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1.
Biochemistry ; 52(36): 6211-8, 2013 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-23952581

RESUMO

Hydroxylamine oxidoreductase (HAO) is a 24-heme homotrimeric enzyme that catalyzes the conversion of hydroxylamine to nitrite in nitrifying bacteria: a key reaction in the nitrogen cycle. One heme in each HAO monomer is a highly unusual heme P460 that is the site of catalysis. This was proposed to be a c-type heme that contained an additional porphyrin-tyrosine cross-link. Here, we report the crystal structure of HAO from Nitrosomonas europaea to 2.1 Å resolution that defines a different model compatible with the crystallographic and biochemical data. The structure reveals that heme P460 contains two covalent cross-links between the porphyrin and a Tyr residue. In addition, the enzyme was purified from source, and an unknown physiological HAO binding partner was present within the crystal (annotated in the genome as hypothetical protein NE1300). NE1300 may play a structural role in the ternary complex with cytochrome c554, the physiological electron acceptor of HAO.


Assuntos
Heme/análogos & derivados , Oxirredutases/química , Cristalografia por Raios X , Heme/química , Espectrometria de Massas , Modelos Moleculares , Simulação de Acoplamento Molecular , Nitrosomonas europaea/enzimologia , Oxirredutases/isolamento & purificação
2.
Acta Crystallogr Sect F Struct Biol Cryst Commun ; 65(Pt 12): 1296-8, 2009 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-20054133

RESUMO

Hydroxylamine oxidoreductase (HAO) from Nitrosomonas europaea is a homotrimeric protein that catalyzes the oxidation of hydroxylamine to nitrite. Each monomer, with a molecular weight of 67.1 kDa, contains seven c-type hemes and one heme P460, the porphyrin ring of which is covalently linked to a tyrosine residue from an adjacent subunit. HAO was first crystallized and structurally characterized at a resolution of 2.8 A in 1997. The structure was solved in space group P6(3) and suffered from merohedral twinning. Here, a crystallization procedure is presented that yielded untwinned crystals belonging to space group P2(1)2(1)2, which diffracted to 2.25 A resolution and contained one trimer in the asymmetric unit. The unit-cell parameters were a = 140.7, b = 142.6, c = 107.4 A.


Assuntos
Nitrosomonas europaea/enzimologia , Oxirredutases/química , Cristalização , Cristalografia por Raios X , Heme/química , Estrutura Quaternária de Proteína , Subunidades Proteicas , Tirosina/química
3.
Environ Microbiol ; 10(11): 3140-9, 2008 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-18973625

RESUMO

Bacterial aerobic ammonium oxidation and anaerobic ammonium oxidation (anammox) are important processes in the global nitrogen cycle. Key enzymes in both processes are the octahaem cytochrome c (OCC) proteins, hydroxylamine oxidoreductase (HAO) of aerobic ammonium-oxidizing bacteria (AOB), which catalyses the oxidation of hydroxylamine to nitrite, and hydrazine oxidoreductase (HZO) of anammox bacteria, which converts hydrazine to N(2). While the genomes of AOB encode up to three nearly identical copies of hao operons, genome analysis of Candidatus'Kuenenia stuttgartiensis' showed eight highly divergent octahaem protein coding regions as possible candidates for the HZO. Based on their phylogenetic relationship and biochemical characteristics, the sequences of these eight gene products grouped in three clusters. Degenerate primers were designed on the basis of available gene sequences with the aim to detect hao and hzo genes in various ecosystems. The hao primer pairs amplified gene fragments from 738 to 1172 bp and the hzo primer pairs amplified gene fragments from 289 to 876 bp in length, when tested on genomic DNA isolated from a variety of AOB and anammox bacteria. A selection of these primer pairs was also used successfully to amplify and analyse the hao and hzo genes in community DNA isolated from different ecosystems harbouring both AOB and anammox bacteria. We propose that OCC protein-encoding genes are suitable targets for molecular ecological studies on both aerobic and anaerobic ammonium-oxidizing bacteria.


