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EC Number
General Information
Commentary
Reference
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) from Desulfovibrio desulfuricans and formate dehydrogenase (Fdh) from Escherichia coli K-12, 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
more
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, Arg354,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-bisPGD 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 bacteria like Desulfovibrio desulfuricans ATCC 27774 and Escherichia coli K12, where nitrate reduction catalyzed by Nap is coupled to an energy conserving process, the genes napG and napH are always present
more
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
physiological function
the Nap enzyme from Cupriavidus necator catalyzes nitrate reduction to consume the excess of reducing equivalents generated by consumption of the carbon source
physiological function
the Nap enzyme from Rhodobacter sphaeroides catalyzes nitrate reduction to consume the excess of reducing equivalents generated by consumption of the carbon source
physiological function
the Nap enzyme from Shewanella gelidimarina catalyzes nitrate reduction to consume the excess of reducing equivalents generated by consumption of the carbon source
more
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-bisPGD 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 bacteria like Desulfovibrio desulfuricans ATCC 27774 and Escherichia coli K12, where nitrate reduction catalyzed by Nap is coupled to an energy conserving process, the genes napG and napH are always present
evolution
genotyping of different strains from M and G populations, overview. The only mutated gene shared between the strains from populations M and G is bll4572, this gene is mutated in all six strains
metabolism
NasST regulates the nitrate-mediated response of nosZ and napE genes, from the dissimilatory denitrification pathway, regulation of nos and nap genes by the NasST system in the absence of nitrate in mutant strains, overview
more
modeling of regulation of nap and nos genes by NasST system in Bradyrhizobium japonicum strain USDA110 and nasS and Nos++ mutant strains
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