BRENDA - Enzyme Database
show all sequences of 1.1.1.282

Insights into the function of RifI2: structural and biochemical investigation of a new shikimate dehydrogenase family protein

Peek, J.; Garcia, C.; Lee, J.; Christendat, D.; Biochim. Biophys. Acta 1834, 516-523 (2013)

Data extracted from this reference:

Cloned(Commentary)
Cloned (Commentary)
Organism
recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21 gold
Pseudomonas putida
Crystallization (Commentary)
Crystallization (Commentary)
Organism
RifI2 X-ray diffraction structure determination and analysis at 2.15 A resolution, modelling
Pseudomonas putida
Engineering
Protein Variants
Commentary
Organism
N193D
site-directed mutagenesis, inactive mutant
Pseudomonas putida
N193L
site-directed mutagenesis, inactive mutant
Pseudomonas putida
N193Q
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Pseudomonas putida
N193S
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Pseudomonas putida
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.43
-
NAD+
pH 8.8, 25°C, with quinate
Pseudomonas putida
0.71
-
NAD+
pH 8.8, 25°C, with shikimate
Pseudomonas putida
1.88
-
L-quinate
pH 8.8, 25°C, with NAD+
Pseudomonas putida
2.18
-
shikimate
pH 8.8, 25°C, with NADP+
Pseudomonas putida
2.65
-
NADP+
pH 8.8, 25°C, with shikimate
Pseudomonas putida
3.38
-
shikimate
pH 8.8, 25°C, with NAD+
Pseudomonas putida
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
additional information
divalent cations are not required for the activity of RifI2, as the reaction rate is not altered in the presence of 5 mM Ca2+, Mg2+, Mn2+, or Zn2+. Similarly, the reaction is not affected by the addition of 10 mM EDTA to chelate any endogenous divalent cations associated with the enzyme
Pseudomonas putida
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
L-quinate + NAD+
Pseudomonas putida
-
3-dehydroquinate + NADH + H+
-
-
?
L-quinate + NAD+
Pseudomonas putida KT 2240
-
3-dehydroquinate + NADH + H+
-
-
?
shikimate + NAD+
Pseudomonas putida
-
3-dehydroshikimate + NADH + H+
-
-
?
shikimate + NAD+
Pseudomonas putida KT 2240
-
3-dehydroshikimate + NADH + H+
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Pseudomonas putida
Q88JP1
-
-
Pseudomonas putida KT 2240
Q88JP1
-
-
Purification (Commentary)
Purification (Commentary)
Organism
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21 gold by nickel affinity chromatography, dialysis, tag cleavage through TEV protease and removal by nickel affinity chromatography, followed by gel filtration
Pseudomonas putida
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
L-quinate + NAD+
-
740100
Pseudomonas putida
3-dehydroquinate + NADH + H+
-
-
-
?
L-quinate + NAD+
-
740100
Pseudomonas putida KT 2240
3-dehydroquinate + NADH + H+
-
-
-
?
shikimate + NAD+
-
740100
Pseudomonas putida
3-dehydroshikimate + NADH + H+
-
-
-
?
shikimate + NAD+
-
740100
Pseudomonas putida KT 2240
3-dehydroshikimate + NADH + H+
-
-
-
?
shikimate + NADP+
very low activity with NADP+
740100
Pseudomonas putida
3-dehydroshikimate + NADPH + H+
-
-
-
?
shikimate + NADP+
very low activity with NADP+
740100
Pseudomonas putida KT 2240
3-dehydroshikimate + NADPH + H+
-
-
-
?