Assuntos
Proteínas de Bactérias/genética , Grupo dos Citocromos c/metabolismo , Microbiologia Ambiental , Hidrazinas/metabolismo , Hidroxilamina/metabolismo , Oxirredutases/genética , Reação em Cadeia da Polimerase/métodos , Sequência de Aminoácidos , Primers do DNA , DNA Bacteriano/química , DNA Bacteriano/genética , Dados de Sequência Molecular , Filogenia , Alinhamento de Sequência , Análise de Sequência de DNA
4.
Mycoses ; 51(4): 301-7, 2008 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-18924261

RESUMO

This study aimed at screen for antimicrobial activity present in the non-rubber constituents of rubber latex of Hevea brasiliensis against various microbial strains. An antimicrobial protein, hevein was extracted from the bottom fraction after centrifugation and purified by acetone fractionation and anion exchange chromatography on a DEAE-Sepharose Fast Flow column. This procedure was more efficient and rapid than the previously described procedures. The antimicrobial activity was investigated and revealed that hevein, a small (4.7 kDa) cysteine-rich protein, had strong antimicrobial activity, especially against Candida spp. including Candida albicans, Candida tropicalis and Candida krusei. The MIC80 value for hevein was as low as 12 microg ml(-1) with C. tropicalis ATCC 750. Higher MIC80 values were obtained for C. albicans ATCC 10231 (95 microg ml(-1)) and C. krusei ATCC 6258 (190 microg ml(-1)). To confirm the antifungal activity, hevein also inhibited the growth of those fungi in a disk diffusion assay and its inhibition was enhanced when a Hevea latex protease inhibitor was also included. Hevein at a concentration of 30 microg ml(-1) also caused a Ca2+-dependent aggregation of C. tropicalis yeast cells. These data indicate that hevein can inhibit the growth of certain potential oral fungal pathogens.


Assuntos
Anti-Infecciosos/isolamento & purificação , Anti-Infecciosos/farmacologia , Peptídeos Catiônicos Antimicrobianos/isolamento & purificação , Peptídeos Catiônicos Antimicrobianos/farmacologia , Candida/efeitos dos fármacos , Hevea/química , Látex/química , Lectinas de Plantas/isolamento & purificação , Lectinas de Plantas/farmacologia , Sequência de Aminoácidos , Anti-Infecciosos/química , Peptídeos Catiônicos Antimicrobianos/química , Cryptococcus neoformans/efeitos dos fármacos , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Positivas/efeitos dos fármacos , Testes de Sensibilidade Microbiana , Dados de Sequência Molecular , Peso Molecular , Lectinas de Plantas/química
5.
Environ Microbiol ; 10(11): 3150-63, 2008 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-18761666

RESUMO

The biogeochemical nitrogen cycle is mediated by many groups of microorganisms that harbour octahaem cytochromes c (OCC). In this study molecular evolutionary analyses and the conservation of predicted functional residues and secondary structure were employed to investigate the descent of OCC proteins related to hydroxylamine oxidoreductase (HAO) and hydrazine oxidoreductase (HZO) from pentahaem cytochrome c nitrite reductase (NrfA). An octahaem cytochrome cnitrite reductase (ONR) was shown to be a possible intermediate in the process. Analysis of genomic neighbourhoods of OCC protein-encoding genes revealed adjacent conserved genes whose products, together with HAO, provide a path of electron transfer to quinone and constitute a functional catabolic module. The latter has evolved more than once under a variety of functional pressures on the catabolic lifestyles of their bacterial hosts. Structurally, the archetypical long helices in the large C-terminal domain of the proteins as well as the distal axial ligands to most haems were highly conserved in NrfA and all descendents. Residues known to be involved in the nitrite reductase activity of NrfA including the 'CxxCK' motif at the catalytic haem, the substrate and Ca binding sites, and the nitrite and ammonium channels were conserved in the eight representatives of ONR. In the latter, a unique cysteine has been inserted above the active site. The 64 other OCC proteins differed from ONR by the absence of the 'CxxCK' motif, the channel residues and most of the Ca-binding residues and the conserved presence of an 'Asp-His' pair inserted above the active site as well as the tyrosine that forms an intersubunit cross-link to the catalytic haem of HAO. Our proposed scenario of evolution of OCC proteins in the HAO family from NrfA is supported by (i) homology based on sequence and structure, (ii) its wide distribution among bacterial taxa, (iii) the dedicated interaction with specific proteins, and it is (iv) congruent with geological history.


