BRENDA - Enzyme Database
show all sequences of 1.9.6.1

Characterization of a periplasmic nitrate reductase in complex with its biosynthetic chaperone

Dow, J.M.; Grahl, S.; Ward, R.; Evans, R.; Byron, O.; Norman, D.G.; Palmer, T.; Sargent, F.; FEBS J. 281, 246-260 (2014)

Data extracted from this reference:

Activating Compound
Activating Compound
Commentary
Organism
Structure
NapD
a small (9.3 kDa) cytoplasmic protein that is essential for Nap activity, role for NapD in the insertion of the molybdenum cofactor. The NapD cysteine residues (C8 and C32) are not conserved and a cysteine-free variant of NapD complements a DELTAnapD strain for restoration of NapA activity. A NapD C8S/C32A variant remains attached to the NapA signal peptide. Copurification of recombinant NapA complexed with N-terminally His-tagged NapD activator by nickel afinity chromatography
Escherichia coli
Cloned(Commentary)
Commentary
Organism
gene napA, enzyme NapA is encoded, along with its periplasmic di-heme c-type cytochrome redox partner NapB, in the seven gene nap operon, coexpression of NapA with His-tagged NapD activator in Escherichia coli strains MC4100 and BL21(DE3), recombinant expression of MTSL-labelled MalE-NapASP fusion mutant S4C/S24C in Escherichia coli strain BL21(DE3), subcloning in Escherichia coli strain LCB2048
Escherichia coli
Crystallization (Commentary)
Crystallization
Organism
purified recombinant NapDNHis/NapA complex, small angle X-ray scattering analysis, modelling
Escherichia coli
Engineering
Amino acid exchange
Commentary
Organism
S4C/S24C
site-directed mutagenesis, native, NapD results in a loss of some of the spin labels from the NapA signal peptide possibly due to the surface-exposed native cysteine residues of NapD. The NapD cysteine residues (C8 and C32) are not conserved and a cysteine-free variant of NapD complements a DELTAnapD strain for restoration of NapA activity. A NapD C8S/C32A variant remains attached to the NapA signal peptide
Escherichia coli
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
periplasm
NapA is exported to the periplasm in a folded form by the twin-arginine protein transport (Tat) pathway. NapA is subject to Tat proofreading prior to export by the Tat pathway
Escherichia coli
-
-
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Fe2+
in the cofactor heme and the [4Fe-4S] cluster
Escherichia coli
Molybdenum
in the molybdenum cofactor. Role for NapD in the insertion of the molybdenum cofactor
Escherichia coli
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2 ferrocytochrome + 2 H+ + nitrate
Escherichia coli
-
2 ferricytochrome + nitrite
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
P33937
-
-
Purification (Commentary)
Commentary
Organism
copurification of recombinant NapA complexed with N-terminally His-tagged NapD activator by nickel afinity chromatography from Escherichia coli strains MC4100 and BL21(DE3)
Escherichia coli
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2 ferrocytochrome + 2 H+ + nitrate
-
742486
Escherichia coli
2 ferricytochrome + nitrite
-
-
-
?