Subunits
Subunits
Commentary
Organism
dimer
distinct mode of dimerization in which the individual molecules interact in a back-to-front manner, overview. The molecules of the RifI2 dimer associate via hydrophobic interactions between residues on alpha-helix alpha8 of the first molecule and alpha10' of the second molecule. In addition, the side chain of Gln167 on apha-helix alpha8 forms a hydrogen bond with the guanidinium group of Arg243' on beta-strand beta10'. A second hydrogen bond to Arg243' may be made by Asn171. Asp53 and Arg56 on alpha-helix alpha2 bind the imidazole ring of His31' on alpha-helix alpha1'
Pseudomonas putida
Synonyms
Synonyms
Commentary
Organism
RifI2
-
Pseudomonas putida
SDH/QDH
-
Pseudomonas putida
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.0055
-
NAD+
pH 8.8, 25°C, with quinate
Pseudomonas putida
0.0063
-
L-quinate
pH 8.8, 25°C, with NAD+
Pseudomonas putida
0.022
-
NADP+
pH 8.8, 25°C, with shikimate
Pseudomonas putida
0.027
-
shikimate
pH 8.8, 25°C, with NADP+
Pseudomonas putida
2.8
-
NAD+
pH 8.8, 25°C, with shikimate
Pseudomonas putida
3.9
-
shikimate
pH 8.8, 25°C, with NAD+
Pseudomonas putida
Cofactor
Cofactor
Commentary
Organism
Structure
additional information
in the RifI2 structure, the NADP+-specifying motif is replaced with Asp-Pro-Ser-Thr-Ala-Arg (residues 156-161). The side chain of Asp156 binds to the adenine ribose of NAD+, while its negative charge is predicted to repel the additional phosphate of NADP+. RifI2 possesses low apparent binding affinity for NADP+. Analysis of the cofactor-binding sites of the RifI2–NAD+ complex and structure comparison, inportance of the invariant residue Asn193 in the cofactor-binding site, overview
Pseudomonas putida
NAD+
the C-terminal domain of each protomer in the RifI2 asymmetric unit contains a bound molecule of NAD+, Cofactor binding structure and mechanism, detailed overview
Pseudomonas putida
NADH
-
Pseudomonas putida
Cloned(Commentary) (protein specific)
Commentary
Organism
recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21 gold
Pseudomonas putida
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
additional information
in the RifI2 structure, the NADP+-specifying motif is replaced with Asp-Pro-Ser-Thr-Ala-Arg (residues 156-161). The side chain of Asp156 binds to the adenine ribose of NAD+, while its negative charge is predicted to repel the additional phosphate of NADP+. RifI2 possesses low apparent binding affinity for NADP+. Analysis of the cofactor-binding sites of the RifI2–NAD+ complex and structure comparison, inportance of the invariant residue Asn193 in the cofactor-binding site, overview
Pseudomonas putida
NAD+
the C-terminal domain of each protomer in the RifI2 asymmetric unit contains a bound molecule of NAD+, Cofactor binding structure and mechanism, detailed overview
Pseudomonas putida
NADH
-
Pseudomonas putida
Crystallization (Commentary) (protein specific)
Crystallization
Organism
RifI2 X-ray diffraction structure determination and analysis at 2.15 A resolution, modelling
Pseudomonas putida
Engineering (protein specific)
Protein Variants
Commentary
Organism
N193D
site-directed mutagenesis, inactive mutant
Pseudomonas putida
N193L
site-directed mutagenesis, inactive mutant
Pseudomonas putida
N193Q
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Pseudomonas putida
N193S
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Pseudomonas putida
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.43
-
NAD+
pH 8.8, 25°C, with quinate
Pseudomonas putida
0.71
-
NAD+
pH 8.8, 25°C, with shikimate
Pseudomonas putida
1.88
-
L-quinate
pH 8.8, 25°C, with NAD+
Pseudomonas putida
2.18
-
shikimate
pH 8.8, 25°C, with NADP+
Pseudomonas putida
2.65
-
NADP+
pH 8.8, 25°C, with shikimate
Pseudomonas putida
3.38
-
shikimate
pH 8.8, 25°C, with NAD+
Pseudomonas putida
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
additional information
divalent cations are not required for the activity of RifI2, as the reaction rate is not altered in the presence of 5 mM Ca2+, Mg2+, Mn2+, or Zn2+. Similarly, the reaction is not affected by the addition of 10 mM EDTA to chelate any endogenous divalent cations associated with the enzyme
Pseudomonas putida
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
L-quinate + NAD+
Pseudomonas putida
-
3-dehydroquinate + NADH + H+
-
-
?
L-quinate + NAD+
Pseudomonas putida KT 2240
-
3-dehydroquinate + NADH + H+
-
-
?
shikimate + NAD+
Pseudomonas putida
-
3-dehydroshikimate + NADH + H+
-
-
?
shikimate + NAD+
Pseudomonas putida KT 2240
-
3-dehydroshikimate + NADH + H+
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21 gold by nickel affinity chromatography, dialysis, tag cleavage through TEV protease and removal by nickel affinity chromatography, followed by gel filtration
Pseudomonas putida
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
L-quinate + NAD+
-
740100
Pseudomonas putida
3-dehydroquinate + NADH + H+
-
-
-
?
