BRENDA - Enzyme Database
show all sequences of 1.13.11.66

Crystal structure of PnpCD, a two-subunit hydroquinone 1,2-dioxygenase, reveals a novel structural class of Fe2+-dependent dioxygenases

Liu, S.; Su, T.; Zhang, C.; Zhang, W.M.; Zhu, D.; Su, J.; Wei, T.; Wang, K.; Huang, Y.; Guo, L.; Xu, S.; Zhou, N.Y.; Gu, L.; J. Biol. Chem. 290, 24547-24560 (2015)

Data extracted from this reference:

Cloned(Commentary)
Cloned (Commentary)
Organism
genes pnpCD, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
Pseudomonas sp.
Crystallization (Commentary)
Crystallization (Commentary)
Organism
purified full-length or proteolytically truncated PnpCD in apo form and in complex with Fe3+ or substrate analogue hydroxybenzonitrile and Cd2+, i.e. apo-PnpCD, PnpCD-Fe3+, and PnpCD-Cd2+-HBN, sitting-drop vapor diffusion method, 15-20 mg/ml protein in 10mM Tris-HCl, pH 8.0, and 100 mM NaCl, is mixed with reservoir solution containing 0.2 M sodium thiocyanate, 20% w/v PEG 3350, 20°C, method optimization, X-ray diffraction structure determination and analysis
Pseudomonas sp.
Engineering
Protein Variants
Commentary
Organism
E248Q
site-directed mutagenesis, the mutation results in complete loss of enzyme activity
Pseudomonas sp.
F264A
site-directed mutagenesis, the mutation results in almost complete loss of enzyme activity
Pseudomonas sp.
F79A
site-directed mutagenesis, the mutation results in almost complete loss of enzyme activity
Pseudomonas sp.
L252A
site-directed mutagenesis, the mutation results in a 70% loss of enzyme activity
Pseudomonas sp.
L313A
site-directed mutagenesis, the mutation results in almost complete loss of enzyme activity
Pseudomonas sp.
V315A
site-directed mutagenesis, the mutation results in a 50% loss of enzyme activity
Pseudomonas sp.
W230A
site-directed mutagenesis, the mutation results in a 70% loss of enzyme activity
Pseudomonas sp.
W273a
site-directed mutagenesis, the mutation results in almost complete loss of enzyme activity
Pseudomonas sp.
W76A
site-directed mutagenesis, the mutation results in almost complete loss of enzyme activity
Pseudomonas sp.
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Fe2+
a Fe2+-dependent dioxygenase, selectively utilizes Fe2+for its catalytic reaction. Four residues of enzyme PnpD, His256, Asn258, Glu262, and His303, coordinate the iron ion
Pseudomonas sp.
Fe3+
binding structure, overview
Pseudomonas sp.
additional information
Fe3+, Mn2+, Co2+, Ni2+, Cu2+, and Cd2+ cannot substitute for Fe2+
Pseudomonas sp.
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
4-nitrophenol + O2
Pseudomonas sp.
-
?
-
-
?
benzene-1,4-diol + O2
Pseudomonas sp.
-
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Pseudomonas sp.
C1I210 AND C1I209
beta- and alpha-subunit
-
Purification (Commentary)
Purification (Commentary)
Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
Pseudomonas sp.
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
4-nitrophenol + O2
-
745331
Pseudomonas sp.
?
-
-
-
?
benzene-1,4-diol + O2
-
745331
Pseudomonas sp.
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
-
-
-
?
Subunits
Subunits
Commentary
Organism
heterotetramer
2 * 38300, subunit alpha, + 2 * 18000, subunit beta
Pseudomonas sp.
More
the PnpCD structure contains a pseudo cupin and an iron metallocenter in the catalytic PnpD. Both the PnpC and the C-terminal domains of PnpD comprise a conserved cupin fold, whereas PnpC cannot form a competent metal binding pocket as can PnpD cupin, structure analysis, overview
Pseudomonas sp.
Synonyms
Synonyms
Commentary
Organism
PnpCD
-
Pseudomonas sp.
two-subunit hydroquinone 1,2-dioxygenase
-
Pseudomonas sp.
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Pseudomonas sp.
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Pseudomonas sp.
Cloned(Commentary) (protein specific)
Commentary
Organism
genes pnpCD, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
Pseudomonas sp.
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified full-length or proteolytically truncated PnpCD in apo form and in complex with Fe3+ or substrate analogue hydroxybenzonitrile and Cd2+, i.e. apo-PnpCD, PnpCD-Fe3+, and PnpCD-Cd2+-HBN, sitting-drop vapor diffusion method, 15-20 mg/ml protein in 10mM Tris-HCl, pH 8.0, and 100 mM NaCl, is mixed with reservoir solution containing 0.2 M sodium thiocyanate, 20% w/v PEG 3350, 20°C, method optimization, X-ray diffraction structure determination and analysis
Pseudomonas sp.