Assuntos
Bactérias Aeróbias/enzimologia , Bactérias Anaeróbias/enzimologia , Proteínas de Bactérias/genética , Grupo dos Citocromos c/genética , Evolução Molecular , Motivos de Aminoácidos , Sequência de Aminoácidos , Amônia , Bactérias Aeróbias/genética , Bactérias Anaeróbias/genética , Sítios de Ligação , Sequência Conservada , Grupo dos Citocromos c/química , Modelos Biológicos , Filogenia , Estrutura Secundária de Proteína , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos
6.
Biochemistry ; 47(25): 6539-51, 2008 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-18505274

RESUMO

Cytochrome c(m552) (cyt c(m552)) from the ammonia-oxidizing Nitrosomonas europaea is encoded by the cycB gene, which is preceded in a gene cluster by three genes encoding proteins involved in the oxidation of hydroxylamine: hao, hydroxylamine oxidoreductase; orf2, a putative membrane protein; cycA, cyt c(554). By amino acid sequence alignment of the core tetraheme domain, cyt c(m552) belongs to the NapC/TorC family of tetra- or pentaheme cytochrome c species involved in electron transport from membrane quinols to a variety of periplasmic electron shuttles leading to terminal reductases. However, cyt c(m552) is thought to reduce quinone with electrons originating from HAO. In this work, the tetrahemic 27 kDa cyt c(m552) from N. europaea was purified after extraction from membranes using Triton X-100 with subsequent exchange into n-dodecyl beta-d-maltoside. The cytochrome had a propensity to form strong SDS-resistant dimers likely mediated by a conserved GXXXG motif present in the putative transmembrane segment. Optical spectra of the ferric protein contained a broad ligand-metal charge transfer band at approximately 625 nm indicative of a high-spin heme. Mossbauer spectroscopy of the reduced (57)Fe-enriched protein revealed the presence of high-spin and low-spin hemes in a 1:3 ratio. Multimode EPR spectroscopy of the native state showed signals from an electronically interacting high-spin/low-spin pair of hemes. Upon partial reduction, a typical high-spin heme EPR signal was observed. No EPR signals were observed from the other two low-spin hemes, indicating an electronic interaction between these hemes as well. UV-vis absorption data indicate that CO (ferrous enzyme) or CN(-) (ferric or ferrous enzyme) bound to more than one and possibly all hemes. Other anionic ligands did not bind. The four ferrous hemes of the cytochrome were rapidly oxidized in the presence of oxygen. Comparative modeling, based on the crystal structure and conserved residues of the homologous NrfH protein from Desulfovibrio of cyt c(m552), predicted some structural elements, including a Met-ligated high-spin heme in a quinone-binding pocket, and likely axial ligands to all four hemes.


Assuntos
Amônia/metabolismo , Proteínas de Bactérias/metabolismo , Grupo dos Citocromos c/metabolismo , Nitrosomonas europaea/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Grupo dos Citocromos c/química , Grupo dos Citocromos c/genética , Espectroscopia de Ressonância de Spin Eletrônica , Complexo I de Transporte de Elétrons/química , Complexo I de Transporte de Elétrons/genética , Complexo I de Transporte de Elétrons/metabolismo , Eletroforese em Gel de Poliacrilamida , Heme/química , Heme/metabolismo , Ligantes , Proteínas de Membrana/química , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Nitrosomonas europaea/genética , Oxirredução , Conformação Proteica , Multimerização Proteica , Estrutura Terciária de Proteína , Homologia de Sequência de Aminoácidos , Espectroscopia de Mossbauer
7.
Biochemistry ; 46(28): 8340-9, 2007 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-17583915

RESUMO

We have determined the 1.8 A X-ray crystal structure of a monoheme c-type cytochrome, cytochrome P460, from Nitrosomonas europea. The chromophore possesses unusual spectral properties analogous to those of the catalytic heme P460 of hydroxylamine oxidoreductase (HAO), the only known heme in biology to withdraw electrons from an iron-coordinated substrate. The analysis reveals a homodimeric structure and elucidates a new c-type cytochrome fold that is predominantly beta-sheet. In addition to the two cysteine thioether links to the porphyrin typical of c-type hemes, there is a third proteinaceous link involving a conserved lysine. The covalent bond is between the lysine side-chain nitrogen and the 13'-meso carbon of the heme, which, following cross-link formation, is sp3-hybridized, demonstrating the loss of conjugation at this position within the porphyrin. The structure has implications for the analogous tyrosine-heme meso carbon cross-link observed in HAO.


