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Literature summary extracted from

  • Singh, S.; Stavrinides, J.; Christendat, D.; Guttman, D.S.
    A phylogenomic analysis of the shikimate dehydrogenases reveals broadscale functional diversification and identifies one functionally distinct subclass (2008), Mol. Biol. Evol., 25, 2221-2232.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.25 five putative SDH-encoding genes amplified and cloned into either a modified pET28a vector or the p15TVLIC vector, a ligation-independent vector due to incompatible cloning sites between the insert and pET28.3. Expressed in either the Escherichia coli strain BL21 gold (p15TV-LIC constructs) or the Escherichia coli BL21CodonPlus (pET28.3constructs) Pseudomonas putida KT2440
1.1.1.25 SDH-encoding gene is amplified by polymerase chain reaction from Pseudomonas putida KT2440 genomic DNA using primers with incorporated restriction sites. Resulting product is cloned into a vector and expressed in the Escherichia coli strain BL21 with appropriate antibiotics. Pseudomonas putida
1.1.1.25 SDH-encoding gene is amplified by polymerase chain reaction from Pseudomonas putida KT2440 genomic DNA using primers with incorporated restriction sites. Resulting product is cloned into vector and expressed in the Escherichia coli strain BL21 with appropriate antibiotics. Pseudomonas putida
1.1.1.282 five putative SDH-encoding genes amplified and cloned into either a modified pET28a vector or the p15TVLIC vector, a ligation-independent vector due to incompatible cloning sites between the insert and pET28.3. Expressed in either the Escherichia coli strain BL21 gold (p15TV-LIC constructs) or the Escherichia coli BL21CodonPlus (pET28.3constructs) Pseudomonas putida KT2440

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.1.1.25 additional information
-
 additional information no measurable activity with NAD+ Pseudomonas putida
1.1.1.25 additional information
-
 additional information no measurable activity with NADH+ Pseudomonas putida
1.1.1.25 additional information
-
 additional information no measurable activity with quinate Pseudomonas putida
1.1.1.25 additional information
-
 additional information no measurable activity with shikimate Pseudomonas putida
1.1.1.25 0.0046
-
 shikimate pH 8.8, presence of 2 mM NADP+ Pseudomonas putida
1.1.1.25 0.0073
-
 NADP+ pH 8.8, presence of 2 mM shikimate Pseudomonas putida
1.1.1.25 0.0786
-
 shikimate pH 8.8, presence of 2 mM NAD+ Pseudomonas putida
1.1.1.25 0.0786
-
 shikimate in the presence of 2 mM NAD+ Pseudomonas putida KT2440
1.1.1.25 0.105
-
 shikimate pH 8.8, presence of 2 mM NADP+ Pseudomonas putida
1.1.1.25 0.105
-
 shikimate in the presence of 2 mM NADP+ Pseudomonas putida KT2440
1.1.1.25 0.112
-
 NADP+ pH 8.8, presence of 2 mM shikimate Pseudomonas putida
1.1.1.25 0.112
-
 NADP+ in the presence of shikimate Pseudomonas putida KT2440
1.1.1.25 0.351
-
 shikimate pH 8.8, presence of 2 mM NAD+ Pseudomonas putida
1.1.1.25 0.572
-
 NAD+ pH 8.8, presence of 2 mM shikimate Pseudomonas putida
1.1.1.25 0.783
-
 quinate pH 8.8, presence of 2 mM NAD+ Pseudomonas putida
1.1.1.25 1.083
-
 NAD+ pH 8.8, presence of 2 mM quinate Pseudomonas putida
1.1.1.25 4.2
-
 shikimate pH 8.8, presence of 2 mM NAD+ Pseudomonas putida
1.1.1.25 5.4
-
 NAD+ pH 8.8, presence of 2 mM shikimate Pseudomonas putida
1.1.1.25 5.43
-
 NAD+ pH 8.8, presence of 2 mM shikimate Pseudomonas putida
1.1.1.25 5.43
-
 NAD+ in the presence of shikimate Pseudomonas putida KT2440
1.1.1.282 0.572
-
 NAD+ in the presence of shikimate Pseudomonas putida KT2440
1.1.1.282 0.783
-
 quinate in the presence of 2 mM NAD+ Pseudomonas putida KT2440
1.1.1.282 1.083
-
 NAD+ in the presence of quinate Pseudomonas putida KT2440
1.1.1.282 4.2
-
 shikimate in the presence of 2 mM NAD+ Pseudomonas putida KT2440

