BRENDA - Enzyme Database show
show all sequences of 1.13.11.3

Roles of the equatorial tyrosyl iron ligand of protocatechuate 3,4-dioxygenase in catalysis

Valley, M.P.; Brown, C.K.; Burk, D.L.; Vetting, M.W.; Ohlendorf, D.H.; Lipscomb, J.D.; Biochemistry 44, 11024-11039 (2005)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
the enzyme containing the Y408E mutation is expressed in Pseudomonas fluorescens; the enzymes containing the Y408C, Y408F and Y408H mutation are expressed in Escherichia coli
Pseudomonas putida
Engineering
Amino acid exchange
Commentary
Organism
Y408C
iron is tightly bound. The structure reveals no significant mutation-related changes except in the immediate vicinity of the altered amino acid (rmsd over all atoms = 0.2-0.3 A). The new amino acid does not coordinate to the iron, because the side chain is shorter than that of Tyr. In contrast to the wild-type enzyme, Tyr447 remains bound to the iron, as a result, a monodentate substrate complex is formed between the iron and protocatechuate 04. Protocatechuate does not shift into a chelated orientation. Inhibitors like 4-hydroybenzoate and 3-hydroybenzoate bind more tighly to the mutant enzyme, whereas the substrate protocatechuate binds less tightly.
Pseudomonas putida
Y408E
iron is tightly bound. The structure reveals no significant mutation-related changes except in the immediate vicinity of the altered amino acid (rmsd over all atoms = 0.2-0.3 A). The new amino acid does not coordinate to the iron, because the side chain is shorter than that of Tyr. In contrast to the wild-type enzyme, Tyr447 remains bound to the iron, as a result, a monodentate substrate complex is formed between the iron and protocatechuate 04. Protocatechuate does not shift into a chelated orientation.
Pseudomonas putida
Y408F
iron is not tightly bound, the Y408F mutant does not reconstitute above half-occupancy and loses color during crystallization attempts. Inhibitors like 4-hydroybenzoate and 3-hydroybenzoate bind more tighly to the mutant enzyme, whereas the substrate protocatechuate binds less tightly.
Pseudomonas putida
Y408H
iron is tightly bound. The structure reveals no significant mutation-related changes except in the immediate vicinity of the altered amino acid (rmsd over all atoms = 0.2-0.3 A). The new amino acid does not coordinate to the iron, because the side chain is shorter than that of Tyr. In contrast to the wild-type enzyme, Tyr447 remains bound to the iron, as a result, a monodentate substrate complex is formed between the iron and protocatechuate 04. Protocatechuate does not shift into a chelated orientation. Inhibitors like 4-hydroybenzoate and 3-hydroybenzoate bind more tighly to the mutant enzyme, whereas the substrate protocatechuate binds less tightly.
Pseudomonas putida
Inhibitors
Inhibitors
Commentary
Organism
Structure
3-hydroxybenzoate
optical titration at 25°C
Pseudomonas putida
4-hydroxybenzoate
optical titration at 25°C
Pseudomonas putida
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
rates (s-1) and dissocation constants (microM) for protocatechuate: Y408H: k+2 = 2.8, k-2 = 1.9, k+2 + k-2 = 4.7, K1 = 2600, Kd = 1100, Y408F: k+2 = 0.39, k-2 = 0.46, k+2 + k-2 = 0.85, K1 = 84, Kd = 45, Y408C: k+2 + k-2 = 0.67; substrate dissociation constant for protocatechuate: wild type = 2.5 microM, Y408H = 39 micro M, Y408C = 57 microM
Pseudomonas putida
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Pseudomonas putida
-
reclassified from Pseudomonas aeruginosa
-
Purification (Commentary)
Commentary
Organism
enzymes from Escherichia coli: DEAE-Sepharose Fast Flow column (5.5 x 19 cm), Phenyl-Sepharose CL-4B column (4.5 x 22.5 cm), Sephacryl S-300 column (3 x 97.5 cm); enzymes from Pseudomonas florescens
Pseudomonas putida
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3,4-dihydroxybenzoate + O2
-
671966
Pseudomonas putida
beta-carboxy-cis,cis-muconate
-
-
-
?