Engineering (protein specific)
Protein Variants
Commentary
Organism
E248Q
site-directed mutagenesis, the mutation results in complete loss of enzyme activity
Pseudomonas sp.
F264A
site-directed mutagenesis, the mutation results in almost complete loss of enzyme activity
Pseudomonas sp.
F79A
site-directed mutagenesis, the mutation results in almost complete loss of enzyme activity
Pseudomonas sp.
L252A
site-directed mutagenesis, the mutation results in a 70% loss of enzyme activity
Pseudomonas sp.
L313A
site-directed mutagenesis, the mutation results in almost complete loss of enzyme activity
Pseudomonas sp.
V315A
site-directed mutagenesis, the mutation results in a 50% loss of enzyme activity
Pseudomonas sp.
W230A
site-directed mutagenesis, the mutation results in a 70% loss of enzyme activity
Pseudomonas sp.
W273a
site-directed mutagenesis, the mutation results in almost complete loss of enzyme activity
Pseudomonas sp.
W76A
site-directed mutagenesis, the mutation results in almost complete loss of enzyme activity
Pseudomonas sp.
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
a Fe2+-dependent dioxygenase, selectively utilizes Fe2+for its catalytic reaction. Four residues of enzyme PnpD, His256, Asn258, Glu262, and His303, coordinate the iron ion
Pseudomonas sp.
Fe3+
binding structure, overview
Pseudomonas sp.
additional information
Fe3+, Mn2+, Co2+, Ni2+, Cu2+, and Cd2+ cannot substitute for Fe2+
Pseudomonas sp.
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
4-nitrophenol + O2
Pseudomonas sp.
-
?
-
-
?
benzene-1,4-diol + O2
Pseudomonas sp.
-
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
Pseudomonas sp.
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
4-nitrophenol + O2
-
745331
Pseudomonas sp.
?
-
-
-
?
benzene-1,4-diol + O2
-
745331
Pseudomonas sp.
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
heterotetramer
2 * 38300, subunit alpha, + 2 * 18000, subunit beta
Pseudomonas sp.
More
the PnpCD structure contains a pseudo cupin and an iron metallocenter in the catalytic PnpD. Both the PnpC and the C-terminal domains of PnpD comprise a conserved cupin fold, whereas PnpC cannot form a competent metal binding pocket as can PnpD cupin, structure analysis, overview
Pseudomonas sp.
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Pseudomonas sp.
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Pseudomonas sp.
General Information
General Information
Commentary
Organism
metabolism
the two-subunit hydroquinone 1,2-dioxygenase PnpCD is the ring cleavage enzyme in para-nitrophenol catabolism
Pseudomonas sp.
additional information
the PnpCD structure contains a pseudo cupin and a iron metallocenter in the catalytic PnpD, which adds to understanding of the ring cleavage mechanism of dioxygenases, structure analysis, overview
Pseudomonas sp.
physiological function
hydroquinone 1,2-dioxygenase PnpCD is the key enzyme in the hydroquinone pathway of para-nitrophenol degradation, catalyzes the ring cleavage of hydroquinone to gamma-hydroxymuconic semialdehyde
Pseudomonas sp.
General Information (protein specific)
General Information
Commentary
Organism
metabolism
the two-subunit hydroquinone 1,2-dioxygenase PnpCD is the ring cleavage enzyme in para-nitrophenol catabolism
Pseudomonas sp.
additional information
the PnpCD structure contains a pseudo cupin and a iron metallocenter in the catalytic PnpD, which adds to understanding of the ring cleavage mechanism of dioxygenases, structure analysis, overview
Pseudomonas sp.
physiological function
hydroquinone 1,2-dioxygenase PnpCD is the key enzyme in the hydroquinone pathway of para-nitrophenol degradation, catalyzes the ring cleavage of hydroquinone to gamma-hydroxymuconic semialdehyde
Pseudomonas sp.
Other publictions for EC 1.13.11.66
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)
744430
Ferraroni
The crystal structures of nat ...
Sphingomonas sp., Sphingomonas sp. TTNP3
Biochim. Biophys. Acta
1865
520-530
2017
-
-
-
1
-
-
2
-
-
1
-
2
-
8
-
-
-
1
-
-
-
-
6
2
2
1
-
-
-
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
2
-
-
-
1
-
2
-
-
-
-
-
-
-
-
6
2
1
-
-
-
1
-
-
-
-
1
1
-
-
-
745331
Liu
Crystal structure of PnpCD, a ...
Pseudomonas sp.
