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1.
Microbes Environ ; 32(1): 54-60, 2017 Mar 31.
Article in English | MEDLINE | ID: mdl-28260736

ABSTRACT

Hydrogen sulfide (H2S) is emitted from industrial activities, and several chemotrophs possessing Sox enzymes are used for its removal. Oral malodor is a common issue in the dental field and major malodorous components are volatile sulfur compounds (VSCs), including H2S and methyl mercaptan. Paracoccus pantotrophus is an aerobic, neutrophilic facultatively autotrophic bacterium that possesses sulfur-oxidizing (Sox) enzymes in order to use sulfur compounds as an energy source. In the present study, we cloned the Sox enzymes of P. pantotrophus GB17 and evaluated their VSC-degrading activities for the prevention of oral malodor. Six genes, soxX, soxY, soxZ, soxA, soxB, and soxCD, were amplified from P. pantotrophus GB17. Each fragment was cloned into a vector for the expression of 6×His-tagged fusion proteins in Escherichia coli. Recombinant Sox (rSox) proteins were purified from whole-cell extracts of E. coli using nickel affinity chromatography. The enzyme mixture was investigated for the degradation of VSCs using gas chromatography. Each of the rSox enzymes was purified to apparent homogeneity, as confirmed by SDS-PAGE. The rSox enzyme mixture degraded H2S in dose- and time-dependent manners. All rSox enzymes were necessary for degrading H2S. The H2S-degrading activities of rSox enzymes were stable at 25-80°C, and the optimum pH was 7.0. The amount of H2S produced by periodontopathic bacteria or oral bacteria collected from human subjects decreased after an incubation with rSox enzymes. These results suggest that the combination of rSox enzymes from P. pantotrophus GB17 is useful for the prevention of oral malodor.


Subject(s)
Hydrogen Sulfide/metabolism , Oxidoreductases/metabolism , Paracoccus pantotrophus/enzymology , Paracoccus pantotrophus/metabolism , Recombinant Proteins/metabolism , Biotransformation , Chromatography, Affinity , Chromatography, Gas , Cloning, Molecular , Enzyme Stability , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Hydrogen-Ion Concentration , Oxidation-Reduction , Oxidoreductases/chemistry , Oxidoreductases/genetics , Oxidoreductases/isolation & purification , Paracoccus pantotrophus/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Temperature
2.
Mol Microbiol ; 92(1): 153-63, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24673795

ABSTRACT

It has recently been shown that the biosynthetic route for both the d1 -haem cofactor of dissimilatory cd1 nitrite reductases and haem, via the novel alternative-haem-synthesis pathway, involves siroheme as an intermediate, which was previously thought to occur only as a cofactor in assimilatory sulphite/nitrite reductases. In many denitrifiers (which require d1 -haem), the pathway to make siroheme remained to be identified. Here we identify and characterize a sirohydrochlorin-ferrochelatase from Paracoccus pantotrophus that catalyses the last step of siroheme synthesis. It is encoded by a gene annotated as cbiX that was previously assumed to be encoding a cobaltochelatase, acting on sirohydrochlorin. Expressing this chelatase from a plasmid restored the wild-type phenotype of an Escherichia coli mutant-strain lacking sirohydrochlorin-ferrochelatase activity, showing that this chelatase can act in the in vivo siroheme synthesis. A ΔcbiX mutant in P. denitrificans was unable to respire anaerobically on nitrate, proving the role of siroheme as a precursor to another cofactor. We report the 1.9 Å crystal structure of this ferrochelatase. In vivo analysis of single amino acid variants of this chelatase suggests that two histidines, His127 and His187, are essential for siroheme synthesis. This CbiX can generally be identified in α-proteobacteria as the terminal enzyme of siroheme biosynthesis.