Assuntos
Proteínas de Bactérias/química , Citocromos/química , Heme/química , Nitrosomonas europaea/enzimologia , Cristalografia por Raios X , Dimerização , Lisina/química , Modelos Moleculares , Oxirredutases/química , Dobramento de Proteína , Estrutura Secundária de Proteína
8.
FEBS Lett ; 581(5): 911-6, 2007 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-17292891

RESUMO

Cytochromes-P460 of Nitrosomonas europaea and Methylococcus capsulatus (Bath), and the cytochrome c' of M. capsulatus, believed to be involved in binding or transformation of N-oxides, are shown to represent an evolutionarily related new family of monoheme, approximately 17kDa, cytochromes c found in the genomes of diverse Proteobacteria. All members of this family have a predicted secondary structure predominantly of beta-sheets in contrast to the predominantly alpha-helical cytochromes c' found in photoheterotrophic and denitrifying Proteobacteria.


Assuntos
Citocromos c'/química , Citocromos c'/metabolismo , Citocromos c/química , Citocromos c/metabolismo , Citocromos/química , Citocromos/metabolismo , Sequência de Aminoácidos , Proteínas de Bactérias/química , Proteínas de Bactérias/classificação , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Dicroísmo Circular , Citocromos/classificação , Citocromos/genética , Citocromos c/classificação , Citocromos c/genética , Citocromos c'/classificação , Citocromos c'/genética , Evolução Molecular , Methylococcus capsulatus/genética , Methylococcus capsulatus/metabolismo , Nitrosomonas europaea/genética , Nitrosomonas europaea/metabolismo , Filogenia , Estrutura Secundária de Proteína , Homologia de Sequência de Aminoácidos
10.
Arch Biochem Biophys ; 457(1): 95-104, 2007 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-17078921

RESUMO

1H NMR and visible absorption spectroscopy were used to monitor sixth ligand methionine displacement reactions in four members of the ferricytochrome c-551 family from Pseudomonas aeruginosa, Pseudomonas stutzeri, Pseudomonas stutzeri substrain ZoBell, and Nitrosomonas europae. Potassium cyanide displaces the methionine ligand with very modest changes in the visible spectra, but profound changes in the NMR spectra. The initial product formed kinetically, designated complex I, changes with time and/or heating to a more thermodynamically favored product termed complex II. Spectra indicate that both I and II are actually a family of closely related conformational isomers. Low temperature NMR spectra of complex II indicate that some of the isomers are in chemical exchange on the NMR time scale. High pH also displaces the methionine ligand in a manner similar to the well-known alkaline transition of mitochondrial cytochrome c. However, the reaction occurs at higher pH values and over a narrower pH range for the c-551 family, and the transition pH range is different for the different proteins studied. The final alkaline forms also show peak widths and a number of peaks indicative of multiple conformational isomers.


Assuntos
Proteínas de Bactérias/química , Grupo dos Citocromos c/química , Heme/química , Metionina/química , Nitrosomonas/química , Pseudomonas/química , Espectroscopia de Ressonância de Spin Eletrônica , Concentração de Íons de Hidrogênio , Ligantes , Ressonância Magnética Nuclear Biomolecular , Cianeto de Potássio/química , Conformação Proteica , Isoformas de Proteínas/química
11.
J Inorg Biochem ; 101(1): 173-9, 2007 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-17064778

RESUMO

The impact of protonation and inhibitor binding of the diheme cytochrome c peroxidase (CCP) from Nitrosomonas europaea has been examined by the technique of catalytic protein film voltammetry (PFV). Previous efforts have shown that the low-potential heme active site (L) binds substrate and yields electrocatalysis at an pyrolytic graphite edge electrode, with properties evocative of a high-potential intermediate, with E(m)>540mV (vs. normal hydrogen electrode) [A.L. Bradley, S.E. Chobot, D.M. Arciero, A.B. Hooper, S. J. Elliott, J. Biol. Chem. 279 (2004) 13297-13300]. Here we demonstrate through similar experiments that catalytic PFV generates limiting currents which allow for electrochemically-detected enzymology of the Ne CCP: such as the demonstration that pH-dependent Michaelis-Menten constants (K(m) values) reveal a pK(a) value of 6.5 associated with the "ES" complex. Further, the direct electrocatalysis is shown in the presence of known inhibitors (cyanide and azide), indicating that inhibitor binding occurs at L, and shifts the resulting catalytic midpoint potential in a negative direction. Michaelis-Menten treatment of the limiting currents generated in the presence of variable concentrations of inhibitors showed that cyanide behaved as a competitive inhibitor with a K(i) value of 0.15muM; azide revealed a mixed-mode of inhibition. The observed data were found to support a previous model of electrocatalysis, and the role of proton transfer chemistry in the active site is discussed in terms of a structural model.


