RESUMO
A copper-containing nitrite reductase catalyzes the reduction of nitrite to nitric oxide in the denitrifier Sinorhizobium meliloti 2011 (SmNirK), a microorganism used as bioinoculant in alfalfa seeds. Wild type SmNirK is a homotrimer that contains two copper centers per monomer, one of type 1 (T1) and other of type 2 (T2). T2 is at the interface of two monomers in a distorted square pyramidal coordination bonded to a water molecule and three histidine side chains, H171 and H136 from one monomer and H342 from the other. We report the molecular, catalytic, and spectroscopic properties of the SmNirK variant H342G, in which the interfacial H342 T2 ligand is substituted for glycine. The molecular properties of H342G are similar to those of wild type SmNirK. Fluorescence-based thermal shift assays and FTIR studies showed that the structural effect of the mutation is only marginal. However, the kinetic reaction with the physiological electron donor was significantly affected, which showed a â¼ 100-fold lower turnover number compared to the wild type enzyme. UV-Vis, EPR and FTIR studies complemented with computational calculations indicated that the drop in enzyme activity are mainly due to the void generated in the protein substrate channel by the point mutation. The main structural changes involve the filling of the void with water molecules, the direct coordination to T2 copper ion of the second sphere aspartic acid ligand, a key residue in catalysis and nitrite sensing in NirK, and to the loss of the 3 N-O coordination of T2.
Assuntos
Cobre , Sinorhizobium meliloti , Cobre/química , Nitritos/química , Sinorhizobium meliloti/química , Sinorhizobium meliloti/metabolismo , Histidina/química , Domínio Catalítico , Oxirredução , Ligantes , Glicina , Espectroscopia de Ressonância de Spin Eletrônica , Nitrito Redutases/químicaRESUMO
We report the crystal structure of the copper-containing nitrite reductase (NirK) from the Gram-negative bacterium Sinorhizobium meliloti 2011 (Sm), together with complex structural alignment and docking studies with both non-cognate and the physiologically related pseudoazurins, SmPaz1 and SmPaz2, respectively. S. meliloti is a rhizobacterium used for the formulation of Medicago sativa bionoculants, and SmNirK plays a key role in this symbiosis through the denitrification pathway. The structure of SmNirK, solved at a resolution of 2.5 Å, showed a striking resemblance with the overall structure of the well-known Class I NirKs composed of two Greek key ß-barrel domains. The activity of SmNirK is ~12% of the activity reported for classical NirKs, which could be attributed to several factors such as subtle structural differences in the secondary proton channel, solvent accessibility of the substrate channel, and that the denitrifying activity has to be finely regulated within the endosymbiont. In vitro kinetics performed in homogenous and heterogeneous media showed that both SmPaz1 and SmPaz2, which are coded in different regions of the genome, donate electrons to SmNirK with similar performance. Even though the energetics of the interprotein electron transfer (ET) process is not favorable with either electron donors, adduct formation mediated by conserved residues allows minimizing the distance between the copper centers involved in the interprotein ET process.
Assuntos
Azurina/química , Proteínas de Bactérias/química , Nitrito Redutases/química , Sinorhizobium meliloti/enzimologia , Cristalografia por Raios X , Domínios ProteicosRESUMO
The Cys-His bridge as electron transfer conduit in the enzymatic catalysis of nitrite to nitric oxide by nitrite reductase from Sinorhizobium meliloti 2011 (SmNir) was evaluated by site-directed mutagenesis, steady state kinetic studies, UV-vis and EPR spectroscopic measurements as well as computational calculations. The kinetic, structural and spectroscopic properties of the His171Asp (H171D) and Cys172Asp (C172D) SmNir variants were compared with the wild type enzyme. Molecular properties of H171D and C172D indicate that these point mutations have not visible effects on the quaternary structure of SmNir. Both variants are catalytically incompetent using the physiological electron donor pseudoazurin, though C172D presents catalytic activity with the artificial electron donor methyl viologen (kcat=3.9(4) s-1) lower than that of wt SmNir (kcat=240(50) s-1). QM/MM calculations indicate that the lack of activity of H171D may be ascribed to the Nδ1H OC hydrogen bond that partially shortcuts the T1-T2 bridging Cys-His covalent pathway. The role of the Nδ1H OC hydrogen bond in the pH-dependent catalytic activity of wt SmNir is also analyzed by monitoring the T1 and T2 oxidation states at the end of the catalytic reaction of wt SmNir at pH6 and 10 by UV-vis and EPR spectroscopies. These data provide insight into how changes in Cys-His bridge interrupts the electron transfer between T1 and T2 and how the pH-dependent catalytic activity of the enzyme are related to pH-dependent structural modifications of the T1-T2 bridging chemical pathway.
