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Literature summary extracted from

  • 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 (2002), Biochemistry, 41, 3861-3869.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.1.1.85 gene ulaD, expression as His-tagged protein in strain BL21(DE3), and as selenomethionine-labeled enzyme Escherichia coli

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.1.1.85 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 Escherichia coli

Inhibitors

EC Number Inhibitors Comment Organism Structure
4.1.1.85 L-gulonate 6-phosphate binding structure involving Glu33 and Asp62 and Mg2+ Escherichia coli

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
4.1.1.23 additional information metal-independent reaction Bacillus subtilis
4.1.1.85 Mg2+ dependent on, binding structure involving Glu33 and Asp62, overview Escherichia coli

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.1.1.23 Orotidine 5'-phosphate Bacillus subtilis
-
 UMP + CO2
-
 ?
4.1.1.85 3-dehydro-L-gulonate 6-phosphate + H+ Escherichia coli
-
 L-xylulose 5-phosphate + CO2
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
4.1.1.23 Bacillus subtilis
-
-
-
4.1.1.85 Escherichia coli P39304 gene ulaD
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.1.1.85 recombinant His-tagged UlaD from strain BL21(DE3), the His-tag is removed by thrombin Escherichia coli

Reaction

EC Number Reaction Comment Organism Reaction ID
4.1.1.23 orotidine 5'-phosphate = UMP + CO2 mechanism Bacillus subtilis
a
4.1.1.85 3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2 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, overview Escherichia coli
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.1.1.23 Orotidine 5'-phosphate
-
 Bacillus subtilis UMP + CO2
-
 ?
4.1.1.23 Orotidine 5'-phosphate mechansim, no formation of a vinyl anion intermediate, enzyme structure, the active sites are located at the dimer interface Bacillus subtilis UMP + CO2
-
 ?
4.1.1.85 3-dehydro-L-gulonate 6-phosphate + H+
-
 Escherichia coli L-xylulose 5-phosphate + CO2
-
 ?

Subunits

EC Number Subunits Comment Organism
4.1.1.23 dimer each subunit consists of a (beta/alpha)8-barrel, arranged in an antiparallel manner Bacillus subtilis
4.1.1.85 dimer (beta/alpha)8-barrel enzyme, the active site is located at the dimer interface Escherichia coli

Synonyms

EC Number Synonyms Comment Organism
4.1.1.23 OMPDC
-
 Bacillus subtilis
4.1.1.85 3-keto-L-gulonate 6-phosphate decarboxylase
-
 Escherichia coli
4.1.1.85 KGPDC
-
 Escherichia coli
4.1.1.85 More the enzyme belongs to the orotidine 5'-monophosphate decarboxylase OMPDC suprafamily, overview Escherichia coli