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.1.1.25 quinate + NAD+ Pseudomonas putida the fourth enzyme in the shikimate pathway 3-dehydroquinate + NADH + H+
-
 r
1.1.1.25 quinate + NAD+ Pseudomonas putida KT 2240 the fourth enzyme in the shikimate pathway 3-dehydroquinate + NADH + H+
-
 r
1.1.1.25 shikimate + NAD+ Pseudomonas putida
-
 3-dehydroshikimate + NADH + H+
-
 r
1.1.1.25 shikimate + NAD+ Pseudomonas putida KT 2240
-
 3-dehydroshikimate + NADH + H+
-
 r
1.1.1.25 shikimate + NADP+ Pseudomonas putida the fourth enzyme in the shikimate pathway 3-dehydroshikimate + NADPH + H+
-
 r
1.1.1.25 shikimate + NADP+ Pseudomonas putida KT 2240 the fourth enzyme in the shikimate pathway 3-dehydroshikimate + NADPH + H+
-
 r

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.25 Pseudomonas putida Q88GF6 homolog sdhL
-
1.1.1.25 Pseudomonas putida Q88IJ7 homolog ael1
-
1.1.1.25 Pseudomonas putida Q88JP1 homolog rifl
-
1.1.1.25 Pseudomonas putida Q88K85 homolog ydiB
-
1.1.1.25 Pseudomonas putida Q88RQ5 homolog aroE
-
1.1.1.25 Pseudomonas putida KT 2240 Q88GF6 homolog sdhL
-
1.1.1.25 Pseudomonas putida KT 2240 Q88IJ7 homolog ael1
-
1.1.1.25 Pseudomonas putida KT 2240 Q88JP1 homolog rifl
-
1.1.1.25 Pseudomonas putida KT 2240 Q88K85 homolog ydiB
-
1.1.1.25 Pseudomonas putida KT 2240 Q88RQ5 homolog aroE
-
1.1.1.25 Pseudomonas putida KT2440 Q88IJ7
-
-
1.1.1.25 Pseudomonas putida KT2440 Q88RQ5
-
-
1.1.1.282 Pseudomonas putida KT2440 Q88GF6
-
-
1.1.1.282 Pseudomonas putida KT2440 Q88JP1
-
-
1.1.1.282 Pseudomonas putida KT2440 Q88K85
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.25 by nickel-nitrilotriacetic acid affinity chromatography Pseudomonas putida KT2440
1.1.1.25 Cultures with expressed SDH enzymes are incubated and then induced with 0.4 mM isopropyl-beta-D-thiogalactopyranoside. Harvested cells are disrupted and the insoluble cellular material is removed by centrifugation. The recombinants are purified from other contaminating proteins using nickel-nitrilotriacetic acid affinity chromatography. Protein samples for kinetic studies are dialyzed and stored at 4 °C in 10 mM Tris–HCl, 500 mM NaCl, and 5% glycerol. Pseudomonas putida
1.1.1.25 Cultures with expressed SDH enzymes are incubated and then induced with 0.4 mM isopropyl-beta-D-thiogalactopyranoside. Harvested cells are disrupted and the insoluble cellular material is removed by centrifugation. The recombinants are purified from other contaminating proteins using nickel-nitrilotriacetic acid affinity chromatography. Protein samples for kinetic studies are dialyzed and stored at 4°C in 10 mM Tris-HCl, 500 mM NaCl, and 5% glycerol. Pseudomonas putida
1.1.1.25 Cultures with expressed SDH enzymes are incubated and then induced with 0.4 mM isopropyl-beta-D-thiogalactopyranoside. Harvested cells are disrupted and the insoluble cellular material is removed by centrifugation. The recombinants are purified from other contaminating proteins using nickel-nitrilotriacetic acid affinity chromatography. Protein samples for kinetic studies are dialyzed and stored at 4°C in 10 mM Tris–HCl, 500 mM NaCl, and 5% glycerol. Pseudomonas putida
1.1.1.282 by nickel-nitrilotriacetic acid affinity chromatography Pseudomonas putida KT2440

