BRENDA - Enzyme Database
show all sequences of 1.7.2.4

Role of calcium in secondary structure stabilization during maturation of nitrous oxide reductase

Schneider, L.K.; Einsle, O.; Biochemistry 55, 1433-1440 (2016)

Data extracted from this reference:

Cloned(Commentary)
Cloned (Commentary)
Organism
codon-optimized gene nosZ, from canonical gene cluster nosRZDFYL(X), recombinant overexpression of His6-tagged enzyme and of Strep-tagged enzyme in Escherichia coli strain BL21(DE3)
Shewanella denitrificans
Crystallization (Commentary)
Crystallization (Commentary)
Organism
purified enzyme, sitting drop vapor diffusion method, for His6-tagged Ca2+-bound apo-N2OR enzyme: mixing of 0.0003 ml of 15mg/ml protein solution with 0.0003 ml of well solution containing PEG 3350, 0.2 M ammonium sulfate, and 0.1 M Bis-Tris-HCl, pH 5.5, for Strep-tagged Ca2+-free or -bound apo-N2OR: mixing of 0.0003 ml of 15mg/ml protein solution with 0.0003 ml of well solution containing 25% w/v PEG 3350, 0.2 M lithium sulfate monohydrate, and 0.1 M Tris-HCl, pH 8.5, 7 days, 25C, X-ray diffraction structure determination and analysis, molecular replacement and modelling using structure PDB ID 3SBQ as template. No crystals are obtained for Ca2+-free His6-tagged apo-N2OR
Shewanella denitrificans
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
periplasm
the enzyme contains a signal peptide with the twin-arginine motif S-RR-S-F-M-G that is required for Tat-dependent translocation to the periplasm
Shewanella denitrificans
-
-
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Ca2+
single Ca2+ ion binds to the Ca2+-binding loop coordinated by residues Y251, E255, M263, D269, and S316 and a water molecule, Ca2+ plays a role in secondary structure stabilization during maturation of nitrous oxide reductase, required for structural stability of the binuclear CuA site
Shewanella denitrificans
Cu2+
involved in catalysis. In the absence of Ca2+, substantial parts of the enzyme surrounding the binding sites for the copper ions show structural disorder. Reconstitution of the binuclear CuA site was possible in vitro but required the presence of Ca2+ ions for a stable insertion of the center
Shewanella denitrificans
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
130000
-
gel filtration
Shewanella denitrificans
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
nitrous oxide + 2 reduced cytochrome c
Shewanella denitrificans
-
nitrogen + H2O + 2 cytochrome c
-
-
?
nitrous oxide + 2 reduced cytochrome c
Shewanella denitrificans OS217
-
nitrogen + H2O + 2 cytochrome c
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Shewanella denitrificans
Q12M27
-
-
Shewanella denitrificans OS217
Q12M27
-
-
Purification (Commentary)
Purification (Commentary)
Organism
recombinant His6-tagged enzyme and Strep-tagged enzyme from Escherichia coli strain BL21(DE3) with or without bound calcium by metal affinity and streptavidin chromatography, respectively, followed by gel filtration
Shewanella denitrificans
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
nitrous oxide + 2 reduced cytochrome c
-
741924
Shewanella denitrificans
nitrogen + H2O + 2 cytochrome c
-
-
-
?
nitrous oxide + 2 reduced cytochrome c
the copper enzyme nitrous oxide reductase catalyzes the two-electron reduction of nitrous oxide (N2O) to dinitrogen
741924
Shewanella denitrificans
nitrogen + H2O + 2 cytochrome c
-
-
-
?
nitrous oxide + 2 reduced cytochrome c
-
741924
Shewanella denitrificans OS217
nitrogen + H2O + 2 cytochrome c
-
-
-
?
nitrous oxide + 2 reduced cytochrome c
the copper enzyme nitrous oxide reductase catalyzes the two-electron reduction of nitrous oxide (N2O) to dinitrogen
741924
Shewanella denitrificans OS217
nitrogen + H2O + 2 cytochrome c
-
-
-
?
