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Information on EC 1.9.6.1 - nitrate reductase (cytochrome) and Organism(s) Paracoccus pantotrophus and UniProt Accession Q56350

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Paracoccus pantotrophus
UNIPROT: Q56350 not found.
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The taxonomic range for the selected organisms is: Paracoccus pantotrophus
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
periplasmic nitrate reductase, periplasmic nitrate reductases, napedabc, napabc, nap-alpha, nap-beta, nap enzyme, benzyl viologen-nitrate reductase, napdaghb, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
periplasmic nitrate reductase
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benzyl viologen-nitrate reductase
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periplasmic nitrate reductase
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periplasmic nitrate reductases
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reductase, nitrate (cytochrome)
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respiratory nitrate reductase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2 ferrocytochrome + 2 H+ + nitrate = 2 ferricytochrome + nitrite
show the reaction diagram
sulfur-shift mechanism catalytic mechanism, detailed overview. The mechanism is defined by a change in the Mo ion coordination, which involves a first-to-second shell displacement (shift) of the sulfur from the Cys, resulting in a free coordination position that is used by the enzyme to bind the substrate with a low energy cost, molybdenum coordinates an oxygen atom from the substrate, an oxygen atom from the substrate is transferred to the Mo ion, and later released as a water molecule. The reaction requires two electrons, which are provided by external reducing species, and two protons that are obtained from the solvent either directly or indirectly mediated by residues from the enzyme catalytic pocket
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
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oxidation
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reduction
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PATHWAY SOURCE
PATHWAYS
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-, -
SYSTEMATIC NAME
IUBMB Comments
ferrocytochrome:nitrate oxidoreductase
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CAS REGISTRY NUMBER
COMMENTARY hide
9029-42-9
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2 ferrocytochrome + 2 H+ + nitrate
2 ferricytochrome + nitrite
show the reaction diagram
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-
-
?
nitrate + reduced benzyl viologen
nitrite + oxidized benzyl viologen
show the reaction diagram
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-
-
?
nitrate + reduced methyl viologen
nitrite + oxidized methyl viologen
show the reaction diagram
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-
?
nitrate + reduced methyl viologen
nitrite + oxidized methyl viologen + H2O
show the reaction diagram
additional information
?
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NapAB catalysed nitrate reduction driven by direct electron transfer from the electrode to NapAB, protein film voltammetry. Exploration of the nitrate reductase activity of purified NapAB as a function of electrochemical potential, substrate concentration and pH using protein film voltammetry. Nitrate reduction by NapAB occurs at potentials below approx. 0.1 V at pH 7. These are lower potentials than required for NarGH nitrate reduction. The potentials required for Nap nitrate reduction are also likely to require ubiquinol/ubiquinone ratios higher than are needed to activate the H+-pumping oxidases expressed during aerobic growth where Nap levels are maximal. Thus the operational potentials of Paracoccus pantotrophus NapAB are consistent with a productive role in redox balancing
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?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2 ferrocytochrome + 2 H+ + nitrate
2 ferricytochrome + nitrite
show the reaction diagram
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
cytochrome c
i.e. NapB, contains two c-type hemes and is assembled and secreted into the periplasm by the Ccm (cytochrome c maturation) machinery independently from enzyme NapA. Once in the periplasm they form the heterodimer NapAB
molybdenum cofactor
synthesis of the Mo-pyranopterin cofactor, overview
cytochrome c552
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the enzyme is a complex of a 93000 Da polypeptide and a 16000 Da nitrate-oxidizable cytochrome c552, cytochrome c552 contains two c-type heme moieties
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heme
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contains 1.3 mol heme per mol of protein (assuminga 110-kDa molecular mass)
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe2+
in the heme/cytochrome cofactor
Mo(VI)
coordinates a cysteine and a sulfido residue
Fe
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contains 2.7 mol iron (of which 1.4 mol is presumably non-haem iron) per mol of protein (assuming a 110000 Da molecular mass)
Mo
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contains molybdenum, 0.9 mol molybdenum: 1 mol protein (assuminga 110000 Da molecular mass)
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
azide
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mixed type inhibition
thiocyanate
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competitive
additional information
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insensitive to inhibition by azide
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.045
nitrate
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pH 7, NapAB catalysed nitrate reduction driven by direct electron transfer from the electrode to NapAB, protein film voltammetry
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 9.5
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pH 7.0: about 70% of maximal activity, pH 9.5: about 60% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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mutant strain (M-6) overproduces the enzyme activity under anaerobic growth conditions
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