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.007
-
protocatechuate
for the mutant enzyme Y408H, at 25°C in 50 mM Tris and 2 mM beta-mercaptoethanol, pH 8.5 under saturating protocatechuate and O2 conditions
Pseudomonas putida
0.01
-
protocatechuate
for the mutant enzyme Y408E, at 25°C in 50 mM Tris and 2 mM beta-mercaptoethanol, pH 8.5 under saturating protocatechuate and O2 conditions
Pseudomonas putida
0.011
-
protocatechuate
for the mutant enzyme Y408F, at 25°C in 50 mM Tris and 2 mM beta-mercaptoethanol, pH 8.5 under saturating protocatechuate and O2 conditions
Pseudomonas putida
0.13
-
protocatechuate
for the mutant enzyme Y408C, at 25°C in 50 mM Tris and 2 mM beta-mercaptoethanol, pH 8.5 under saturating protocatechuate and O2 conditions
Pseudomonas putida
100
-
protocatechuate
for the wild-type enzyme, at 25°C in 50 mM Tris and 2 mM beta-mercaptoethanol, pH 8.5 under saturating protocatechuate and O2 conditions
Pseudomonas putida
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8.5
-
maximum activity for the wild type enzyme and the mutants enymes Y408C, Y408F, Y408E and Y408H
Pseudomonas putida
Ki Value [mM]
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
additional information
-
additional information
rates (s-1) and dissociation constants (microM) for 4-hysroxybenzoate: wild type: k+2 = 42, k-2 = 14, k+2 + k-2 = 56, K1 = 700, Kd = 170, Y408H: k+2 + k-2 = 2.3, Y408C: k+2 + k-2 = 0.7, Y408F: k+2 + k-2 = 0.9; substrate dissociation constant for 3-hydroxybenzoate: wild type = 3500 microM, Y408H = 180 microM, Y408E = 210 microM, Y408C = 2500 microM, Y408F = 1800 microM; substrate dissociation constant for 4-hydroxybenzoate: wild type = 300 microM, Y408H = 6.3 microM, Y408C = 51 microM, Y408F = 12 microM
Pseudomonas putida
Cloned(Commentary) (protein specific)
Commentary
Organism
the enzyme containing the Y408E mutation is expressed in Pseudomonas fluorescens; the enzymes containing the Y408C, Y408F and Y408H mutation are expressed in Escherichia coli
Pseudomonas putida
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
Y408C
iron is tightly bound. The structure reveals no significant mutation-related changes except in the immediate vicinity of the altered amino acid (rmsd over all atoms = 0.2-0.3 A). The new amino acid does not coordinate to the iron, because the side chain is shorter than that of Tyr. In contrast to the wild-type enzyme, Tyr447 remains bound to the iron, as a result, a monodentate substrate complex is formed between the iron and protocatechuate 04. Protocatechuate does not shift into a chelated orientation. Inhibitors like 4-hydroybenzoate and 3-hydroybenzoate bind more tighly to the mutant enzyme, whereas the substrate protocatechuate binds less tightly.
Pseudomonas putida
Y408E
iron is tightly bound. The structure reveals no significant mutation-related changes except in the immediate vicinity of the altered amino acid (rmsd over all atoms = 0.2-0.3 A). The new amino acid does not coordinate to the iron, because the side chain is shorter than that of Tyr. In contrast to the wild-type enzyme, Tyr447 remains bound to the iron, as a result, a monodentate substrate complex is formed between the iron and protocatechuate 04. Protocatechuate does not shift into a chelated orientation.
Pseudomonas putida
Y408F
iron is not tightly bound, the Y408F mutant does not reconstitute above half-occupancy and loses color during crystallization attempts. Inhibitors like 4-hydroybenzoate and 3-hydroybenzoate bind more tighly to the mutant enzyme, whereas the substrate protocatechuate binds less tightly.
Pseudomonas putida
Y408H
iron is tightly bound. The structure reveals no significant mutation-related changes except in the immediate vicinity of the altered amino acid (rmsd over all atoms = 0.2-0.3 A). The new amino acid does not coordinate to the iron, because the side chain is shorter than that of Tyr. In contrast to the wild-type enzyme, Tyr447 remains bound to the iron, as a result, a monodentate substrate complex is formed between the iron and protocatechuate 04. Protocatechuate does not shift into a chelated orientation. Inhibitors like 4-hydroybenzoate and 3-hydroybenzoate bind more tighly to the mutant enzyme, whereas the substrate protocatechuate binds less tightly.