Subunits
Subunits
Commentary
Organism
homodimer
2 * 64810, maturated enzyme, sequence calculation, a homodimer with a distinct two-domain architecture in the protomer
Shewanella denitrificans
More
calcium plays a role in secondary structure stabilization during maturation of nitrous oxide reductase. The enzyme contains a signal peptide with the twin-arginine motif S-RR-S-F-M-G that is required for Tat-dependent translocation to the periplasm. Three-dimensional structure analysis, overview
Shewanella denitrificans
Synonyms
Synonyms
Commentary
Organism
N2OR
-
Shewanella denitrificans
nitrous oxide reductase
-
Shewanella denitrificans
NosZ
-
Shewanella denitrificans
Sden_2219
-
Shewanella denitrificans
SdN2OR
-
Shewanella denitrificans
Z-type N2OR
-
Shewanella denitrificans
Cofactor
Cofactor
Commentary
Organism
Structure
cytochrome c
-
Shewanella denitrificans
Cloned(Commentary) (protein specific)
Commentary
Organism
codon-optimized gene nosZ, from canonical gene cluster nosRZDFYL(X), recombinant overexpression of His6-tagged enzyme and of Strep-tagged enzyme in Escherichia coli strain BL21(DE3)
Shewanella denitrificans
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
cytochrome c
-
Shewanella denitrificans
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified enzyme, sitting drop vapor diffusion method, for His6-tagged Ca2+-bound apo-N2OR enzyme: mixing of 0.0003 ml of 15mg/ml protein solution with 0.0003 ml of well solution containing PEG 3350, 0.2 M ammonium sulfate, and 0.1 M Bis-Tris-HCl, pH 5.5, for Strep-tagged Ca2+-free or -bound apo-N2OR: mixing of 0.0003 ml of 15mg/ml protein solution with 0.0003 ml of well solution containing 25% w/v PEG 3350, 0.2 M lithium sulfate monohydrate, and 0.1 M Tris-HCl, pH 8.5, 7 days, 25C, X-ray diffraction structure determination and analysis, molecular replacement and modelling using structure PDB ID 3SBQ as template. No crystals are obtained for Ca2+-free His6-tagged apo-N2OR
Shewanella denitrificans
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
periplasm
the enzyme contains a signal peptide with the twin-arginine motif S-RR-S-F-M-G that is required for Tat-dependent translocation to the periplasm
Shewanella denitrificans
-
-
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Ca2+
single Ca2+ ion binds to the Ca2+-binding loop coordinated by residues Y251, E255, M263, D269, and S316 and a water molecule, Ca2+ plays a role in secondary structure stabilization during maturation of nitrous oxide reductase, required for structural stability of the binuclear CuA site
Shewanella denitrificans
Cu2+
involved in catalysis. In the absence of Ca2+, substantial parts of the enzyme surrounding the binding sites for the copper ions show structural disorder. Reconstitution of the binuclear CuA site was possible in vitro but required the presence of Ca2+ ions for a stable insertion of the center
Shewanella denitrificans
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
130000
-
gel filtration
Shewanella denitrificans
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
nitrous oxide + 2 reduced cytochrome c
Shewanella denitrificans
-
nitrogen + H2O + 2 cytochrome c
-
-
?
nitrous oxide + 2 reduced cytochrome c
Shewanella denitrificans OS217
-
nitrogen + H2O + 2 cytochrome c
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His6-tagged enzyme and Strep-tagged enzyme from Escherichia coli strain BL21(DE3) with or without bound calcium by metal affinity and streptavidin chromatography, respectively, followed by gel filtration
Shewanella denitrificans
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
nitrous oxide + 2 reduced cytochrome c
-
741924
Shewanella denitrificans
nitrogen + H2O + 2 cytochrome c
-
-
-
?
nitrous oxide + 2 reduced cytochrome c
the copper enzyme nitrous oxide reductase catalyzes the two-electron reduction of nitrous oxide (N2O) to dinitrogen
741924
Shewanella denitrificans
nitrogen + H2O + 2 cytochrome c
-
-
-
?
nitrous oxide + 2 reduced cytochrome c
-
741924
Shewanella denitrificans OS217
nitrogen + H2O + 2 cytochrome c
-
-
-
?