Assuntos
Citocromo-c Peroxidase/antagonistas & inibidores , Citocromo-c Peroxidase/metabolismo , Nitrosomonas europaea/enzimologia , Catálise , Citocromo-c Peroxidase/química , Eletroquímica , Modelos Moleculares , Prótons
12.
Chemphyschem ; 7(6): 1258-67, 2006 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-16688708

RESUMO

C-type cytochromes with histidine-methionine (His-Met) iron coordination play important roles in electron-transfer reactions and in enzymes. Low-temperature electron paramagnetic resonance (EPR) spectra of low-spin ferric cytochromes c can be divided into two groups, depending on the spread of g values: the normal rhombic ones with small g anisotropy and g(max) below 3.2, and those featuring large g anisotropy with g(max) between 3.3 and 3.8, also denoted as highly axial low spin (HALS) species. Herein we present the detailed magnetic properties of cytochrome c(553) from Bacillus pasteurii (g(max) 3.36) and cytochrome c(552) from Nitrosomonas europaea (g(max) 3.34) over the pH range 6.2 to 8.2. Besides being structurally very similar, cytochrome c(553) shows the presence of a minor rhombic species at pH 6.2 (6 %), whereas cytochrome c(552) has about 25 % rhombic species over pH 7.5. The detailed Mössbauer analysis of cytochrome c(552) confirms the presence of these two low-spin ferric species (HALS and rhombic) together with an 8 % ferrous form with parameters comparable to the horse cytochrome c. Both EPR and Mössbauer data of axial cytochromes c with His-Met iron coordination are consistent with an electronic (d(xy))(2) (d(xz))(2) (d(yz))(1) ground state, which is typical for Type I model hemes.


Assuntos
Grupo dos Citocromos c/química , Citocromos/química , Espectroscopia de Ressonância de Spin Eletrônica/métodos , Histidina/química , Metionina/química , Espectroscopia de Mossbauer/métodos , Anisotropia , Bacillus/metabolismo , Biofísica/métodos , Elétrons , Concentração de Íons de Hidrogênio , Ligantes , Espectroscopia de Ressonância Magnética , Nitrosomonas/metabolismo
13.
Artigo em Inglês | MEDLINE | ID: mdl-16582494

RESUMO

Cytochrome P460 from Nitrosomonas europaea, a novel mono-heme protein containing an unusual cross-link between a conserved lysine and the porphyrin ring, has been recombinantly expressed and purified from Escherichia coli. The protein crystallizes readily and diffraction to 1.7 angstroms has been obtained in-house. The crystals belong to the trigonal space group P3(1/2)21, with unit-cell parameters a = b = 53.3, c = 127.1 angstroms, and contain one monomer in the asymmetric unit.


Assuntos
Citocromos/química , Nitrosomonas europaea/enzimologia , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/isolamento & purificação , Proteínas de Bactérias/metabolismo , Sequência de Bases , Clonagem Molecular , Sequência Conservada , Cristalização , Citocromos/genética , Citocromos/isolamento & purificação , Citocromos/metabolismo , Primers do DNA , Hemeproteínas/química , Lisina , Espectrometria de Massas , Reação em Cadeia da Polimerase , Difração de Raios X
14.
J Am Chem Soc ; 128(13): 4330-7, 2006 Apr 05.
Artigo em Inglês | MEDLINE | ID: mdl-16569009

RESUMO

The tetraheme cytochrome c(554) (cyt c(554)) from Nitrosomonas europaea is believed to function as an electron-transfer protein from hydroxylamine oxidoreductase (HAO). We show here that cyt c(554) also has significant NO reductase activity. The protein contains one high-spin and three low-spin c-type hemes. HAO catalyzed reduction of the cyt c(554), ligand binding, intermolecular electron transfer, and kinetics of NO reduction by cyt c(554) have been investigated. We detect the formation of a NO-bound ferrous heme species in cyt c(554) by EPR and Mössbauer spectroscopies during the HAO catalyzed oxidation of hydroxylamine, indicating that N-oxide intermediates produced from HAO readily bind to cyt c(554). In the half-reduced state of cyt c(554), we detect a spin interaction between the [FeNO](7) state of heme 2 and the low-spin ferric state of heme 4. We find that ferrous cyt c(554) will reduce NO at a rate greater than 16 s(-1), which is comparable to rates of other known NO reductases. Carbon monoxide or nitrite are shown not to bind to the reduced protein, and previous results indicate the reactions with O(2) are slow and that a variety of ligands will not bind in the oxidized state. Thus, the enzymatic site is highly selective for NO. The NO reductase activity of cyt c(554) may be important during ammonia oxidation in N. europaea at low oxygen concentrations to detoxify NO produced by reduction of nitrite or incomplete oxidation of hydroxylamine.