Pseudomonas putida
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
3-hydroxybenzoate
optical titration at 25°C
Pseudomonas putida
4-hydroxybenzoate
optical titration at 25°C
Pseudomonas putida
Ki Value [mM] (protein specific)
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
additional information
-
additional information
rates (s-1) and dissociation constants (microM) for 4-hysroxybenzoate: wild type: k+2 = 42, k-2 = 14, k+2 + k-2 = 56, K1 = 700, Kd = 170, Y408H: k+2 + k-2 = 2.3, Y408C: k+2 + k-2 = 0.7, Y408F: k+2 + k-2 = 0.9; substrate dissociation constant for 3-hydroxybenzoate: wild type = 3500 microM, Y408H = 180 microM, Y408E = 210 microM, Y408C = 2500 microM, Y408F = 1800 microM; substrate dissociation constant for 4-hydroxybenzoate: wild type = 300 microM, Y408H = 6.3 microM, Y408C = 51 microM, Y408F = 12 microM
Pseudomonas putida
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
additional information
-
additional information
rates (s-1) and dissocation constants (microM) for protocatechuate: Y408H: k+2 = 2.8, k-2 = 1.9, k+2 + k-2 = 4.7, K1 = 2600, Kd = 1100, Y408F: k+2 = 0.39, k-2 = 0.46, k+2 + k-2 = 0.85, K1 = 84, Kd = 45, Y408C: k+2 + k-2 = 0.67; substrate dissociation constant for protocatechuate: wild type = 2.5 microM, Y408H = 39 micro M, Y408C = 57 microM
Pseudomonas putida
Purification (Commentary) (protein specific)
Commentary
Organism
enzymes from Escherichia coli: DEAE-Sepharose Fast Flow column (5.5 x 19 cm), Phenyl-Sepharose CL-4B column (4.5 x 22.5 cm), Sephacryl S-300 column (3 x 97.5 cm); enzymes from Pseudomonas florescens
Pseudomonas putida
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3,4-dihydroxybenzoate + O2
-
671966
Pseudomonas putida
beta-carboxy-cis,cis-muconate
-
-
-
?
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.007
-
protocatechuate
for the mutant enzyme Y408H, at 25°C in 50 mM Tris and 2 mM beta-mercaptoethanol, pH 8.5 under saturating protocatechuate and O2 conditions
Pseudomonas putida
0.01
-
protocatechuate
for the mutant enzyme Y408E, at 25°C in 50 mM Tris and 2 mM beta-mercaptoethanol, pH 8.5 under saturating protocatechuate and O2 conditions
Pseudomonas putida
0.011
-
protocatechuate
for the mutant enzyme Y408F, at 25°C in 50 mM Tris and 2 mM beta-mercaptoethanol, pH 8.5 under saturating protocatechuate and O2 conditions
Pseudomonas putida
0.13
-
protocatechuate
for the mutant enzyme Y408C, at 25°C in 50 mM Tris and 2 mM beta-mercaptoethanol, pH 8.5 under saturating protocatechuate and O2 conditions
Pseudomonas putida
100
-
protocatechuate
for the wild-type enzyme, at 25°C in 50 mM Tris and 2 mM beta-mercaptoethanol, pH 8.5 under saturating protocatechuate and O2 conditions
Pseudomonas putida
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8.5
-
maximum activity for the wild type enzyme and the mutants enymes Y408C, Y408F, Y408E and Y408H
Pseudomonas putida
Other publictions for EC 1.13.11.3
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
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)
741660
Zhang
Improvement of the Stabilizat ...
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183
1035-1048
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742982
Mulla
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Biodegradation of 3-chloroben ...
Bacillus sp. (in: Bacteria), Bacillus sp. (in: Bacteria) OS13
J. Environ. Chem. Eng.
4
1423-1431
2016
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743818
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Highly efficient and stable n ...
Pseudomonas putida
Sci. Rep.
6
33572
2016
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742063
Sainsbury
Chemical intervention in bact ...
Rhodococcus jostii
Bioorg. Chem.