Subunits
Subunits
Commentary
Organism
More
PELDOR analysis of recombinant MTSL-labelled MalE-NapASP fusion mutant S4C/S24C alone or in complex with NapD, comparison of bound, NMR-derived NapASP helix from PDB ID 2PQ4 versus free generated helix, positions of the spin labels in the two conformations of the signal peptide, overview
Escherichia coli
Cofactor
Cofactor
Commentary
Organism
Structure
cytochrome c
di-heme cytochrome c redox partner, NapB
Escherichia coli
molybdenum cofactor
-
Escherichia coli
[4Fe-4S] cluster
-
Escherichia coli
Activating Compound (protein specific)
Activating Compound
Commentary
Organism
Structure
NapD
a small (9.3 kDa) cytoplasmic protein that is essential for Nap activity, role for NapD in the insertion of the molybdenum cofactor. The NapD cysteine residues (C8 and C32) are not conserved and a cysteine-free variant of NapD complements a DELTAnapD strain for restoration of NapA activity. A NapD C8S/C32A variant remains attached to the NapA signal peptide. Copurification of recombinant NapA complexed with N-terminally His-tagged NapD activator by nickel afinity chromatography
Escherichia coli
Cloned(Commentary) (protein specific)
Commentary
Organism
gene napA, enzyme NapA is encoded, along with its periplasmic di-heme c-type cytochrome redox partner NapB, in the seven gene nap operon, coexpression of NapA with His-tagged NapD activator in Escherichia coli strains MC4100 and BL21(DE3), recombinant expression of MTSL-labelled MalE-NapASP fusion mutant S4C/S24C in Escherichia coli strain BL21(DE3), subcloning in Escherichia coli strain LCB2048
Escherichia coli
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
cytochrome c
di-heme cytochrome c redox partner, NapB
Escherichia coli
molybdenum cofactor
-
Escherichia coli
[4Fe-4S] cluster
-
Escherichia coli
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant NapDNHis/NapA complex, small angle X-ray scattering analysis, modelling
Escherichia coli
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
S4C/S24C
site-directed mutagenesis, native, NapD results in a loss of some of the spin labels from the NapA signal peptide possibly due to the surface-exposed native cysteine residues of NapD. The NapD cysteine residues (C8 and C32) are not conserved and a cysteine-free variant of NapD complements a DELTAnapD strain for restoration of NapA activity. A NapD C8S/C32A variant remains attached to the NapA signal peptide
Escherichia coli
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
periplasm
NapA is exported to the periplasm in a folded form by the twin-arginine protein transport (Tat) pathway. NapA is subject to Tat proofreading prior to export by the Tat pathway
Escherichia coli
-
-
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
in the cofactor heme and the [4Fe-4S] cluster
Escherichia coli
Molybdenum
in the molybdenum cofactor. Role for NapD in the insertion of the molybdenum cofactor
Escherichia coli
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2 ferrocytochrome + 2 H+ + nitrate
Escherichia coli
-
2 ferricytochrome + nitrite
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
copurification of recombinant NapA complexed with N-terminally His-tagged NapD activator by nickel afinity chromatography from Escherichia coli strains MC4100 and BL21(DE3)
Escherichia coli
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2 ferrocytochrome + 2 H+ + nitrate
-
742486
Escherichia coli
2 ferricytochrome + nitrite
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
More
PELDOR analysis of recombinant MTSL-labelled MalE-NapASP fusion mutant S4C/S24C alone or in complex with NapD, comparison of bound, NMR-derived NapASP helix from PDB ID 2PQ4 versus free generated helix, positions of the spin labels in the two conformations of the signal peptide, overview
Escherichia coli
General Information
General Information
Commentary
Organism
additional information
NapD is a small cytoplasmic protein that is essential for the activity of the periplasmic nitrate reductase and binds tightly to the twinarginine signal peptide of NapA. NapA is structured in its unbound form. The NapA signal peptide undergoes conformational rearrangement upon interaction with NapD. NapA is at least partially folded when bound by its NapD partner. The NapD chaperone binds primarily at the NapA signal peptide in this system and points towards a role for NapD in the insertion of the molybdenum cofactor
Escherichia coli
physiological function
Escherichia coli is a Gram-negative bacterium that can use nitrate during anaerobic respiration. The catalytic subunit of the involved periplasmic nitrate reductase NapA contains two types of redox cofactor and is exported across the cytoplasmic membrane by the twin-arginine protein transport pathway
Escherichia coli
General Information (protein specific)
General Information
Commentary
Organism
additional information
NapD is a small cytoplasmic protein that is essential for the activity of the periplasmic nitrate reductase and binds tightly to the twinarginine signal peptide of NapA. NapA is structured in its unbound form. The NapA signal peptide undergoes conformational rearrangement upon interaction with NapD. NapA is at least partially folded when bound by its NapD partner. The NapD chaperone binds primarily at the NapA signal peptide in this system and points towards a role for NapD in the insertion of the molybdenum cofactor
Escherichia coli
physiological function
Escherichia coli is a Gram-negative bacterium that can use nitrate during anaerobic respiration. The catalytic subunit of the involved periplasmic nitrate reductase NapA contains two types of redox cofactor and is exported across the cytoplasmic membrane by the twin-arginine protein transport pathway
Escherichia coli
Other publictions for EC 1.9.6.1
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)
741478
Cerqueira
Periplasmic nitrate reductase ...
Desulfovibrio desulfuricans, Methylotenera mobilis, Methylotenera mobilis JLW8
Acc. Chem. Res.
48
2875-2884
2015
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1
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1
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3
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3
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1
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1
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3
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3
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1
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1
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2
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3
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5
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1
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1
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5
5
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742645
Lopez
The periplasmic nitrate reduc ...