Assuntos
Grupo dos Citocromos c/metabolismo , Heme/metabolismo , Nitrosomonas europaea/enzimologia , Oxirredutases/metabolismo , Catálise , Grupo dos Citocromos c/química , Espectroscopia de Ressonância de Spin Eletrônica , Heme/química , Hidroxilamina/química , Cinética , Oxirredução , Oxirredutases/química , Espectroscopia de Mossbauer
15.
Appl Environ Microbiol ; 71(9): 5371-82, 2005 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-16151127

RESUMO

Comparison of the organization and sequence of the hao (hydroxylamine oxidoreductase) gene clusters from the gammaproteobacterial autotrophic ammonia-oxidizing bacterium (aAOB) Nitrosococcus oceani and the betaproteobacterial aAOB Nitrosospira multiformis and Nitrosomonas europaea revealed a highly conserved gene cluster encoding the following proteins: hao, hydroxylamine oxidoreductase; orf2, a putative protein; cycA, cytochrome c(554); and cycB, cytochrome c(m)(552). The deduced protein sequences of HAO, c(554), and c(m)(552) were highly similar in all aAOB despite their differences in species evolution and codon usage. Phylogenetic inference revealed a broad family of multi-c-heme proteins, including HAO, the pentaheme nitrite reductase, and tetrathionate reductase. The c-hemes of this group also have a nearly identical geometry of heme orientation, which has remained conserved during divergent evolution of function. High sequence similarity is also seen within a protein family, including cytochromes c(m)(552), NrfH/B, and NapC/NirT. It is proposed that the hydroxylamine oxidation pathway evolved from a nitrite reduction pathway involved in anaerobic respiration (denitrification) during the radiation of the Proteobacteria. Conservation of the hydroxylamine oxidation module was maintained by functional pressure, and the module expanded into two separate narrow taxa after a lateral gene transfer event between gamma- and betaproteobacterial ancestors of extant aAOB. HAO-encoding genes were also found in six non-aAOB, either singly or tandemly arranged with an orf2 gene, whereas a c(554) gene was lacking. The conservation of the hao gene cluster in general and the uniqueness of the c(554) gene in particular make it a suitable target for the design of primers and probes useful for molecular ecology approaches to detect aAOB.


Assuntos
Amônia/metabolismo , Evolução Molecular , Família Multigênica , Oxirredutases/genética , Proteobactérias/enzimologia , Sequência de Aminoácidos , Betaproteobacteria/enzimologia , Betaproteobacteria/genética , Chromatiaceae/enzimologia , Chromatiaceae/genética , Sequência Conservada , Dados de Sequência Molecular , Nitrosomonas europaea/enzimologia , Nitrosomonas europaea/genética , Oxirredução , Oxirredutases/química , Oxirredutases/metabolismo , Filogenia , Proteobactérias/genética , Análise de Sequência de DNA
16.
J Am Chem Soc ; 127(10): 3531-44, 2005 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-15755175

RESUMO

The electronic structure of the red copper site in nitrosocyanin is defined relative to that of the well understood blue copper site of plastocyanin by using low-temperature absorption, circular dichroism, magnetic circular dichroism, resonance Raman, EPR and X-ray absorption spectroscopies, combined with DFT calculations. These studies indicate that the principal electronic structure change in the red copper site is the sigma rather than the pi donor interaction of the cysteine sulfur with the Cu 3d(x2-y2) redox active molecular orbital (RAMO). Further, MCD data show that there is an increase in ligand field strength due to an increase in coordination number, whereas resonance Raman spectra indicate a weaker Cu-S bond. The latter is supported by the S K-edge data, which demonstrate a less covalent thiolate interaction with the RAMO of nitrosocyanin at 20% relative to plastocyanin at 38%. EXAFS results give a longer Cu-S(Cys) bond distance in nitrosocyanin (2.28 A) compared to plastocyanin (2.08 A) and also show a large change in structure with reduction of the red copper site. The red copper site is the only presently known blue copper-related site with an exogenous water coordinated to the copper. Density functional calculations reproduce the experimental properties and are used to determine the specific protein structure contributions to exogenous ligand binding in red copper. The relative orientation of the CuNNS and the CuSC(beta) planes (determined by the protein sequence) is found to be key in generating an exchangeable coordination position at the red copper active site. The exogenous water ligation at the red copper active site greatly increases the reorganization energy (by approximately 1.0 eV) relative to that of the blue copper protein site, making the red site unfavorable for fast outer-sphere electron transfer, while providing an exchangeable coordination position for inner-sphere electron transfer.