Subject(s)
Bacterial Proteins/chemistry , Catalytic Domain , Ferrochelatase/chemistry , Heme/analogs & derivatives , Paracoccus pantotrophus/enzymology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Crystallography, X-Ray , Ferrochelatase/genetics , Ferrochelatase/metabolism , Heme/biosynthesis , Histidine/genetics , Models, Molecular , Mutation , Paracoccus pantotrophus/genetics , Protein Structure, Tertiary
3.
Appl Environ Microbiol ; 79(14): 4455-64, 2013 Jul.
Article in English | MEDLINE | ID: mdl-23686269

ABSTRACT

During chemolithoautotrophic thiosulfate oxidation, the phylogenetically diverged proteobacteria Paracoccus pantotrophus, Tetrathiobacter kashmirensis, and Thiomicrospira crunogena rendered steady enrichment of (34)S in the end product sulfate, with overall fractionation ranging between -4.6‰ and +5.8‰. The fractionation kinetics of T. crunogena was essentially similar to that of P. pantotrophus, albeit the former had a slightly higher magnitude and rate of (34)S enrichment. In the case of T. kashmirensis, the only significant departure of its fractionation curve from that of P. pantotrophus was observed during the first 36 h of thiosulfate-dependent growth, in the course of which tetrathionate intermediate formation is completed and sulfate production starts. The almost-identical (34)S enrichment rates observed during the peak sulfate-producing stage of all three processes indicated the potential involvement of identical S-S bond-breaking enzymes. Concurrent proteomic analyses detected the hydrolase SoxB (which is known to cleave terminal sulfone groups from SoxYZ-bound cysteine S-thiosulfonates, as well as cysteine S-sulfonates, in P. pantotrophus) in the actively sulfate-producing cells of all three species. The inducible expression of soxB during tetrathionate oxidation, as well as the second leg of thiosulfate oxidation, by T. kashmirensis is significant because the current Sox pathway does not accommodate tetrathionate as one of its substrates. Notably, however, no other Sox protein except SoxB could be detected upon matrix-assisted laser desorption ionization mass spectrometry analysis of all such T. kashmirensis proteins as appeared to be thiosulfate inducible in 2-dimensional gel electrophoresis. Instead, several other redox proteins were found to be at least 2-fold overexpressed during thiosulfate- or tetrathionate-dependent growth, thereby indicating that there is more to tetrathionate oxidation than SoxB alone.


Subject(s)
Alcaligenaceae/metabolism , Hydrolases/metabolism , Paracoccus pantotrophus/metabolism , Piscirickettsiaceae/metabolism , Proteome/metabolism , Thiosulfates/metabolism , Autotrophic Processes , Bacterial Proteins/metabolism , Disulfides/metabolism , Oxidation-Reduction , Paracoccus pantotrophus/enzymology , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Sulfur Isotopes/metabolism , Two-Dimensional Difference Gel Electrophoresis
4.
Org Lett ; 14(8): 1982-5, 2012 Apr 20.
Article in English | MEDLINE | ID: mdl-22480179

ABSTRACT

A new reductase, CgKR2, with the ability to reduce ethyl 2-oxo-4-phenylbutyrate (OPBE) to ethyl (R)-2-hydroxy-4-phenylbutyrate ((R)-HPBE), an important chiral precursor for angiotensin-converting enzyme (ACE) inhibitors, was discovered. For the first time, (R)-HPBE with >99% ee was produced via bioreduction of OPBE at 1 M without external addition of cofactors. The space-time yield (700 g·L(-1)·d(-1)) was 27 times higher than the highest record.


Subject(s)
Angiotensin-Converting Enzyme Inhibitors/chemical synthesis , Oxidoreductases/metabolism , Phenylbutyrates/chemical synthesis , Angiotensin-Converting Enzyme Inhibitors/chemistry , Angiotensin-Converting Enzyme Inhibitors/metabolism , Candida/enzymology , Escherichia coli/drug effects , Molecular Structure , Paracoccus pantotrophus/enzymology , Phenylbutyrates/chemistry , Phenylbutyrates/metabolism , Stereoisomerism
5.
J Biol Inorg Chem ; 16(6): 881-8, 2011 Aug.
Article in English | MEDLINE | ID: mdl-21547574

ABSTRACT

The activation mechanism of Pseudomonas stutzeri cytochrome c peroxidase (CCP) was probed through the mediated electrochemical catalysis by its physiological electron donor, P. stutzeri cytochrome c-551. A comparative study was carried out, by performing assays with the enzyme in the resting oxidized state as well as in the mixed-valence activated form, using cyclic voltammetry and a pyrolytic graphite membrane electrode. In the presence of both the enzyme and hydrogen peroxide, the peak-like signal of cytochrome c-551 is converted into a sigmoidal wave form characteristic of an E(r)C'(i) catalytic mechanism. An intermolecular electron transfer rate constant of (4 ± 1) × 10(5) M(-1) s(-1) was estimated for both forms of the enzyme, as well as a similar Michaelis-Menten constant. These results show that neither the intermolecular electron transfer nor the catalytic activity is kinetically controlled by the activation mechanism of CCP in the case of the P. stutzeri enzyme. Direct enzyme catalysis using protein film voltammetry was unsuccessful for the analysis of the activation mechanism, since P. stutzeri CCP undergoes an undesirable interaction with the pyrolytic graphite surface. This interaction, previously reported for the Paracoccus pantotrophus CCP, induces the formation of a non-native conformation state of the electron-transferring haem, which has a redox potential 200 mV lower than that of the native state and maintains peroxidatic activity.