L-quinate + NAD+
-
740100
Pseudomonas putida KT 2240
3-dehydroquinate + NADH + H+
-
-
-
?
shikimate + NAD+
-
740100
Pseudomonas putida
3-dehydroshikimate + NADH + H+
-
-
-
?
shikimate + NAD+
-
740100
Pseudomonas putida KT 2240
3-dehydroshikimate + NADH + H+
-
-
-
?
shikimate + NADP+
very low activity with NADP+
740100
Pseudomonas putida
3-dehydroshikimate + NADPH + H+
-
-
-
?
shikimate + NADP+
very low activity with NADP+
740100
Pseudomonas putida KT 2240
3-dehydroshikimate + NADPH + H+
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
dimer
distinct mode of dimerization in which the individual molecules interact in a back-to-front manner, overview. The molecules of the RifI2 dimer associate via hydrophobic interactions between residues on alpha-helix alpha8 of the first molecule and alpha10' of the second molecule. In addition, the side chain of Gln167 on apha-helix alpha8 forms a hydrogen bond with the guanidinium group of Arg243' on beta-strand beta10'. A second hydrogen bond to Arg243' may be made by Asn171. Asp53 and Arg56 on alpha-helix alpha2 bind the imidazole ring of His31' on alpha-helix alpha1'
Pseudomonas putida
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.0055
-
NAD+
pH 8.8, 25°C, with quinate
Pseudomonas putida
0.0063
-
L-quinate
pH 8.8, 25°C, with NAD+
Pseudomonas putida
0.022
-
NADP+
pH 8.8, 25°C, with shikimate
Pseudomonas putida
0.027
-
shikimate
pH 8.8, 25°C, with NADP+
Pseudomonas putida
2.8
-
NAD+
pH 8.8, 25°C, with shikimate
Pseudomonas putida
3.9
-
shikimate
pH 8.8, 25°C, with NAD+
Pseudomonas putida
General Information
General Information
Commentary
Organism
additional information
enzyme RifI2 lacks a conserved C-terminal alpha-helix
Pseudomonas putida
General Information (protein specific)
General Information
Commentary
Organism
additional information
enzyme RifI2 lacks a conserved C-terminal alpha-helix
Pseudomonas putida
KCat/KM [mM/s]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.0034
-
L-quinate
pH 8.8, 25°C, with NAD+
Pseudomonas putida
0.0083
-
NADP+
pH 8.8, 25°C, with shikimate
Pseudomonas putida
0.012
-
shikimate
pH 8.8, 25°C, with NADP+
Pseudomonas putida
0.013
-
NAD+
pH 8.8, 25°C, with quinate
Pseudomonas putida
1.15
-
shikimate
pH 8.8, 25°C, with NAD+
Pseudomonas putida
3.95
-
NAD+
pH 8.8, 25°C, with shikimate
Pseudomonas putida
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.0034
-
L-quinate
pH 8.8, 25°C, with NAD+
Pseudomonas putida
0.0083
-
NADP+
pH 8.8, 25°C, with shikimate
Pseudomonas putida
0.012
-
shikimate
pH 8.8, 25°C, with NADP+
Pseudomonas putida
0.013
-
NAD+
pH 8.8, 25°C, with quinate
Pseudomonas putida
1.15
-
shikimate
pH 8.8, 25°C, with NAD+
Pseudomonas putida
3.95
-
NAD+
pH 8.8, 25°C, with shikimate
Pseudomonas putida
Other publictions for EC 1.1.1.282
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Synonyms
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
740881
Garcia
The role of the ydiB gene, whi ...
Escherichia coli, Escherichia coli JM101
J. Mol. Microbiol. Biotechnol.
27
11-21
2016
-
1
1
-
1
-
-
-
-
-
-
6
-
12
-
-
-
-
-
-
-
-
6
-
3
-
-
-
-
-
-
-
2
-
-
-
-
1
1
2
-
1
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
739956
Peek
The shikimate dehydrogenase fa ...
Corynebacterium glutamicum, Corynebacterium glutamicum ATCC 13032
Arch. Biochem. Biophys.