Salmonella enterica, Salmonella enterica SL1344 AND CAL128
Infect. Immun.
83
3470-3478
2015
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1
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1
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1
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2
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6
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2
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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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2
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2
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-
-
-
-
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3
3
-
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-
741958
Jacques
Kinetics of substrate inhibit ...
Rhodobacter sphaeroides, Rhodobacter sphaeroides DSM 158
Biochim. Biophys. Acta
1837
1801-1809
2014
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-
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1
1
1
1
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2
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4
1
1
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1
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1
1
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742380
Sanchez
The nitrate-sensing NasST sys ...
Bradyrhizobium japonicum, Bradyrhizobium japonicum JCM 10833
Environ. Microbiol.
16
3263-3274
2014
-
-
1
-
1
-
-
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1
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5
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2
3
3
2
-
-
742486
Dow
Characterization of a peripla ...
Escherichia coli
FEBS J.
281
246-260
2014
1
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1
1
1
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1
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2
2
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742319
Gonzalez
-
Periplasmic nitrate reductase ...
Anaeromyxobacter dehalogenans, Bradyrhizobium japonicum, Campylobacter jejuni subsp. jejuni, Campylobacter jejuni subsp. jejuni ATCC 700819, Cupriavidus necator, Cupriavidus necator H16 / ATCC 23440 / NCIB 10442 / S-10-1, Desulfitobacterium hafniense, Desulfovibrio desulfuricans, Escherichia coli, Paracoccus denitrificans, Paracoccus pantotrophus, Paracoccus pantotrophus GB17, Pseudomonas sp., Pseudomonas sp. G-179, Rhodobacter sphaeroides, Shewanella gelidimarina, Shewanella oneidensis, Wolinella succinogenes
Coord. Chem. Rev.
257
315-331
2013
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-
14
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14
28
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18
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18
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14
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18
14
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42
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14
42
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14
28
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18
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18
14
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25
25
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742648
Cerqueira
The sulfur shift an activatio ...
Desulfovibrio desulfuricans
Inorg. Chem.
52
10766-10772
2013
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1
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1
2
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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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1
1
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712967
Simpson
The periplasmic nitrate reduct ...
Shewanella amazonensis, Shewanella amazonensis SB2B, Shewanella baltica, Shewanella baltica OS155, Shewanella baltica OS185, Shewanella baltica OS195, Shewanella baltica OS223, Shewanella denitrificans, Shewanella denitrificans OS217, Shewanella frigidimarina, Shewanella halifaxensis, Shewanella loihica, Shewanella loihica PV-4, Shewanella oneidensis, Shewanella oneidensis MR-1 / ATCC 700550, Shewanella pealeana, Shewanella piezotolerans, Shewanella piezotolerans WP3, Shewanella putrefaciens, Shewanella putrefaciens CN-32, Shewanella sediminis, Shewanella sp., Shewanella sp. ANA-3, Shewanella sp. MR-4, Shewanella sp. MR-7, Shewanella sp. W3-18-1, Shewanella woodyi
Microbiology
156
302-312
2010
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42
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27
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27
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696917
Durvasula
Effect of periplasmic nitrate ...
Paracoccus pantotrophus
Biotechnol. Prog.
25
973-979
2009
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1
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1
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698636
Stewart
Catabolite repression control ...
Paracoccus pantotrophus
J. Bacteriol.
191
996-1005
2009
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1
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1
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699015
Hofmann
Density functional theory stud ...
Desulfovibrio desulfuricans
J. Biol. Inorg. Chem.
14
1023-1035
2009
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699199
Cerqueira
The effect of the sixth sulfur ...
Desulfovibrio desulfuricans
J. Comput. Chem.
30
2466-2484
2009
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711653
Van Alst
Compensatory periplasmic nitra ...
Pseudomonas aeruginosa
Can. J. Microbiol.
55
1133-1144
2009
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1
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684990
Gates
Voltammetric characterization ...
Paracoccus pantotrophus
Biochem. J.
409
159-168
2008
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695337
Coelho
Heterodimeric nitrate reductas ...
Cupriavidus necator H16
Acta Crystallogr. Sect. F
63
516-519
2007
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674891
Jepson
Spectropotentiometric and stru ...
Escherichia coli
J. Biol. Chem.
282
6425-6437
2006
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