Subject(s)
Bacterial Proteins/metabolism , Cytochrome-c Peroxidase/metabolism , Electron Transport/physiology , Enzyme Activation , Pseudomonas stutzeri/enzymology , Bacterial Proteins/chemistry , Catalysis , Cytochrome-c Peroxidase/chemistry , Electrochemistry , Oxidation-Reduction , Paracoccus pantotrophus/enzymology
6.
Phys Chem Chem Phys ; 13(17): 7720-31, 2011 May 07.
Article in English | MEDLINE | ID: mdl-21423952

ABSTRACT

In protein film electrochemistry a redox protein of interest is studied as an electroactive film adsorbed on an electrode surface. For redox enzymes this configuration allows quantification of the relationship between catalytic activity and electrochemical potential. Considered as a function of enzyme environment, i.e., pH, substrate concentration etc., the activity-potential relationship provides a fingerprint of activity unique to a given enzyme. Here we consider the nature of the activity-potential relationship in terms of both its cellular impact and its origin in the structure and catalytic mechanism of the enzyme. We propose that the activity-potential relationship of a redox enzyme is tuned to facilitate cellular function and highlight opportunities to test this hypothesis through computational, structural, biochemical and cellular studies.


Subject(s)
Enzymes/chemistry , Nitrate Reductase/chemistry , Nitrates/chemistry , Biocatalysis , Electrochemical Techniques/methods , Electrochemistry , Enzymes/metabolism , Kinetics , Models, Molecular , Nitrate Reductase/metabolism , Nitrates/metabolism , Oxidation-Reduction , Paracoccus pantotrophus/enzymology , Structure-Activity Relationship
7.
Biochem Soc Trans ; 39(1): 236-42, 2011 Jan.
Article in English | MEDLINE | ID: mdl-21265780

ABSTRACT

Bacterial cellular metabolism is renowned for its metabolic diversity and adaptability. However, certain environments present particular challenges. Aerobic metabolism of highly reduced carbon substrates by soil bacteria such as Paracoccus pantotrophus presents one such challenge since it may result in excessive electron delivery to the respiratory redox chain when compared with the availability of terminal oxidant, O2. The level of a periplasmic ubiquinol-dependent nitrate reductase, NAP, is up-regulated in the presence of highly reduced carbon substrates. NAP oxidizes ubiquinol at the periplasmic face of the cytoplasmic membrane and reduces nitrate in the periplasm. Thus its activity counteracts the accumulation of excess reducing equivalents in ubiquinol, thereby maintaining the redox poise of the ubiquinone/ubiquinol pool without contributing to the protonmotive force across the cytoplasmic membrane. Although P. pantotrophus NapAB shows a high level of substrate specificity towards nitrate, the enzyme has also been reported to reduce selenate in spectrophotometric solution assays. This transaction draws on our current knowledge concerning the bacterial respiratory nitrate reductases and extends the application of PFE (protein film electrochemistry) to resolve and quantify the selenate reductase activity of NapAB.


Subject(s)
Bacterial Proteins/metabolism , Nitrate Reductases/metabolism , Nitrates/metabolism , Selenium Compounds/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Electrochemical Techniques , Isoenzymes/chemistry , Isoenzymes/genetics , Isoenzymes/metabolism , Models, Molecular , Nitrate Reductases/chemistry , Nitrate Reductases/genetics , Oxidation-Reduction , Paracoccus pantotrophus/enzymology , Periplasm/enzymology , Protein Conformation , Selenic Acid , Selenium/metabolism , Ubiquinone/analogs & derivatives , Ubiquinone/metabolism
8.
Biochem J ; 435(1): 217-25, 2011 Apr 01.
Article in English | MEDLINE | ID: mdl-21244362

