Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:1.7.1.4 (nitrite reductase)
1,847 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The central tunnel of the eight-bladed beta-propeller domain of cytochrome cd1 (nitrite reductase) is seen, from a 1.28 A resolution structure, to contain hydrogen donors and acceptors that are satisfied by interaction either with water or the d1 haem. The d1 haem, although bound by an extensive network of hydrogen bonds, is not distorted in its binding pocket and is confirmed to have exactly the dioxoisobacteriochlorin structure proposed from chemical studies. A biological rationale is advanced for the undistorted structure of the d1 haem and the large number of hydrogen bonds it makes. The beta-propeller domain can be closely superimposed on that of methanol dehydrogenase despite the enzymes sharing no common sequence motifs and using a different set of interactions to "Velcro" close the propeller. The sequence and likely structural relationships between cytochrome cd1 or methanol dehydrogenase and other predicted eight-bladed beta-propeller domains in proteins, such as the pyrolloquinoline quinone-dependent alcohol dehydrogenase, are discussed and compared with other propeller proteins. From sequencing the nirS gene of Thiosphaera pantotropha, it is established that the amino acid sequence deduced previously in part from X-ray diffraction data at lower resolution was largely correct, as was the proposal that eight N-terminal amino acid residues were not seen in the structure. The unusual haem iron environments in both the c-type cytochrome domain, with His/His coordination, and the d1-type cytochrome domain with Tyr/His coordination are related to the functions of the redox centres.
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PMID:Cytochrome cd1 structure: unusual haem environments in a nitrite reductase and analysis of factors contributing to beta-propeller folds. 919 11

In the hydrophobic patch of azurin from Pseudomonas aeruginosa, an electric dipole was created by changing Met44 into Lys and Met64 into Glu. The effect of this dipole on the electron-transfer properties of azurin was investigated. From a spectroscopic characterization (NMR, EPR and ultraviolet-visible) it was found that both the copper site and the overall structure of the [Lys44, Glu64]azurin were not disturbed by the two mutations. A small perturbation of the active site at high pH, similar to that observed for [Lys44]azurin, occurs in the double mutant. At neutral pH the electron-self-exchange rate constant of the double mutant shows a decrease of three orders of magnitude compared with the wild-type value. The possible reasons for this decrease are discussed. Electron transfer with the proposed physiological redox partners cytochrome c551 and nitrite reductase have been investigated and the data analyzed in the Marcus framework. From this analysis it is confirmed that the hydrophobic patch of azurin is the interaction site with both partners, and that cytochrome c551 uses its hydrophobic patch and nitrite reductase a negatively charged surface area for the electron transfer.
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PMID:Electron-transfer properties of Pseudomonas aeruginosa [Lys44, Glu64]azurin. 924 43

The role of the blue copper protein azurin and cytochrome C551 as the possible electron donors to nitrite reductase in the dissimilatory nitrate reduction pathway in Pseudomonas aeruginosa have been investigated. It was shown by an in vivo approach with mutant strains of P. aeruginosa deficient in one or both of these electron-transfer proteins that cytochrome C551, but not azurin, is functional in this pathway. Expression studies demonstrated the presence of azurin in both aerobic and anaerobic cultures. A sharp increase in azurin expression was observed when cultures were shifted from exponential to stationary phase. The stationary-phase sigma factor, sigma s, was shown to be responsible for this induction. In addition, one of the two promoters transcribing the azu gene was regulated by the anaerobic transcriptional regulator ANR. An azurin-deficient mutant was more sensitive to hydrogen peroxide and paraquat than the wild-type P. aeruginosa. These results suggest a physiological role of azurin in stress situations like those encountered in the transition to the stationary phase.
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PMID:In vivo studies disprove an obligatory role of azurin in denitrification in Pseudomonas aeruginosa and show that azu expression is under control of rpoS and ANR. 930 69

Soluble cytochromes c-552 were purified from two strains of the hydrogenothrophic species Alcaligenes eutrophus and their amino acid sequences determined. The two cytochromes were found to have 5 differences out of a total of 89 residues. The proteins are clearly related to the cytochromes c8 (formerly called Pseudomonas cytochromes c-551), but require a single residue insertion after the methionine sixth heme ligand relative to the Pseudomonas aeruginosa protein. The consensus residues Trp56 and Trp77, characteristic for the c8 family, are also present in the Alcaligenes proteins. Overall, the Alcaligenes cytochromes are only 43% identical to the Pseudomonas proteins which average 68% identity to one another. They are also only 45% identical to cytochrome c8 from Hydrogenobacter thermophilus, another hydrogenothrophic species, which indicates that the hydrogen utilizing bacteria are not more closely related to one another than they are to other species. The finding of cytochrome c8 in Alcaligenes eutrophus completes the recent characterization of a cytochrome cd1-nitrite reductase from this bacterial species and suggests the existence of the same denitrification pathway as in Pseudomonas where these two proteins are reaction partners.
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PMID:Cytochromes c-552 from two strains of the hydrogenotrophic bacterium Alcaligenes eutrophus are sequence homologs of the cytochromes c8 from the denitrifying pseudomonads. 943 5