nitrous oxide + 2 reduced cytochrome c
the copper enzyme nitrous oxide reductase catalyzes the two-electron reduction of nitrous oxide (N2O) to dinitrogen
741924
Shewanella denitrificans OS217
nitrogen + H2O + 2 cytochrome c
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
homodimer
2 * 64810, maturated enzyme, sequence calculation, a homodimer with a distinct two-domain architecture in the protomer
Shewanella denitrificans
More
calcium plays a role in secondary structure stabilization during maturation of nitrous oxide reductase. The enzyme contains a signal peptide with the twin-arginine motif S-RR-S-F-M-G that is required for Tat-dependent translocation to the periplasm. Three-dimensional structure analysis, overview
Shewanella denitrificans
General Information
General Information
Commentary
Organism
malfunction
involved in catalysis. In the absence of Ca2+, substantial parts of the enzyme surrounding the binding sites for the copper ions show structural disorder. Reconstitution of the binuclear CuA site was possible in vitro but required the presence of Ca2+ ions for a stable insertion of the center
Shewanella denitrificans
additional information
SdN2OR is a Z-type N2OR, structure modelling
Shewanella denitrificans
General Information (protein specific)
General Information
Commentary
Organism
malfunction
involved in catalysis. In the absence of Ca2+, substantial parts of the enzyme surrounding the binding sites for the copper ions show structural disorder. Reconstitution of the binuclear CuA site was possible in vitro but required the presence of Ca2+ ions for a stable insertion of the center
Shewanella denitrificans
additional information
SdN2OR is a Z-type N2OR, structure modelling
Shewanella denitrificans
Other publictions for EC 1.7.2.4
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)
742390
Sanchez
Regulation of nitrous oxide r ...
Bradyrhizobium diazoefficiens
Environ. Microbiol. Rep.
9
389-396
2017
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1
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3
2
2
3
-
-
742753
Johnston
Spectroscopic definition of t ...
Marinobacter hydrocarbonoclasticus, Marinobacter hydrocarbonoclasticus 617
J. Am. Chem. Soc.
139
4462-4476
2017
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-
-
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1
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1
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1
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741924
Schneider
Role of calcium in secondary ...
Shewanella denitrificans, Shewanella denitrificans OS217
Biochemistry
55
1433-1440
2016
-
-
1
1
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2
1
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4
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2
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4
2
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2
2
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-
742384
Qu
Transcriptional and metabolic ...
Paracoccus denitrificans
Environ. Microbiol.
18
2951-2963
2016
-
-
1
-
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1
-
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1
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1
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3
1
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1
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2
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1
1
1
1
-
-
741746
Zhang
Response of denitrifying gene ...
uncultured bacterium
Appl. Microbiol. Biotechnol.
99
4059-4070
2015
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1
-
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1
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-
-
-
-
-
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1
1
1
1
-
-
742272
Johnston
Protonation state of the Cu4S ...
Paracoccus pantotrophus, Pseudomonas stutzeri
Chem. Sci.
6
5670-5679
2015
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741677
Wyman
Denitrifying alphaproteobacte ...
alpha proteobacterium 4N, Trichodesmium erythraeum, Trichodesmium erythraeum IMS01, uncultured Alphaproteobacteria bacterium
Appl. Environ. Microbiol.
79
2670-2681
2013
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3
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8
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3
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4
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6
6
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725551
Ertem
N-O bond cleavage mechanism(s) ...
Paracoccus denitrificans
J. Biol. Inorg. Chem.
17
687-698
2012
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725648
Fujita
Direct electron transfer from ...
Achromobacter cycloclastes
J. Inorg. Biochem.
115
163-173
2012
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3
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1
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4
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2
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726100
DellAcqua
Biochemical characterization o ...
Marinobacter hydrocarbonoclasticus
Philos. Trans. R. Soc. Lond. B Biol. Sci.
367
1204-1212
2012
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726523
Wan
Expression of the nos operon p ...
Pseudomonas stutzeri, Pseudomonas stutzeri ATCC 14405
Transgenic Res.
21
593-603
2012
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724958
Fernandes
The multicopper oxidase from t ...
Pyrobaculum aerophilum
FEBS J.
277
3176-3189
2010
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2
2
700984
Savelieff
Experimental evidence for a li ...
Paracoccus denitrificans
Proc. Natl. Acad. Sci. USA
105
7919-7924
2008
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698268
Fujita
Insights into the mechanism of ...
Achromobacter cycloclastes
Inorg. Chem.
46
613-615
2007
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1
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1
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698456
Ghosh
Spectroscopic, computational, ...