566
85-99
2015
-
2
2
2
-
-
-
5
-
-
-
6
-
4
-
-
-
4
-
-
-
-
9
2
2
2
-
-
4
2
-
-
4
-
-
-
-
2
2
4
2
-
-
-
-
-
5
-
-
-
6
-
-
-
-
-
-
-
-
9
2
2
-
-
4
2
-
-
-
-
8
8
-
-
-
740724
Guo
Molecular characterization of ...
Populus trichocarpa, Populus trichocarpa Nisqually-1
J. Biol. Chem.
289
23846-23858
2014
-
-
1
-
-
-
-
5
-
-
-
3
-
5
-
-
1
-
-
7
-
-
3
-
5
1
-
-
-
1
-
-
2
-
-
-
-
-
1
2
-
-
-
-
-
-
5
-
-
-
3
-
-
-
1
-
7
-
-
3
-
1
-
-
-
1
-
-
-
-
4
4
-
-
-
724089
Kubota
Characterization of shikimate ...
Corynebacterium glutamicum
Appl. Microbiol. Biotechnol.
97
8139-8149
2013
-
-
1
-
1
-
-
6
-
-
2
3
-
1
-
-
1
-
-
-
-
-
5
1
3
-
-
-
5
2
1
-
3
-
-
-
-
-
1
3
-
1
-
-
-
-
6
-
-
2
3
-
-
-
1
-
-
-
-
5
1
-
-
-
5
2
1
-
-
1
1
1
1
5
5
727115
Höppner
Enzyme-substrate complexes of ...
Corynebacterium glutamicum, Corynebacterium glutamicum ATCC 13032
Biol. Chem.
394
1505-1516
2013
-
-
-
1
-
-
-
8
-
-
-
5
-
7
-
-
-
-
-
-
-
-
5
1
4
1
-
-
8
2
-
-
3
-
-
-
-
-
-
3
1
-
-
-
-
-
8
-
-
-
5
-
-
-
-
-
-
-
-
5
1
1
-
-
8
2
-
-
-
-
1
1
-
8
8
740100
Peek
Insights into the function of ...
Pseudomonas putida, Pseudomonas putida KT 2240
Biochim. Biophys. Acta
1834
516-523
2013
-
-
1
1
4
-
-
6
-
1
-
4
-
5
-
-
1
-
-
-
-
-
6
1
2
-
-
-
6
-
-
-
3
-
-
-
-
-
1
3
1
4
-
-
-
-
6
-
1
-
4
-
-
-
1
-
-
-
-
6
1
-
-
-
6
-
-
-
-
-
1
1
-
6
6
694093
Singh
A phylogenomic analysis of the ...
Pseudomonas putida KT2440
Mol. Biol. Evol.
25
2221-2232
2008
-
-
3
-
-
-
-
4
-
-
-
-
-
3
-
-
3
-
-
-
-
3
11
-
6
-
-
-
4
-
-
-
3
-
-
-
-
-
3
3
-
-
-
-
-
-
4
-
-
-
-
-
-
-
3
-
-
-
3
11
-
-
-
-
4
-
-
-
-
-
-
-
-
-
-
667700
Singh
Structure of Arabidopsis dehyd ...
Arabidopsis thaliana
Biochemistry
45
10406
2006
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
1
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
656292
Lindner
Site-directed mutagenesis of t ...
Escherichia coli
J. Biol. Chem.
280
7162-7169
2005
-
2
-
-
8
-
-
30
-
-
3
-
-
3
-
-
-
-
-
-
-
-
4
1
2
-
-
-
30
-
-
-
4
-
-
-
-
2
-
4
-
8
-
-
-
-
30
-
-
3
-
-
-
-
-
-
-
-
-
4
1
-
-
-
30
-
-
-
-
-
-
-
-
-
-
669328
Singh
Crystal structure of a novel s ...
Enterococcus faecalis, Enterococcus faecium, Lactiplantibacillus plantarum, Listeria monocytogenes, Salmonella enterica subsp. enterica serovar Typhimurium, Shigella flexneri, Streptococcus pyogenes, Escherichia coli, Haemophilus influenzae
J. Biol. Chem.
280
17101-17108
2005
-
-
-
-
-
-
-
-
-
-
-
-
-
9
-
-
-
-
-
-
-
-
9
-
18
-
-
-
-
-
-
-
8
-
-
-
-
-
-
8
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
9
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
644536
Michel
Structures of shikimate dehydr ...
Escherichia coli
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The role of quinate dehydrogen ...
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