Assuntos
Proteínas de Bactérias/química , Cobre/química , Metaloproteínas/química , Proteínas de Bactérias/isolamento & purificação , Sítios de Ligação , Dicroísmo Circular , Cristalografia por Raios X , Espectroscopia de Ressonância de Spin Eletrônica , Metaloproteínas/isolamento & purificação , Modelos Moleculares , Estrutura Molecular , Nitrosomonas europaea/química , Oxirredução , Análise Espectral Raman
17.
J Biol Chem ; 279(14): 13297-300, 2004 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-14973133

RESUMO

Here the cytochrome c peroxidase (CcP) from Nitrosomonas europaea is examined using the technique of catalytic protein film voltammetry. Submonolayers of the bacterial diheme enzyme at a pyrolytic graphite edge electrode give catalytic, reductive signals in the presence of the substrate hydrogen peroxide. The resulting waveshapes indicate that CcP is bound non-covalently in a highly active configuration. The native enzyme has been shown to possess two heme groups of low and high potential (L and H, -260 and +450 mV versus hydrogen, respectively), and here we find that the catalytic waves of the N. europaea enzyme have a midpoint potential of >500 mV and a shape that corresponds to a 1-electron process. The signals increase in magnitude with hydrogen peroxide concentration, revealing Michaelis-Menten kinetics and K(m) = 55 microm. The midpoint potentials shift with substrate concentration, indicating the electrochemically active species observed in our data corresponds to a catalytic species. The potentials also shift with respect to pH, and the pH dependence is interpreted in terms of a two pK(a) model for proton binding. Together the data show that the electrochemistry of the N. europaea cytochrome c peroxidase is unlike other peroxidases studied to date, including other bacterial enzymes. This is discussed in terms of a catalytic model for the N. europaea enzyme and compared with other cytochrome c peroxidases.


Assuntos
Citocromo-c Peroxidase/química , Citocromo-c Peroxidase/metabolismo , Nitrosomonas europaea/enzimologia , Eletroquímica , Ativação Enzimática/efeitos dos fármacos , Ativação Enzimática/fisiologia , Enzimas Imobilizadas , Peróxido de Hidrogênio/farmacologia , Concentração de Íons de Hidrogênio , Modelos Químicos , Oxirredução
18.
Eur J Biochem ; 270(9): 1935-41, 2003 May.
Artigo em Inglês | MEDLINE | ID: mdl-12709052

RESUMO

The heme of cytochrome P460 of Nitrosomonas europaea, which is covalently crosslinked to two cysteines of the polypeptide as with all c-type cytochromes, has an additional novel covalent crosslink to lysine 70 of the polypeptide [Arciero, D.M. & Hooper, A.B. (1997) FEBS Lett.410, 457-460]. The protein can catalyze the oxidation of hydroxylamine. The gene for this protein, cyp, was expressed in Pseudomonas aeruginosa strain PAO lacI, resulting in formation of a holo-cytochrome P460 which closely resembled native cytochrome P460 purified from N. europaea in its UV-visible spectroscopic, ligand binding and catalytic properties. Mutant versions of cytochrome P460 of N. europaea in which Lys70 70 was replaced by Arg, Ala, or Tyr, retained ligand-binding ability but lost catalytic ability and differed in optical spectra which, instead, closely resembled those of cytochromes c'. Tryptic fragments containing the c-heme joined only by two thioether linkages were observed by MALDI-TOF for the mutant cytochromes P460 K70R and K70A but not in wild-type cytochrome P460, consistent with the structural modification of the c-heme only in the wild-type cytochrome. The present observations support the hypothesized evolutionary relationship between cytochromes P460 and cytochromes c' in N. europaea and M. capsulatus[Bergmann, D.J., Zahn, J.A., & DiSpirito, A.A. (2000) Arch. Microbiol. 173, 29-34], confirm the importance of a heme-crosslink to the spectroscopic properties and catalysis and suggest that the crosslink might form auto-catalytically.