Achromobacter cycloclastes, Marinobacter hydrocarbonoclasticus
J. Am. Chem. Soc.
129
3955-3965
2007
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6
2
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699384
Fujita
Anaerobic purification, charac ...
Achromobacter cycloclastes, Achromobacter cycloclastes IAM1013
J. Inorg. Biochem.
101
1836-1844
2007
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700303
Bingham
-
Magnetic circular dichroism an ...
Paracoccus pantotrophus
Mol. Phys.
105
2169-2176
2007
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671444
Horn
Nitrous oxide reductase genes ...
Dechloromonas denitrificans, Flavobacterium denitrificans, Pseudomonas sp., Pseudomonas sp. ED3
Appl. Environ. Microbiol.
72
1019-1026
2006
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671455
Sameshima-Saito
Symbiotic Bradyrhizobium japon ...
Bradyrhizobium japonicum, Bradyrhizobium japonicum USDA 110
Appl. Environ. Microbiol.
72
2526-2532
2006
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671469
Henry
Quantitative detection of the ...
Achromobacter cycloclastes, Alcaligenes faecalis, Bradyrhizobium japonicum, Ensifer adhaerens, Ensifer adhaerens SN611, Hyphomicrobium denitrificans, Pseudomonas denitrificans (nomen rejiciendum), Pseudomonas denitrificans (nomen rejiciendum) CCUG 2519, Pseudomonas fluorescens, Pseudomonas fluorescens C7R12, Sinorhizobium meliloti, Sinorhizobium meliloti 50
Appl. Environ. Microbiol.
72
5181-5189
2006
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12
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672074
Taubner
Structural studies of Apo NosL ...
Achromobacter cycloclastes
Biochemistry
45
12240-12252
2006
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1
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674195
Gorelsky
Mechanism of N2O reduction by ...
Pseudomonas sp.
J. Am. Chem. Soc.
128
278-290
2006
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675403
Paraskevopoulos
Insight into catalysis of nitr ...
Achromobacter cycloclastes 1013, Achromobacter cycloclastes
J. Mol. Biol.
362
55-65
2006
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660478
Mattila
How does nitrous oxide reducta ...
Paracoccus denitrificans, Rhodobacter sphaeroides
Proteins
59
708-722
2005
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2
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4
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5
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673234
Rasmussen
Formation of a cytochrome c-ni ...
Paracoccus pantotrophus
Dalton Trans.
2005
3501-3506
2005
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1
1
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4
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673622
Wunsch
NosX function connects to nitr ...
Paracoccus denitrificans
FEBS Lett.
579
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2005
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657567
Velasco
Molecular characterization of ...
Bradyrhizobium japonicum
Antonie van Leeuwenhoek
85
229-235
2004
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658979
Chan
Reductively activated nitrous ...
Achromobacter cycloclastes
J. Am. Chem. Soc.
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2004
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394516
Haltia
The crystal structure of nitro ...
Paracoccus denitrificans
Biochem. J.
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2003
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1
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659085
Yamaguchi
Characterization of nitrous ox ...
Hyphomicrobium denitrificans, Hyphomicrobium denitrificans A3151
J. Biochem.
134
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2003
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4
1
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1
1
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659880
Arai
Transcriptional regulation of ...
Pseudomonas aeruginosa
Microbiology
149
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2003
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1
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1
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1
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394517
Rasmussen
Multiple forms of the catalyti ...
Paracoccus pantotrophus
Biochem. J.
364
807-815
2002
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5
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2
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394518
Rasmussen
The catalytic center in nitrou ...
Paracoccus pantotrophus, Pseudomonas stutzeri
Biochemistry
39
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2000
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2
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1
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2
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2
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2
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2
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2
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394519
Prudencio
Purification, Characterization ...
Marinobacter hydrocarbonoclasticus, Marinobacter hydrocarbonoclasticus 617
Biochemistry
39
3899-3907
2000
-
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1
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1
3
2
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6
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1
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1
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2
-
2
1
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394520
Brown
A novel type of catalytic copp ...
Marinobacter hydrocarbonoclasticus, Marinobacter hydrocarbonoclasticus 617
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7
191-195
2000
-
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1
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1
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7
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1
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2
1
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394521
Sato
Anaerobic purification and cha ...
