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Literature summary for 1.1.1.25 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)

Cloned (Comment) Organism
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
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
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

KM Value [mM]

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

Natural Substrates/ Products (Substrates)

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

Organism

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

Purification (Commentary)

Purification (Comment) Organism
by nickel-nitrilotriacetic acid affinity chromatography Pseudomonas putida KT2440
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
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
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

Storage Stability

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

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
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 ?
-
?
quinate + NAD(P)+
-
Pseudomonas putida KT2440 3-dehydroquinate + NAD(P)H + H+
-
?
quinate + NAD+ the fourth enzyme in the shikimate pathway Pseudomonas putida 3-dehydroquinate + NADH + H+
-
r
quinate + NAD+ the fourth enzyme in the shikimate pathway Pseudomonas putida KT 2240 3-dehydroquinate + NADH + H+
-
r
shikimate + NAD(P)+
-
Pseudomonas putida KT2440 3-dehydroshikimate + NAD(P)H + H+
-
?
shikimate + NAD+
-
Pseudomonas putida 3-dehydroshikimate + NADH + H+
-
r
shikimate + NAD+
-
Pseudomonas putida KT2440 3-dehydroshikimate + NADH + H+
-
r
shikimate + NAD+
-
Pseudomonas putida KT 2240 3-dehydroshikimate + NADH + H+
-
r
shikimate + NADP+ the fourth enzyme in the shikimate pathway Pseudomonas putida 3-dehydroshikimate + NADPH + H+
-
r
shikimate + NADP+ the fourth enzyme in the shikimate pathway Pseudomonas putida KT 2240 3-dehydroshikimate + NADPH + H+
-
r

Synonyms

Synonyms Comment Organism
ael1
-
Pseudomonas putida
ael1
-
Pseudomonas putida KT2440
AroE
-
Pseudomonas putida
AroE
-
Pseudomonas putida KT2440
rifI
-
Pseudomonas putida
SDH
-
Pseudomonas putida
SDH
-
Pseudomonas putida KT2440
sdhL
-
Pseudomonas putida
shikimate dehydrogenase
-
Pseudomonas putida

Temperature Optimum [°C]

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

Turnover Number [1/s]

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

pH Optimum

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

Cofactor

Cofactor Comment Organism Structure
NAD(P)+
-
Pseudomonas putida KT2440
NAD+
-
Pseudomonas putida
NADP+
-
Pseudomonas putida