the prokaryotic nitrate reductases can be subgrouped as respiratory nitrate reductases (Nar), assimilatory nitrate reductases (Nas), and periplasmic nitrate reductases (Nap). Periplasmic nitrate reductase (Nap) and formate dehydrogenase (Fdh), both belonging to the DMSO reductase family, subfamily I, have a very similar structure, but very different activities. The show key differences that tune them for completely different functions in living cells. Both enzymes share almost identical three-dimensional protein foldings and active sites, in terms of coordination number, geometry and nature of the ligands. The substrates of both enzymes (nitrate and formate) are polyatomic anions that also share similar charge and stereochemistry. In terms of the catalytic mechanism, both enzymes have a common activation mechanism (the sulfur-shift mechanism) that ensures a constant coordination number around the metal ion during the catalytic cycle. In spite of these similarities, they catalyze very different reactions: Nap abstracts an oxygen atom from nitrate releasing nitrite, whereas FdH catalyzes a hydrogen atom transfer from formate and releases carbon dioxide. Detailed comparison, overview. A key difference between the catalytic mechanisms of Nap and FdH is the fact that only Mo is used to reduce nitrate but in Fdhs both Mo and W are catalytically competent to oxidize formate to carbon dioxide
physiological function
additional information
the enzyme shows a sulfur-shift mechanism catalytic mechanism, the active site is deeply buried and centered on the Mo atom, which is hexacoordinated to four sulfur atoms of two pyranopterin guanosine dinucleotides, one inorganic sulfur, and one S (Nap) atom from the side chain of a Cys, structure. Above the region of the metal center, the enzyme presents an arginine residue, that is proposed to be key for stabilization and substrate binding. The side chain of this residues probably interacts electrostatically with the substrates, compensating for the negative charge and favoring their interaction with the negatively charged active site. Comparisons of reaction mechanisms of members of the DMSO reductase family and structure analysis and modelling, overview. The NapA (product of the napA gene) is the catalytic subunit that contains the Mo-bis-PGD and one 4Fe-4S center involved in electron transfer. Similar to other periplasmic Mo- and W-enzymes, immature NapA contains a signal peptide that is recognized by the TAT (twin arginine translocator) system. Prior to translocation, the two metallic cofactors are incorporated into NapA with the aid of the chaperone NapD, which accompanies the assembled metalloenzyme to the transporter, maturation mechanism of Mo. NapB contains two c-type hemes and is assembled and secreted into the periplasm by the Ccm (cytochrome c maturation) machinery independently from NapA. Once in the periplasm they form the heterodimer NapAB, except in the case of monomeric Naps. It is remarkable that napM is present only when the napB gene is absent. NapM is a tetrahemic c-type cytochrome. This cytochrome may mediate electron transfer to NapA in a similar way that NapB does in heterodimeric Naps. NapC is a membrane-anchored protein harboring four c-type hemes belonging to the NapC/NirT family. In some bacteria, where nitrate reduction catalyzed by Nap is coupled to an energy conserving process, the genes napG and napH are always present. Nap from Paracoccus pantotrophus catalyzes nitrate reduction to consume the excess of reducing equivalents generated by consumption of the carbon source, which is in agreement with the lack of napG and napH genes
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
NAPA_PARPN
831
0
92618
Swiss-Prot
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
110000
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gel filtration
16000
90000
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x * 16000 + x * 90000, SDS-PAGE
93000
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1 * 93000 + 1 * 16000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
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x * 16000 + x * 90000, SDS-PAGE
dimer
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1 * 93000 + 1 * 16000, SDS-PAGE
additional information
the catalytic subunit of Nap is usually encoded in a nap operon together with accessory proteins involved in its maturation (chaperones) and redox proteins that transfer reducing equivalents from the physiological electron donor (quinone pool) to the active site of the enzyme, nap enzyme domain structure analysis, overview
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene nap and nap gene cluster, genetic organization and sequence comparisons
expressed in Escherichia coli
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Gates, A.J.; Richardson, D.J.; Butt, J.N.
Voltammetric characterization of the aerobic energy-dissipating nitrate reductase of Paracoccus pantotrophus: exploring the activity of a redox-balancing enzyme as a function of electrochemical potential
Biochem. J.
409
159-168
2008
Paracoccus pantotrophus
Manually annotated by BRENDA team
Berks, B.C.; Ferguson, S.J.; Moir, J.W.; Richardson, D.J.
Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions.
Biochim. Biophys. Acta
1232
97-173
1995
Cupriavidus necator, Escherichia coli, Paracoccus denitrificans, Paracoccus pantotrophus
Manually annotated by BRENDA team
Durvasula, K.; Jantama, K.; Fischer, K.; Vega, A.; Koopman, B.; Svoronos, S.A.
Effect of periplasmic nitrate reductase on diauxic lag of Paracoccus pantotrophus
Biotechnol. Prog.
25
973-979
2009
Paracoccus pantotrophus (Q56350), Paracoccus pantotrophus
Manually annotated by BRENDA team
Berks, B.C.; Richardson, D.J.; Robinson, C.; Reilly, A.; Aplin, R.T.; Ferguson, S.J.
Purification and characterization of the periplasmic nitrate reductase from Thiosphaera pantotropha
Eur. J. Biochem.
220
117-124
1994
Paracoccus pantotrophus
Manually annotated by BRENDA team
Stewart, V.; Bledsoe, P.J.; Chen, L.L.; Cai, A.
Catabolite repression control of napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12
J. Bacteriol.
191
996-1005
2009
Paracoccus pantotrophus
Manually annotated by BRENDA team
Gonzalez, P.; Rivas, M.; Mota, C.; Brondino, C.; Moura, I.; Moura, J.
Periplasmic nitrate reductases and formate dehydrogenases biological control of the chemical properties of Mo and W for fine tuning of reactivity, substrate specificity and metabolic role
Coord. Chem. Rev.
257
315-331
2013
Anaeromyxobacter dehalogenans (Q2IPE7), Bradyrhizobium japonicum, Campylobacter jejuni subsp. jejuni (Q9PPD9), Campylobacter jejuni subsp. jejuni ATCC 700819 (Q9PPD9), Cereibacter sphaeroides (Q53176), Cupriavidus necator (P39185), Cupriavidus necator H16 / ATCC 23440 / NCIB 10442 / S-10-1 (P39185), Desulfitobacterium hafniense (A0A098B5Y5), Desulfovibrio desulfuricans (P81186), Escherichia coli (P33937), Paracoccus denitrificans (A1BB88), Paracoccus pantotrophus (Q56350), Paracoccus pantotrophus GB17 (Q56350), Pseudomonas sp. (Q9RC05), Pseudomonas sp. G-179 (Q9RC05), Shewanella gelidimarina (E2F391), Shewanella oneidensis, Wolinella succinogenes
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Manually annotated by BRENDA team