ABSTRACT

Cytochrome cd1 nitrite reductase is a haem-containing enzyme responsible for the reduction of nitrite into NO, a key step in the anaerobic respiratory process of denitrification. The active site of cytochrome cd1 contains the unique d1 haem cofactor, from which NO must be released. In general, reduced haems bind NO tightly relative to oxidized haems. In the present paper, we present experimental evidence that the reduced d1 haem of cytochrome cd1 from Paracoccus pantotrophus releases NO rapidly (k=65-200 s(-1)); this result suggests that NO release is the rate-limiting step of the catalytic cycle (turnover number=72 s(-1)). We also demonstrate, using a complex of the d1 haem and apomyoglobin, that the rapid dissociation of NO is largely controlled by the d1 haem cofactor itself. We present a reaction mechanism proposed to be applicable to all cytochromes cd1 and conclude that the d1 haem has evolved to have low affinity for NO, as compared with other ferrous haems.


Subject(s)
Bacterial Proteins/metabolism , Cytochromes/metabolism , Heme/analogs & derivatives , Nitric Oxide/metabolism , Nitrite Reductases/metabolism , Paracoccus pantotrophus/enzymology , Apoproteins/metabolism , Biocatalysis , Denitrification , Heme/metabolism , Kinetics , Models, Molecular , Myoglobin/metabolism , Oxidation-Reduction , Photolysis
9.
J Biol Inorg Chem ; 16(2): 209-15, 2011 Feb.
Article in English | MEDLINE | ID: mdl-20963615

ABSTRACT

In this work it is demonstrated that the characterization of c-type haem containing proteins by electrochemical techniques needs to be cautiously performed when using pyrolytic graphite electrodes. An altered form of the cytochromes, which has a redox potential 300 mV lower than that of the native state and displays peroxidatic activity, can be induced by interaction with the pyrolytic graphite electrode. Proper control experiments need to be performed, as altered conformations of the enzymes containing c-type haems can show activity towards the enzyme substrate. The work was focused on the study of the activation mechanism and catalytic activity of cytochrome c peroxidase from Paracoccus pantotrophus. The results could only be interpreted with the assignment of the observed non-turnover and catalytic signals to a non-native conformation state of the electron-transferring haem. The same phenomenon was detected for Met-His monohaem cytochromes (mitochondrial cytochrome c and Desulfovibrio vulgaris cytochrome c-553), as well as for the bis-His multihaem cytochrome c(3) from Desulfovibrio gigas, showing that this effect is independent of the axial coordination of the c-type haem protein. Thus, the interpretation of electrochemical signals of c-type (multi)haem proteins at pyrolytic graphite electrodes must be carefully performed, to avoid misassignment of the signals and incorrect interpretation of catalytic intermediates.


Subject(s)
Carbon/chemistry , Electrochemistry/methods , Electrodes , Hemeproteins/chemistry , Cytochrome-c Peroxidase/chemistry , Paracoccus pantotrophus/enzymology , Protein Structure, Secondary
10.
Inorg Chem ; 50(2): 409-11, 2011 Jan 17.
Article in English | MEDLINE | ID: mdl-21142117

ABSTRACT

The bacterial sulfane dehydrogenase SoxCD is a distantly related member of the sulfite oxidase (SO) enzyme family that is proposed to oxidize protein-bound sulfide (sulfane) of SoxY as part of a multienzyme mechanism of thiosulfate metabolism. This study characterized the molybdenum cofactor of SoxCD1, comprising the catalytic molybdopterin subunit SoxC and the truncated c-type cytochrome subunit SoxD1. Electron paramagnetic resonance spectroscopy of the Mo(V) intermediate generated by dithionite reduction revealed low- and high-pH species with g and A((95,97)Mo) matrices nearly identical to those of SO, indicating a similar pentacoordinate active site in SoxCD1. However, no sulfite-induced reduction to Mo(V) was detected, nor could a strongly coupled (1)H signal or a phosphate-inhibited species be generated. This indicates that the outer coordination sphere controls substrate binding in SoxCD, permitting access only to protein-bound sulfur via the C-terminal tail of SoxY.


