number 4.1.1.85)
ExplorEnz
ExPASy
KEGG
MetaCyc
NCBI: PubMed, Protein, Nucleotide, Structure, Genome, OMIM
IUBMB Enzyme Nomenclature
PROSITE Database of protein families and domains
SYSTERS
Protein Mutant Database
InterPro (database of protein families, domains and functional sites)