Cleavage of chromosomal DNA from Pseudomonas aeruginosa PAO by Spel and Dpnl has been used together with PFGE and Southern hybridization to establish the map location of the following principal denitrification genes: narGH (encoding the large and small subunits of respiratory nitrate reductase), nirS (cytochrome-cd1 nitrite reductase), nirE (uroporphyrinogen-III methyltransferase for haem d1 biosynthesis), norCB (nitric-oxide reductase complex), nosZ (nitrous-oxide reductase) and nosA (an outer-membrane protein and OprC homologue). The study also included several genes related to anaerobic or microaerophilic metabolism: napA (encoding the catalytic subunit of the periplasmic nitrate reductase), ccoN (catalytic subunit of the cytochrome-cbb3 oxidase), hemN (oxygen-independent coproporphyrinogen-III oxidase), an fnr-like regulatory gene, and azu and fdxA (electron carriers azurin and ferredoxin, respectively). Genes necessary for denitrification are concentrated at 20 to 36 min on the P. aeruginosa chromosome, where they form three separate loci, the nir-nor, nar and nos gene clusters. Genomic DNA of Pseudomonas stutzeri ZoBell was also subjected to Spel restriction and Southern analysis to assign denitrification genes to individual fragments. A homologue of nosA encoding a putative component of the Cu-processing apparatus for nitrous-oxide reductase was identified. In both P. aeruginosa and P. stutzeri there is evidence for the linkage of anr (fnrA) with hemN and ccoN; and for the presence of a napA gene.
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PMID:Localization of denitrification genes on the chromosomal map of Pseudomonas aeruginosa. 949 81

Cytochrome c552 is the terminal component of the formate-dependent nitrite reduction pathway of Escherichia coli. In addition to four 'typical' haem-binding motifs, CXXCH-, characteristic of c-type cytochromes, the N-terminal region of NrfA includes a motif, CWSCK. Peptides generated by digesting the cytochrome from wild-type bacteria with cyanogen bromide followed by trypsin were analysed by on-line HPLC MS/MS in parent scanning mode. A strong signal at mass 619, corresponding to haem, was generated by fragmentation of a peptide of mass 1312 that included the sequence CWSCK. Neither this signal nor the haem-containing peptide of mass 1312 was detected in parallel experiments with cytochrome that had been purified from a transformant unable to synthesize NrfE, NrfF and NrfG: this is consistent with our previous report that NrfE and NrfG (but not NrfF) are essential for formate-dependent nitrite reduction. Redox titrations clearly revealed the presence of high and low mid-point potential redox centres. The best fit to the experimental data is for three n=1 components with mid-point redox potentials (pH 7.0) of +45 mV (21% of the total absorbance change), -90 mV (36% of the total) and -210mV (43% of the total). Plasmids in which the lysine codon of the cysteine-lysine motif, AAA, was changed to the histidine codon CAT (to create a fifth 'typical' haem c-binding motif), or to the isoleucine and leucine codons, ATT and CTT, were unable to transform a Nrf deletion mutant to Nrf+ or to restore formate-dependent nitrite reduction to the transformants. The presence of a 50 kDa periplasmic c-type cytochrome was confirmed by staining proteins separated by SDS-PAGE for covalently bound haem, but the methyl-viologen-dependent nitrite reductase activities associated with the mutated proteins, although still detectable, were far lower than that of the native protein. The combined data establish not only that there is a haem group bound covalently to the cysteine-lysine motif of cytochrome c552 but also that one or more products of the last three genes of the nrf operon are essential for the haem ligation to this motif.
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PMID:Involvement of products of the nrfEFG genes in the covalent attachment of haem c to a novel cysteine-lysine motif in the cytochrome c552 nitrite reductase from Escherichia coli. 959 8