Subject(s)
Coenzymes/chemistry , Metalloproteins/chemistry , Paracoccus pantotrophus/enzymology , Pteridines/chemistry , Catalytic Domain , Chlorides/chemistry , Electron Spin Resonance Spectroscopy , Hydrogen-Ion Concentration , Ligands , Molybdenum Cofactors , Paracoccus pantotrophus/genetics , Sulfur/chemistry
11.
J Biol Chem ; 286(10): 8349-8360, 2011 Mar 11.
Article in English | MEDLINE | ID: mdl-21147779

ABSTRACT

The sulfur cycle enzyme sulfane dehydrogenase SoxCD is an essential component of the sulfur oxidation (Sox) enzyme system of Paracoccus pantotrophus. SoxCD catalyzes a six-electron oxidation reaction within the Sox cycle. SoxCD is an α(2)ß(2) heterotetrameric complex of the molybdenum cofactor-containing SoxC protein and the diheme c-type cytochrome SoxD with the heme domains D(1) and D(2). SoxCD(1) misses the heme-2 domain D(2) and is catalytically as active as SoxCD. The crystal structure of SoxCD(1) was solved at 1.33 Å. The substrate of SoxCD is the outer (sulfane) sulfur of Cys-110-persulfide located at the C-terminal peptide swinging arm of SoxY of the SoxYZ carrier complex. The SoxCD(1) substrate funnel toward the molybdopterin is narrow and partially shielded by side-chain residues of SoxD(1). For access of the sulfane-sulfur of SoxY-Cys-110 persulfide we propose that (i) the blockage by SoxD-Arg-98 is opened via interaction with the C terminus of SoxY and (ii) the C-terminal peptide VTIGGCGG of SoxY provides interactions with the entrance path such that the cysteine-bound persulfide is optimally positioned near the molybdenum atom. The subsequent oxidation reactions of the sulfane-sulfur are initiated by the nucleophilic attack of the persulfide anion on the molybdenum atom that is, in turn, reduced. The close proximity of heme-1 to the molybdopterin allows easy acceptance of the electrons. Because SoxYZ, SoxXA, and SoxB are already structurally characterized, with SoxCD(1) the structures of all key enzymes of the Sox cycle are known with atomic resolution.


Subject(s)
Bacterial Proteins/chemistry , Molybdenum/chemistry , Oxidoreductases/chemistry , Paracoccus pantotrophus/enzymology , Sulfur/chemistry , Bacterial Proteins/genetics , Crystallography, X-Ray , Oxidation-Reduction , Oxidoreductases/genetics , Paracoccus pantotrophus/genetics , Peptides/chemistry , Peptides/genetics , Protein Structure, Quaternary , Protein Structure, Tertiary , Structure-Activity Relationship
12.
Biochemistry ; 50(1): 17-24, 2011 Jan 11.
Article in English | MEDLINE | ID: mdl-21110519

ABSTRACT

A new way to study the electrochemical properties of proteins by coupling front-face fluorescence spectroscopy with an optically transparent thin-layer electrochemical cell is presented. First, the approach was examined on the basis of the redox-dependent conformational changes in tryptophans in cytochrome c, and its redox potential was successfully determined. Second, an electrochemically induced fluorescence analysis of periplasmic thiol-disulfide oxidoreductases SoxS and SoxW was performed. SoxS is essential for maintaining chemotrophic sulfur oxidation of Paracoccus pantotrophus active in vivo, while SoxW is not essential. According to the potentiometric redox titration of tryptophan fluorescence, the midpoint potential of SoxS was -342 ± 8 mV versus the standard hydrogen electrode (SHE') and that of SoxW was -256 ± 10 mV versus the SHE'. The fluorescence properties of the thioredoxins are presented and discussed together with the intrinsic fluorescence contribution of the tyrosines.


Subject(s)
Bacterial Proteins/chemistry , Cytochromes c/chemistry , Oxidoreductases/chemistry , Paracoccus pantotrophus/chemistry , Spectrometry, Fluorescence/instrumentation , Thioredoxins/chemistry , Amino Acid Sequence , Animals , Electrochemical Techniques/instrumentation , Electrochemical Techniques/methods , Equipment Design , Horses , Molecular Sequence Data , Oxidation-Reduction , Paracoccus pantotrophus/enzymology , Spectrometry, Fluorescence/methods
13.
Biotechnol Prog ; 25(4): 973-9, 2009.
Article in English | MEDLINE | ID: mdl-19399903

