Literature summary for 1.1.1.267 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 .

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Cloned(Commentary)

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

Crystallization (Commentary)

Crystallization (Comment)	Organism
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

Crystallization (Comment)

Organism

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

Inhibitors	Comment	Organism	Structure
fosmidomycin	-	Vibrio vulnificus

Metals/Ions

Metals/Ions	Comment	Organism
Mg2+	activates	Vibrio vulnificus
Mn2+	activates	Vibrio vulnificus
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)

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

Organism

Organism	UniProt	Comment	Textmining
Vibrio vulnificus	Q8DBF5	-	-
Vibrio vulnificus CMCP6	Q8DBF5	-	-

Purification (Commentary)

Purification (Comment)	Organism
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)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
1-deoxy-D-xylulose 5-phosphate + NADPH + H+	-	Vibrio vulnificus	2-C-methyl-D-erythritol 4-phosphate + NADP+	-	?
1-deoxy-D-xylulose 5-phosphate + NADPH + H+	i.e. DXP	Vibrio vulnificus	2-C-methyl-D-erythritol 4-phosphate + NADP+	-	?
1-deoxy-D-xylulose 5-phosphate + NADPH + H+	-	Vibrio vulnificus CMCP6	2-C-methyl-D-erythritol 4-phosphate + NADP+	-	?
1-deoxy-D-xylulose 5-phosphate + NADPH + H+	i.e. DXP	Vibrio vulnificus CMCP6	2-C-methyl-D-erythritol 4-phosphate + NADP+	-	?
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	?	-	-
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

Subunits	Comment	Organism
homodimer	-	Vibrio vulnificus

Synonyms

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

Cofactor

Cofactor	Comment	Organism	Structure
NADP+	-	Vibrio vulnificus
NADPH	-	Vibrio vulnificus

General Information

General Information	Comment	Organism
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
additional information	enzyme active site structure analysis	Vibrio vulnificus