A molecular model of QH-ADH, the quinohaemoprotein alcohol dehydrogenase from Comamonas testosteroni, has been built by homology modelling. Sequence similarity of N-terminal residues 1-570 with the alpha-subunit of quinoprotein methanol dehydrogenases (MDHs) from Methylophilus methylotrophus W3A1 and Methylobacterium extorquens provided a basis for the design of the PQQ-binding domain of QH-ADH. Minimal sequence similarity with cytochrome c551 from Ectothiorhodospira halophila and cytochrome c5 from Azotobacter vinelandii has been used to model the C-terminal haem c-binding domain, residues 571-677, absent in MDHs. Distance constraints inferred from 19F-NMR relaxation studies of trifluoromethylphenylhydrazine-derivatized PQQ bound to QH-ADH apoenzyme as well as theoretical relations for optimal electron transfer have been employed to position the haem- and PQQ-binding domains relative to each other. The homology model obtained shows overall topological similarity with the crystal structure of cd1-nitrite reductase from Thiosphera pantotropha. The proposed model accounts for the following: (i) the site that is sensitive to in vivo proteolytic attack; (ii) the substrate specificity in comparison with MDHs; (iii) changes of the spectral properties of the haem c upon reconstitution of apo-enzyme with PQQ; (iv) electronic interaction between haem and PQQ; and (v) enantioselectivity in the conversion of a chiral sec alcohol.
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PMID:Homology model of the quinohaemoprotein alcohol dehydrogenase from Comamonas testosteroni. 961 42

The nirQOP operon, which is located between the genes for nitrite reductase and nitric oxide reductase in Pseudomonas aeruginosa, encodes a putative ATP-binding protein and two putative transmembrane proteins. Phylogenetic analysis showed that NirO belongs to the family of subunit III of cytochrome oxidases but is distantly related to the other bacterial or mitochondrial proteins. P. aeruginosa strains that lacked the nirOP genes had all enzyme activities for denitrification and could grow under anaerobic conditions with nitrate or nitrite as an electron acceptor. However, the energy conservation efficiency of anaerobic respiration was lower in these strains than in strains harboring the nirOP gene.
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PMID:The role of the nirQOP genes in energy conservation during anaerobic growth of Pseudomonas aeruginosa. 983 35

Pseudomonas stutzeri is a facultative anaerobic bacterium with the capability of denitrification. In searching for regulators that control the expression of this trait in response to oxygen withdrawal, we have found an unprecedented multiplicity of four genes encoding transcription factors of the FNR family. The fnrA gene encodes a genuine FNR-type regulator, which is expressed constitutively and controls the cytochrome cbb3-type terminal oxidase (the cco operon), cytochrome c peroxidase (the ccp gene) and the oxygen-independent coproporphyrinogen III oxidase (the hemN gene), in addition to its previously demonstrated role in arginine catabolism (the arc operon). The fnr homologues dnrD, dnrE and dnrS encode regulators of a new subgroup within the FNR family. Their main distinctive feature is the lack of cysteine residues for complexing the [4Fe-4S] centre of redox-active FNR-type regulators. However, they form a phylogenetic lineage separate from the FixK branch of FNR proteins, which also lack this cysteine signature. We have studied the expression of the dnr genes under aerobic, oxygen-limited and denitrifying conditions. DnrD is a key regulator of denitrification by selective activation of the genes for cytochrome cd1 nitrite reductase and NO reductase. The dnrD gene is part of the 30 kb region carrying denitrification genes of P. stutzeri. Transcription of dnrD was activated in O2-limited cells and particularly strongly in denitrifying cells, but was not under the control of FnrA. In response to denitrifying growth conditions, dnrD was transcribed as part of an operon together with genes downstream and upstream of dnrD. dnrS was found about 9 kb upstream of dnrD, next to the nrdD gene for anaerobic ribonucleotide reductase. The transcription of dnrS required FnrA in O2-limited cells. Mutation of dnrS affected nrdD and the expression of ferredoxin I as an element of the oxidative stress response. The dnrE gene is part of the nar region encoding functions for respiratory nitrate reduction. We found the highest amount of dnrE transcripts in aerobically nitrate-challenged cells. The gene was transcribed from two promoters, P1 and P2, of which promoter P1 was under the control of the nitrate response regulator NarL. The multiplicity of FNR factors in P. stutzeri underlines the versatility of the FNR scaffold to serve for transcriptional regulation directed at anaerobic or nitrate-activated metabolic processes.
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PMID:Multiple transcription factors of the FNR family in denitrifying Pseudomonas stutzeri: characterization of four fnr-like genes, regulatory responses and cognate metabolic processes. 1020 42

A periplasmic protein able to transfer electrons from cytoplasmic membrane to the periplasmic nitrite reductase (cytochrome cd1) has been purified from the anoxically grown cytochrome c550 mutant strain Pd2121 and shown to be pseudoazurin by several independent criteria (molecular mass, copper content, visible spectrum, N-terminal amino acid sequence). Under our assay conditions, the half-saturation of electron transport occurred at about 10 microM pseudoazurin; the reaction was retarded by increasing ionic strength.
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PMID:Pseudoazurin mediates periplasmic electron flow in a mutant strain of Paracoccus denitrificans lacking cytochrome c550. 1021 31


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