Assuntos
Proteínas de Bactérias/metabolismo , Grupo dos Citocromos c/metabolismo , Citocromos/metabolismo , Nitrosomonas/enzimologia , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Grupo dos Citocromos c/química , Citocromos/química , Citocromos/genética , Heme/química , Mutação , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Análise Espectral
19.
J Am Chem Soc ; 125(7): 1738-47, 2003 Feb 19.
Artigo em Inglês | MEDLINE | ID: mdl-12580599

RESUMO

The tetraheme cytochrome c(554) (cyt c(554)) from Nitrosomonas europaea is an essential electron transfer component in the biological oxidation of ammonia. The protein contains one 5-coordinate heme and three bis-His coordinated hemes in a 3D arrangement common to a newly characterized class of multiheme proteins. The ligand binding, electrochemical properties, and heme-heme interactions are investigated with Mössbauer and X- and Q-band (parallel/perpendicular mode) EPR spectroscopy. The results indicate that the 5-coordinate heme will not bind the common heme ligands, CN(-), F(-), CO, and NO in a wide pH range. Thus, cyt c(554) functions only in electron transfer. Analysis of a series of electrochemically poised and chemically reduced samples allows assignment of reduction potentials for heme 1 through 4 of +47, +47, -147, and -276 mV, respectively. The spectroscopic results indicate that the hemes are weakly exchange-coupled (J approximately -0.5 cm(-)(1)) in two separate pairs and in accordance with the structure: hemes 2/4 (high-spin/low-spin), hemes 1/3 (low-spin/low-spin). There is no evidence of exchange coupling between the pairs. A comparison of the reduction potentials between homologous hemes of cyt c(554) and other members of this new class of multiheme proteins is discussed. Heme 1 has a unique axial N(delta)-His coordination which contributes to a higher potential relative to the homologous hemes of hydroxylamine oxidoreductase (HAO) and the split-Soret cytochrome. Heme 2 is 300 mV more positive than heme 4 of HAO, which is attributed to hydroxide coordination to heme 4 of HAO.


Assuntos
Grupo dos Citocromos c/química , Nitrosomonas/química , Grupo dos Citocromos c/metabolismo , Eletroquímica , Espectroscopia de Ressonância de Spin Eletrônica/métodos , Ligantes , Modelos Moleculares , Nitrosomonas/metabolismo , Oxirredução , Espectroscopia de Mossbauer/métodos , Titulometria
20.
Biochemistry ; 41(14): 4603-11, 2002 Apr 09.
Artigo em Inglês | MEDLINE | ID: mdl-11926822

RESUMO

Hydroxylamine oxidoreductase (HAO) from the autotrophic nitrifying bacterium Nitrosomonas europaea catalyzes the oxidation of NH2OH to NO2-. The enzyme contains eight hemes per subunit which participate in catalysis and electron transport. NO is found to bind to the enzyme and inhibit electron flow to the acceptor protein, cytochrome c554. NO is found to oxidize either partially or fully reduced HAO, but NO will not reduce ferric HAO. Since NO can be reduced but not oxidized to product by HAO, NO is not considered to be a long-lived intermediate in the catalytic mechanism. Substrate oxidation occurs in the presence of bound NO or cyanide, suggesting a second interaction site for substrate with HAO and providing a means for recovery of the NO-inhibited form of the enzyme. Upon addition of NO to oxidized HAO, the integer-spin EPR signal from the active site vanishes, an IR band from NO appears at 1920 cm(-1), and a diamagnetic quadrupole iron doublet appears in Mössbauer spectroscopy with delta = 0.06 mm/s and DeltaEq = 2.1 mm/s. The NO stretching frequency and Mössbauer parameters are characteristic of an [FeNO]6 heme complex. New Mössbauer data on ferric myoglobin-NO are also presented for comparison. The results indicate that NO binds to heme P460 and that the loss of the integer-spin EPR signal is due to the conversion of heme P460 to a diamagnetic S = 0 state and concomitant loss of magnetic interaction with neighboring heme 6. In previous studies where the heme P460-heme 6 interaction was affected by substrate or cyanide binding, a signal attributable to heme 6 was not observable. In contrast, in this work, the NO-induced loss of the signal is accompanied by the appearance of a previously unobserved large g(max) (or HALS) low-spin EPR signal from heme 6.


Assuntos
Óxido Nítrico/química , Oxirredutases/química , Espectroscopia de Ressonância de Spin Eletrônica , Óxido Nítrico/metabolismo , Nitrosomonas/enzimologia , Oxirredução , Oxirredutases/isolamento & purificação , Oxirredutases/metabolismo , Conformação Proteica , Subunidades Proteicas , Espectrofotometria , Espectroscopia de Infravermelho com Transformada de Fourier , Espectroscopia de Mossbauer
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