60
102-109
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742046
Guzik
Degradation potential of prot ...
Stenotrophomonas maltophilia, Stenotrophomonas maltophilia KB2
BioMed Res. Int.
2014
138768
2014
4
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3
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743122
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Protocatechuate 3,4-dioxygena ...
Stenotrophomonas maltophilia, Stenotrophomonas maltophilia KB2
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24
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4
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725655
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Pseudomonas pseudoalcaligenes, Pseudomonas pseudoalcaligenes KF707
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56
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726481
Da Silva
-
The effects of trace elements, ...
Leifsonia sp.
Sci. Agric. (Piracicaba, Braz.)
70
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1
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726535
Guzik
Influence of metal ions on bio ...
Stenotrophomonas maltophilia, Stenotrophomonas maltophilia KB2
World J. Microbiol. Biotechnol.
29
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2013
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712295
Zhao
PcaO positively regulates pcaH ...
Corynebacterium glutamicum
J. Bacteriol.
192
1565-1572
2010
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702976
Guzik
Isolation and characterization ...
Stenotrophomonas maltophilia, Stenotrophomonas maltophilia KB2
Braz. J. Microbiol.
40
285-291
2009
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704290
Zimmermann
Role of Acinetobacter baylyi C ...
Acinetobacter baylyi, Acinetobacter baylyi Crc
J. Bacteriol.
191
2834-2842
2009
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686803
Kim
Molecular cloning and function ...
Chromohalobacter sp. HS-2, Chromohalobacter sp. HS2
FEMS Microbiol. Lett.
280
235-241
2008
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697244
Bubinas
-
Degradation of naphthalene by ...
Geobacillus sp.
Cent. Eur. J. Biol.
3
61-68
2008
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Bubinas
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Protocatechuate 3,4-dioxygenas ...
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2007
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Pau
Spectroscopic and electronic s ...
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Deletion mutations caused by D ...
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674004
Kurahashi
Trigonal-bipyramidal geometry ...
Pseudomonas putida
Inorg. Chem.
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7709-7721
2006
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Borowski
Mechanism for Catechol Ring Cl ...
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Parulekar
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Multiple pathways for the biod ...
Pseudomonas mendocina
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85-89
2005
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671966
Valley
Roles of the equatorial tyrosy ...
Pseudomonas putida
Biochemistry
44
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2005
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1
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5
1
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677115
Shen
Key enzymes of the protocatech ...
Corynebacterium glutamicum
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48
241-249
2005
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1
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657551
Brown
Biophysical analyses of design ...
Acinetobacter sp., Pseudomonas putida
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555-585
2004
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7
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18
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7
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7
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2
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18
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695732
Buchan
Diverse organization of genes ...
Roseovarius nubinhibens ISM, Ruegeria pomeroyi, Sagittula stellata E-37, Sulfitobacter sp.
Appl. Environ. Microbiol.
70
1658-1668
2004
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4
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1
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439514
Kahng
Enhanced detection and charact ...
Acinetobacter lwoffii, Acinetobacter lwoffii K24
Biochem. Biophys. Res. Commun.
295
903-909
2002
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1
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2
1
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439513
Contzen
Cloning of the genes for a 4-s ...
Agrobacterium tumefaciens, Hydrogenophaga palleronii
Mol. Microbiol.
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199-205
2001
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2
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5
1
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439510
Buchan
Key aromatic-ring-cleaving enz ...
Roseobacter sp., Sagittula stellata
Appl. Environ. Microbiol.
66
4662-4672
2000
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1
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1
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5
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2
1
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439511
Patil
The use of protocatechuate dio ...
Burkholderia cepacia
Anal. Biochem.
286
187-192
2000
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1
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1
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1
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439512
Vetting
Structure of Acinetobacter str ...
Acinetobacter sp.
Biochemistry
39
7943-7955
2000
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1
1
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1
1
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439509
D'Argenio
Substitution, insertion, delet ...
Acinetobacter sp.
J. Bacteriol.
181
6478-6487
1999
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1
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439508
Frazee
The axial tyrosinate Fe3+ liga ...
no activity in Pseudomonas fluorescens, Pseudomonas putida
Biochemistry
37
2131-2144
1998
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1
1
1
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6
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6
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1
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1
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1
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3
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439506
Orville
Crystal structures of substrat ...
