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Literature summary extracted from

  • Ussin, N.K.; Bagnell, A.M.; Offermann, L.R.; Abdulsalam, R.; Perdue, M.L.; Magee, P.; Chruszcz, M.
    Structural characterization of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus (2018), Biochim. Biophys. Acta, 1866, 1209-1215 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.267 gene dxr, sequence comparisons, recombinant expression of N-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3) Vibrio vulnificus

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.1.1.267 purified recombinant enzyme in apoform, or in complex with inhibitors fosmidomycin or FR900098 and Mn2+, or in complex with arginine, or in phosphate-free condition, hanging and sitting drop vapor diffusion methods, mixing of 12 mg/ml protein in 10 mM Tris-HCl, pH 7.4, and 150 mM NaCl, at 25°C, with reservoir solution of different compositions, crystallization conditions, overview, X-ray diffraction structure determination and analysis, molecular replacement using the Escherichia coli Dxr enzyme structure (PDB ID 1Q0L) as a starting model, modeling Vibrio vulnificus

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.1.1.267 fosmidomycin
-
Vibrio vulnificus

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.1.1.267 Mg2+ activates Vibrio vulnificus
1.1.1.267 Mn2+ activates Vibrio vulnificus
1.1.1.267 additional information Dxrs require a divalent metal for their activity. The enzymes may use Mg2+ or Mn2+ cations. The enzyme forms a dimeric assembly and contains a metal ion in the active site. The residues coordinating the metal are parts of two highly conserved protein fragments: 148-PVDSEHXA-155 and 227-NKGLEXIE-234. The first of these fragments is bridging the N- and C-terminal domains. Residues E152 and E231 are the major residues involved in metal binding, and in three crystal structure cases they are the only amino acids involved in interactions with the metal. In the fourth case the metal ion is coordinated by D150, E152 and E231 (PDB ID 5KRR, chain B) Vibrio vulnificus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.1.1.267 1-deoxy-D-xylulose 5-phosphate + NADPH + H+ Vibrio vulnificus
-
2-C-methyl-D-erythritol 4-phosphate + NADP+
-
?
1.1.1.267 1-deoxy-D-xylulose 5-phosphate + NADPH + H+ Vibrio vulnificus CMCP6
-
2-C-methyl-D-erythritol 4-phosphate + NADP+
-
?

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.267 Vibrio vulnificus Q8DBF5
-
-
1.1.1.267 Vibrio vulnificus CMCP6 Q8DBF5
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.267 recombinant N-terminally His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis, and gel filtration, followed by tag cleavage through TEV protease, and another step of nickel affinity chromatography, and terminated by gel filtration Vibrio vulnificus

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.267 1-deoxy-D-xylulose 5-phosphate + NADPH + H+
-
Vibrio vulnificus 2-C-methyl-D-erythritol 4-phosphate + NADP+
-
?
1.1.1.267 1-deoxy-D-xylulose 5-phosphate + NADPH + H+ i.e. DXP Vibrio vulnificus 2-C-methyl-D-erythritol 4-phosphate + NADP+
-
?
1.1.1.267 1-deoxy-D-xylulose 5-phosphate + NADPH + H+
-
Vibrio vulnificus CMCP6 2-C-methyl-D-erythritol 4-phosphate + NADP+
-
?
1.1.1.267 1-deoxy-D-xylulose 5-phosphate + NADPH + H+ i.e. DXP Vibrio vulnificus CMCP6 2-C-methyl-D-erythritol 4-phosphate + NADP+
-
?
1.1.1.267 additional information VvDxr residues S186, H209, S222, N227 and K228 may participate in binding of the DXP substrate's phosphate moiety. These residues are conserved. H209 is a part of a flexible loop (209-HPXWXMG-115) that closes on the active site upon substrate binding. While H209 interacts with the phosphate group, W211 and M213 shield the remaining part of Dxp from solvent Vibrio vulnificus ?
-
-
1.1.1.267 additional information VvDxr residues S186, H209, S222, N227 and K228 may participate in binding of the DXP substrate's phosphate moiety. These residues are conserved. H209 is a part of a flexible loop (209-HPXWXMG-115) that closes on the active site upon substrate binding. While H209 interacts with the phosphate group, W211 and M213 shield the remaining part of Dxp from solvent Vibrio vulnificus CMCP6 ?
-
-

Subunits

EC Number Subunits Comment Organism
1.1.1.267 homodimer
-
Vibrio vulnificus

Synonyms

EC Number Synonyms Comment Organism
1.1.1.267 1-deoxy-D-xylulose 5-phosphate reductoisomerase
-
Vibrio vulnificus
1.1.1.267 DXR
-
Vibrio vulnificus
1.1.1.267 VvDxr
-
Vibrio vulnificus

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.267 NADP+
-
Vibrio vulnificus
1.1.1.267 NADPH
-
Vibrio vulnificus

General Information

EC Number General Information Comment Organism
1.1.1.267 metabolism the enzyme is involved in the 2-methyl-D-erythritol-4-phosphate (MEP) terpenoid biosynthetic pathway catalyzing the second step, pathway overview Vibrio vulnificus
1.1.1.267 additional information enzyme active site structure analysis Vibrio vulnificus