Storage Stability

EC Number Storage Stability Organism
1.1.1.25 4°C, 10 mM Tris-HCl buffer, pH 7.5, 500 mM NaCl, 5% glycerol Pseudomonas putida KT2440
1.1.1.282 4°C, 10 mM Tris-HCl buffer, pH 7.5, 500 mM NaCl, 5% glycerol Pseudomonas putida KT2440
1.1.1.282 4°C, 10 mM Tris–HCl buffer, pH 7.5, 500 mM NaCl, 5% glycerol Pseudomonas putida KT2440

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.25 additional information broad extent to which the SDH enzyme superfamily has diversified. 5 evolutionarily distinct SDH homologs in the genome of the common soil-inhabiting bacterium, Pseudomonas putida KT2440 Pseudomonas putida KT2440 ?
-
 ?
1.1.1.25 quinate + NAD(P)+
-
 Pseudomonas putida KT2440 3-dehydroquinate + NAD(P)H + H+
-
 ?
1.1.1.25 quinate + NAD+ the fourth enzyme in the shikimate pathway Pseudomonas putida 3-dehydroquinate + NADH + H+
-
 r
1.1.1.25 quinate + NAD+ the fourth enzyme in the shikimate pathway Pseudomonas putida KT 2240 3-dehydroquinate + NADH + H+
-
 r
1.1.1.25 shikimate + NAD(P)+
-
 Pseudomonas putida KT2440 3-dehydroshikimate + NAD(P)H + H+
-
 ?
1.1.1.25 shikimate + NAD+
-
 Pseudomonas putida 3-dehydroshikimate + NADH + H+
-
 r
1.1.1.25 shikimate + NAD+
-
 Pseudomonas putida KT2440 3-dehydroshikimate + NADH + H+
-
 r
1.1.1.25 shikimate + NAD+
-
 Pseudomonas putida KT 2240 3-dehydroshikimate + NADH + H+
-
 r
1.1.1.25 shikimate + NADP+ the fourth enzyme in the shikimate pathway Pseudomonas putida 3-dehydroshikimate + NADPH + H+
-
 r
1.1.1.25 shikimate + NADP+ the fourth enzyme in the shikimate pathway Pseudomonas putida KT 2240 3-dehydroshikimate + NADPH + H+
-
 r
1.1.1.282 L-quinate + NAD+
-
 Pseudomonas putida KT2440 3-dehydroquinate + NADH + H+
-
 r
1.1.1.282 additional information broad extent to which the SDH enzyme superfamily has diversified. 5 evolutionarily distinct SDH homologs in the genome of the common soil-inhabiting bacterium, Pseudomonas putida KT2440 Pseudomonas putida KT2440 ?
-
 ?
1.1.1.282 quinate + NAD(P)+
-
 Pseudomonas putida KT2440 3-dehydroquinate + NAD(P)H + H+
-
 ?
1.1.1.282 shikimate + NAD(P)+
-
 Pseudomonas putida KT2440 3-dehydroshikimate + NAD(P)H + H+
-
 ?
1.1.1.282 shikimate + NAD+
-
 Pseudomonas putida KT2440 3-dehydroshikimate + NADH + H+
-
 r

Synonyms

EC Number Synonyms Comment Organism
1.1.1.25 ael1
-
 Pseudomonas putida
1.1.1.25 ael1
-
 Pseudomonas putida KT2440
1.1.1.25 AroE
-
 Pseudomonas putida
1.1.1.25 AroE
-
 Pseudomonas putida KT2440
1.1.1.25 rifI
-
 Pseudomonas putida
1.1.1.25 SDH
-
 Pseudomonas putida
1.1.1.25 SDH
-
 Pseudomonas putida KT2440
1.1.1.25 sdhL
-
 Pseudomonas putida
1.1.1.25 shikimate dehydrogenase
-
 Pseudomonas putida
1.1.1.282 rifI
-
 Pseudomonas putida KT2440
1.1.1.282 SDH
-
 Pseudomonas putida KT2440
1.1.1.282 sdhL
-
 Pseudomonas putida KT2440
1.1.1.282 YdiB
-
 Pseudomonas putida KT2440