J. Biol. Chem.
290
24547-24560
2015
-
-
1
1
9
-
-
-
-
3
-
2
-
1
-
-
1
-
-
-
-
-
2
2
2
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
1
9
-
-
-
-
-
-
3
-
2
-
-
-
1
-
-
-
-
2
2
1
-
-
-
1
-
-
-
-
3
3
-
-
-
745802
Mancini
A copper-induced quinone degr ...
Lactococcus lactis, Lactococcus lactis IL1403
Mol. Microbiol.
95
645-659
2015
-
-
1
-
-
1
1
1
-
2
-
6
-
13
-
-
1
-
-
-
-
-
11
1
3
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
1
-
1
-
1
-
2
-
6
-
-
-
1
-
-
-
-
11
1
1
-
-
-
1
-
-
-
1
1
1
1
-
-
719179
Zhang
Identification of the para-nit ...
Pseudomonas sp.
BMC Microbiol.
12
27
2012
-
-
1
-
-
-
-
-
-
-
1
-
-
8
-
-
1
-
-
-
-
-
2
-
2
1
1
1
-
1
1
2
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
1
-
-
-
-
2
-
1
1
1
-
1
1
2
-
-
-
-
-
-
-
718555
Kolvenbach
Purification and characterizat ...
Sphingomonas sp., Sphingomonas sp. TTNP3
AMB Express
1
08
2011
-
-
-
-
-
-
9
2
-
1
6
-
-
9
-
-
2
-
-
-
2
-
32
2
-
-
-
-
2
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
18
-
2
-
1
6
-
-
-
-
2
-
-
2
-
32
2
-
-
-
2
-
2
-
-
-
-
-
-
2
2
718916
Machonkin
Substrate specificity of Sphin ...
Sphingobium chlorophenolicum
Biochemistry
50
8899-8913
2011
-
-
-
-
-
-
3
12
-
-
-
-
-
1
-
-
-
-
-
-
-
-
8
-
-
-
-
-
9
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
3
-
12
-
-
-
-
-
-
-
-
-
-
-
-
8
-
-
-
-
9
-
-
-
-
-
-
-
-
9
9
719104
Shen
Cloning and characterization o ...
Pseudomonas putida, Pseudomonas putida DLL-E4
Biores. Technol.
101
7516-7522
2010
-
-
-
-
2
-
-
-
-
-
2
-
-
7
-
-
-
-
-
-
-
-
4
2
2
-
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-
2
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2
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-
-
4
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
719327
Yin
Characterization of MnpC, a hy ...
Cupriavidus necator, Cupriavidus necator JMP 134-1
Curr. Microbiol.
61
471-476
2010
-
-
1
-
-
-
-
1
-
2
1
-
-
28
-
-
-
-
-
-
1
3
4
1
1
-
-
-
-
1
1
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1
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1
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2
1
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1
3
4
1
-
-
-
-
1
1
-
-
-
-
-
-
-
-
720066
Machonkin
Determination of the active si ...
Sphingobium chlorophenolicum
J. Biol. Inorg. Chem.
15
291-301
2010
-
-
1
1
5
-
-
-
-
1
-
-
-
1
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-
-
-
-
-
-
-
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-
1
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1
-
1
5
-
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1
-
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-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
719714
Moonen
Hydroquinone dioxygenase from ...
Pseudomonas fluorescens, Pseudomonas fluorescens ACB
J. Bacteriol.
190
5199-5209
2008
1
-
-
-
-
-
12
1
-
1
3
-
-
13
-
-
1
-
-
-
1
-
14
1
-
-
-
-
1
1
-
-
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1
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-
1
-
-
-
-
-
-
-
12
1
1
-
1
3
-
-
-
-
1
-
-
1
-
14
1
-
-
-
1
1
-
-
-
-
-
-
-
-
-
718727
Xun
Characterization of 2,6-dichlo ...
Sphingobium chlorophenolicum
Biochem. Biophys. Res. Commun.
266
322-325
1999
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-
1
-
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1
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1
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1
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2
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1
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1
1
1
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1
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1
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1
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-
-
2
-
-
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-
1
1
1
-
-
-
-
-
-
-
-
718831
Xu
Evidence that pcpA encodes 2,6 ...
Sphingobium chlorophenolicum
Biochemistry
38
7659-7669
1999
-
-
-
-
-
-
-
-
-
2
1
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1
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1
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1
1
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1
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1
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1
1
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-
-
-
-
-
719693
Miyauchi
Cloning and sequencing of a no ...
Sphingomonas paucimobilis
J. Bacteriol.
181
6712-6719
1999
-
-
1
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3
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1
1
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1
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2
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3
1
1
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1
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3
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1
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3
1
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