Pseudomonas putida
Biochemistry
36
10052-10066
1997
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1
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1
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1
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1
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1
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1
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439507
Orville
Cyanide and nitric oxide bindi ...
Pseudomonas putida
Biochemistry
36
14044-14055
1997
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1
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1
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1
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439505
Hammer
Purification and characterizat ...
Agrobacterium tumefaciens, Agrobacterium tumefaciens S2, Hydrogenophaga palleronii, Hydrogenophaga palleronii S1
Arch. Microbiol.
166
92-100
1996
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26
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3
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4
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4
4
5
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2
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3
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26
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3
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666009
Ohlendorf
Structure of protocatechuate 3 ...
Pseudomonas aeruginosa
J. Mol. Biol.
244
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1994
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Whittaker
Protocatechuate 3,4-dioxygenas ...
Brevibacterium fuscum
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1990
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Orville
Binding of isotopically labele ...
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439498
Wojtas-Wasilewska
-
Immobilization of protocatechu ...
Pleurotus ostreatus
Phytochemistry
27
2731-2733
1988
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439493
Ohlendorf
Determination of the quaternar ...
Pseudomonas putida
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439492
Ludwig
Characterization of crystals o ...
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Chen
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Aromatic metabolism in Rhizobi ...
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Kurane
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Protocatechuate 3,4-dioxygenas ...
Nocardia erythropolis
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48
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Whittaker
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439494
May
-
Protocatechuate 3,4-dioxygenas ...
Pseudomonas sp.
Biochemistry
22
5331-5340
1983
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439496
Walsh
Halogenated protocatechuates a ...
Burkholderia cepacia
J. Biol. Chem.
258
14413-14421
1983
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5
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439490
May
Protocatechuate 3,4-dioxygenas ...
Pseudomonas putida
J. Biol. Chem.
257
12746-12751
1982
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1
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439491
Iwaki
The primary structure of the b ...
Pseudomonas aeruginosa
Arch. Biochem. Biophys.
210
210-223
1981
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439504
Bull
Purification and properties of ...
Pseudomonas putida
J. Biol. Chem.
256
12673-12680
1981
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5
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439501
Durham
Intergeneric evolutionary homo ...
Azotobacter vinelandii
Biochemistry
19
149-155
1980
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9
2
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4
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665455
Satyshur
Preliminary crystallographic s ...
Pseudomonas aeruginosa
J. Biol. Chem.
255
10015-10016
1980
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439488
Mohan
-
Purification and properties of ...
Tecoma stans
Plant Sci. Lett.
16
267-272
1979
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2
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439489
Kohlmiller
The primary structure of the a ...
Pseudomonas putida
J. Biol. Chem.
254
7302-7308
1979
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439495
May
Protocatechuate 3,4-dioxygenas ...
Pseudomonas aeruginosa
Biochemistry
18
5933-5939
1979
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6
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439487
May
Interaction of protocatechuate ...
Pseudomonas putida
Biochemistry
17
1853-1860
1978
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439486
Que
Protocatechuate 3,4-dioxygenas ...
Pseudomonas putida
Biochim. Biophys. Acta
485
60-74
1977
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13
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439500
Hou
Protocatechuate 3, 4-dioxygena ...
Acinetobacter calcoaceticus, Acinetobacter calcoaceticus 80-1
Biochemistry
15
582-588
1976
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2
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19
7
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439485
Zaborsky
Immobilization of protocatechu ...
Pseudomonas aeruginosa
Biochim. Biophys. Acta
289
68-76
1972
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439480
Gibson
-
Assay of enzymes of aromatic m ...
Pseudomonas sp.
Methods Enzymol.
6A
463-478
1971
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439483
Fujisawa
Protocatechuate 3,4-dioxygenas ...
Pseudomonas aeruginosa, Pseudomonas aeruginosa B-10
J. Biol. Chem.
243
2673-2681
1968
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11
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439481
Stanier
Protocatechuic acid oxidase ...
Pseudomonas fluorescens, Pseudomonas fluorescens A.3.12.
J. Biol. Chem.
210
799-808
1954
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439482
Gross
The metabolism of protocatechu ...
Neurospora crassa
J. Biol. Chem.
219
781-796
1954
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2
3
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