Assuntos
Proteínas de Bactérias/metabolismo , Transporte de Elétrons , Nitrito Redutases/metabolismo , Sinorhizobium meliloti/enzimologia , Substituição de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Cobre/química , Cisteína/química , Espectroscopia de Ressonância de Spin Eletrônica , Histidina/química , Modelos Moleculares , Mutagênese Sítio-Dirigida , Mutação de Sentido Incorreto , Nitrito Redutases/química , Nitrito Redutases/genética , Nitritos/metabolismo , Oxirredução , Mutação Puntual , Conformação Proteica , Proteínas Recombinantes/metabolismo , Sinorhizobium meliloti/genética , Espectrofotometria UltravioletaRESUMO
Bradyrhizobium diazoefficiens, a nitrogen-fixing endosymbiont of soybeans, is a model strain for studying rhizobial denitrification. This bacterium can also use nitrate as the sole nitrogen (N) source during aerobic growth by inducing an assimilatory nitrate reductase encoded by nasC located within the narK-bjgb-flp-nasC operon along with a nitrite reductase encoded by nirA at a different chromosomal locus. The global nitrogen two-component regulatory system NtrBC has been reported to coordinate the expression of key enzymes in nitrogen metabolism in several bacteria. In this study, we demonstrate that disruption of ntrC caused a growth defect in B. diazoefficiens cells in the presence of nitrate or nitrite as the sole N source and a decreased activity of the nitrate and nitrite reductase enzymes. Furthermore, the expression of narK-lacZ or nirA-lacZ transcriptional fusions was significantly reduced in the ntrC mutant after incubation under nitrate assimilation conditions. A B. diazoefficiens rpoN 1/2 mutant, lacking both copies of the gene encoding the alternative sigma factor σ54, was also defective in aerobic growth with nitrate as the N source as well as in nitrate and nitrite reductase expression. These results demonstrate that the NtrC regulator is required for expression of the B. diazoefficiens nasC and nirA genes and that the sigma factor RpoN is also involved in this regulation.
Assuntos
Proteínas de Bactérias/genética , Bradyrhizobium/metabolismo , Nitrato Redutase/metabolismo , Nitrito Redutases/metabolismo , Fator sigma/genética , Proteínas de Bactérias/metabolismo , Bradyrhizobium/genética , Bradyrhizobium/crescimento & desenvolvimento , Desnitrificação/fisiologia , Nitrato Redutase/genética , Nitrito Redutases/genética , Glycine max/microbiologiaRESUMO
The effect of metal ions, ferric ion (Fe3+) and molybdenum ion (Mo6+) on the denitrification process of Paracoccus pantotrophus P16 grown under saline conditions was investigated. Results revealed that the dosages of added Fe3+ and Mo6+ significantly accelerated nitrate utilization and nitrite accumulation. Enzymatic studies revealed that the membrane-bound nitrate reductase and the periplasmic nitrite reductase had activities of 998 +/- 28 and 373 +/- 18 nmol (mg protein)-1 min-1, respectively after growing Paracoccus pantotrophus P16 in medium supplemented with 1.5 micron M Fe3+. If provided with 1.5 micron M Fe3+and 2.4 micron M Mo6+, the membrane-bound nitrate reductase activity increased to 6,223 +/- 502 nmol (mg protein)-1 min-1 and the periplasmic nitrite reductase was 344 +/- 20 nmol (mg protein)-1 min-1. The results indicated that an addition of Fe3+ and Mo6+ led to an overstimulation of nitrate reductase activity as compared with nitrite reductase activity. When glucose was supplied, the minimal ratio of carbon per nitrate (C/N) was 2.31 mg C/mg NO3--N with denitrification yield of 0.45 g NO3--N/g C. Addition of ethanol instead of glucose, the minimal ratio of C/N was 1.15 mg C/mg NO3--N with denitrification yield of 1.08 g NO3--N/g C.