Rhodobacter sphaeroides
J. Biochem.
125
864-868
1999
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1
1
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1
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1
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2
1
2
1
1
-
1
-
1
-
-
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-
-
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394522
Sabaty
Nitrite and nitrous oxide redu ...
Rhodobacter sphaeroides
J. Bacteriol.
181
6028-6032
1999
1
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1
-
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-
-
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-
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394523
Ferretti
Biochemical characterization a ...
Achromobacter xylosoxidans
Eur. J. Biochem.
259
651-659
1999
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1
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2
1
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1
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1
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394524
Sato
Characterization of a multi-co ...
Rhodobacter sphaeroides
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3
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1
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3
1
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1
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2
1
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-
-
-
-
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394525
Farrar
CuA and CuZ are variants of th ...
Pseudomonas stutzeri
Proc. Natl. Acad. Sci. USA
95
9891-9896
1998
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1
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1
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-
-
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394526
Hole
Characterization of the membra ...
Thiobacillus denitrificans
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1996
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1
1
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1
2
1
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1
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1
1
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-
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394527
Dreusch
Mutation of the conserved Cys1 ...
Pseudomonas stutzeri
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1
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1
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394528
Zhang
-
The reaction of reduced cytoch ...
Wolinella succinogenes
Biochim. Biophys. Acta
1142
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1993
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394529
Berks
Purification and characterizat ...
Paracoccus pantotrophus, Paracoccus pantotrophus LMD 82.5
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4
1
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1
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3
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1
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3
3
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1
3
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1
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4
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4
1
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1
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665462
SooHoo
Purification and characterizat ...
Pseudomonas aeruginosa, Pseudomonas aeruginosa P2
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266
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Jones
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Denitrification in Flexibacter ...
Solitalea canadensis
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394531
Hulse
Isolation of a high specific a ...
Achromobacter cycloclastes
Biochem. Biophys. Res. Commun.
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1990
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Bonin
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Effects of oxygen on each step ...
Marinobacter hydrocarbonoclasticus
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394533
Teraguchi
Purification and some characte ...
Wolinella succinogenes
J. Biol. Chem.
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1989
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394534
Viebrock
Molecular cloning, heterologou ...
Pseudomonas stutzeri
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1988
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394535
Coyne
Nitrous oxide reduction in nod ...
Rhizobium sp., Rhizobium sp. 8A55
Appl. Environ. Microbiol.
53
1168-1170
1987
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394536
Snyder
Purification and some characte ...
Paracoccus denitrificans
J. Biol. Chem.
262
6515-6525
1987
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1
1
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394538
Michalski
-
Purification and characterizat ...
Rhodobacter sphaeroides
Biochim. Biophys. Acta
872
50-60
1986
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394542
Aida
Temporary low oxygen condition ...
Pseudomonas sp., Pseudomonas sp. G59
Can. J. Microbiol.
32
543-547
1986
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394539
Coyle
Nitrous oxide reductase from d ...
Pseudomonas stutzeri
Eur. J. Biochem.
153
459-467
1985
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1
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2
1
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1
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394540
McEwan
Nitrous oxide reduction by mem ...
Rhodobacter capsulatus, Rhodobacter sphaeroides, Rhodopseudomonas palustris, Rhodopseudomonas palustris PW5, Rhodospirillum rubrum, Rhodospirillum rubrum S1
J. Bacteriol.
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823-830
1985
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6
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6
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394537
Kucera
-
Amperometric assay of activity ...
Paracoccus denitrificans
Collect. Czech. Chem. Commun.
49
2709-2712
1984
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394541
Snyder
Nitrous oxide reductase and th ...
Paracoccus denitrificans, Pseudomonas denitrificans (nomen rejiciendum), Pseudomonas stutzeri
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119
588-592
1984
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6
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394543
Zumft
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A novel kind of multi-copper p ...
Pseudomonas stutzeri
FEBS Lett.
148
107-112
1982
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Matsubara
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Identification of a copper pro ...
Pseudomonas fluorescens
Arch. Microbiol.
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322-328
1982
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394545
Kristjansson
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Partial purification and chara ...
Paracoccus denitrificans
Curr. Microbiol.
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247-251
1981
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Kristjansson
First practical assay for solu ...
Paracoccus denitrificans
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255
704-707
1980
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