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.1.1.25 22
-
 assay at Pseudomonas putida

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.1.1.25 additional information
-
 additional information no measurable activity with NAD+ Pseudomonas putida
1.1.1.25 additional information
-
 additional information no measurable activity with NADH Pseudomonas putida
1.1.1.25 additional information
-
 additional information no measurable activity with NADH+ Pseudomonas putida
1.1.1.25 additional information
-
 additional information no measurable activity with quinate Pseudomonas putida
1.1.1.25 additional information
-
 additional information no measurable activity with shikimate Pseudomonas putida
1.1.1.25 0.077
-
 NADP+ in the presence of quinate Pseudomonas putida KT2440
1.1.1.25 0.16
-
 quinate in the presence of 2 mM NADP+ Pseudomonas putida KT2440
1.1.1.25 1.99
-
 shikimate pH 8.8, presence of 2 mM NAD+ Pseudomonas putida
1.1.1.25 1.99
-
 shikimate in the presence of 2 mM NAD+ Pseudomonas putida KT2440
1.1.1.25 5.3
-
 NADP+ pH 8.8, presence of 2 mM shikimate Pseudomonas putida
1.1.1.25 5.3
-
 NADP+ in the presence of shikimate Pseudomonas putida KT2440
1.1.1.25 5.8
-
 shikimate pH 8.8, presence of 2 mM NADP+ Pseudomonas putida
1.1.1.25 5.8
-
 shikimate in the presence of 2 mM NADP+ Pseudomonas putida KT2440
1.1.1.25 6.72
-
 NAD+ pH 8.8, presence of 2 mM shikimate Pseudomonas putida
1.1.1.25 6.72
-
 NAD+ in the presence of shikimate Pseudomonas putida KT2440
1.1.1.25 31.2
-
 shikimate pH 8.8, presence of 2 mM NAD+ Pseudomonas putida
1.1.1.25 31.2
-
 shikimate in the presence of 2 mM NAD+ Pseudomonas putida KT2440
1.1.1.25 37.7
-
 quinate pH 8.8, presence of 2 mM NAD+ Pseudomonas putida
1.1.1.25 40.7
-
 NAD+ pH 8.8, presence of 2 mM quinate Pseudomonas putida
1.1.1.25 55.7
-
 shikimate pH 8.8, presence of 2 mM NAD+ Pseudomonas putida
1.1.1.25 61.1
-
 NAD+ pH 8.8, presence of 2 mM shikimate Pseudomonas putida
1.1.1.25 97.1
-
 NAD+ pH 8.8, presence of 2 mM shikimate Pseudomonas putida
1.1.1.25 97.1
-
 NAD+ in the presence of shikimate Pseudomonas putida KT2440
1.1.1.25 261.5
-
 NADP+ pH 8.8, presence of 2 mM shikimate Pseudomonas putida
1.1.1.25 261.5
-
 NADP+ in the presence of shikimate Pseudomonas putida KT2440
1.1.1.25 266.2
-
 shikimate pH 8.8, presence of 2 mM NADP+ Pseudomonas putida
1.1.1.25 266.2
-
 shikimate in the presence of 2 mM NADP+ Pseudomonas putida KT2440
1.1.1.282 37.7
-
 quinate in the presence of 2 mM NAD+ Pseudomonas putida KT2440
1.1.1.282 55.7
-
 shikimate in the presence of 2 mM NAD+ Pseudomonas putida KT2440
1.1.1.282 55.7
-
 NAD+ in the presence of quinate Pseudomonas putida KT2440
1.1.1.282 61.1
-
 NAD+ in the presence of shikimate Pseudomonas putida KT2440

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.1.1.25 8.8
-
 assay at Pseudomonas putida

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.25 NAD(P)+
-
 Pseudomonas putida KT2440
1.1.1.25 NAD+
-
 Pseudomonas putida
1.1.1.25 NADP+
-
 Pseudomonas putida
1.1.1.282 NAD(P)+
-
 Pseudomonas putida KT2440