ABSTRACT

Paracoccus pantotrophus expresses two nitrate reductases-membrane bound nitrate reductase (Nar) and periplasmic nitrate reductase (Nap). In growth experiments with two denitrifying species (Paracoccus pantotrophus and Alcaligenes eutrophus) that have both Nap and Nar and two species (Pseudomonas denitrificans and Pseudomonas fluorescens) with Nar only, it was found that diauxic lag is shorter for bacteria that express Nap. In P. pantotrophus, napEDABC encodes the periplasmic nitrate reductase. To analyze the effect of Nap on diauxic lag, the nap operon was deleted from P. pantotrophus. The growth experiments with nap(-) mutant resulted in increased diauxic lag when switched from aerobic to anoxic respiration, suggesting Nap is responsible for shorter lags and helps in adaptation to anoxic metabolism after transition from aerobic conditions.


Subject(s)
Bacterial Proteins/metabolism , Nitrate Reductase/metabolism , Paracoccus pantotrophus/enzymology , Paracoccus pantotrophus/growth & development , Periplasmic Proteins/metabolism , Aerobiosis , Anaerobiosis , Bacterial Proteins/genetics , Nitrate Reductase/genetics , Paracoccus pantotrophus/genetics , Periplasmic Proteins/genetics
14.
Electron. j. biotechnol ; 12(2): 4-5, Apr. 2009. ilus, tab
Article in English | LILACS | ID: lil-551365

ABSTRACT

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.


Subject(s)
Artemia/metabolism , Molybdoferredoxin/metabolism , Paracoccus pantotrophus , Paracoccus pantotrophus/enzymology , Bioaccumulation/analysis , Denitrification
15.
Acta Crystallogr D Biol Crystallogr ; 65(Pt 3): 229-40, 2009 Mar.
Article in English | MEDLINE | ID: mdl-19237745

ABSTRACT

The periplasmic thiol-disulfide oxidoreductase SoxS is beneficial for the sulfur-oxidizing (Sox) phenotype of the facultative chemotrophic bacterium Paracoccus pantotrophus and is not part of the Sox enzyme system. SoxS combines features of thioredoxins, glutaredoxins and the thiol-disulfide oxidoreductases of the Dsb family in structure, target specificity and reaction. The structure of SoxS was solved in oxidized and reduced forms at 2.1 and 1.9 A resolution, respectively. SoxS revealed high structural homology to typical cytoplasmic bacterial thioredoxins. In contrast, SoxS contained the active-site motif Pro-Gly-Cys-Leu-Tyr-Cys that is not present in other thioredoxins. Interestingly, the sequence of this motif is closely related to the Pro-Gly-Cys-Pro-Tyr-Cys sequence of some glutaredoxins and to the Pro-Xaa-Cys-Xaa-Tyr-Cys sequences of some members of the DsbC and DsbG subfamilies of thiol-disulfide oxidoreductases. Furthermore, the proposed substrate of SoxS, the interprotein disulfide of SoxY, Cys110(Y)-Cys110(Y), is structurally similar to oxidized glutathione. However, SoxS is proposed to specifically reduce the interprotein disulfide between two SoxY subunits, releasing a heterodimeric SoxYZ as an active part of the sulfur-oxidation cycle.


Subject(s)
Bacterial Proteins/chemistry , Paracoccus pantotrophus/enzymology , Protein Disulfide Reductase (Glutathione)/chemistry , Sulfur/metabolism , Amino Acid Motifs , Amino Acid Sequence , Bacterial Proteins/metabolism , Bacterial Proteins/physiology , Binding Sites , Crystallography, X-Ray , Dimerization , Disulfides/metabolism , Glutaredoxins/chemistry , Models, Molecular , Molecular Sequence Data , Oxidation-Reduction , Oxidoreductases Acting on Sulfur Group Donors/metabolism , Protein Conformation , Protein Disulfide Reductase (Glutathione)/physiology , Recombinant Fusion Proteins/chemistry , Selenomethionine/chemistry , Sequence Alignment , Sequence Homology, Amino Acid , Structure-Activity Relationship , Thioredoxins/chemistry
16.
FEBS Lett ; 582(25-26): 3701-4, 2008 Oct 29.
Article in English | MEDLINE | ID: mdl-18834882

ABSTRACT

The central protein of the sulfur-oxidizing enzyme system of Paracoccus pantotrophus, SoxYZ, reacts with three different Sox proteins. Its active site Cys110(Y) is on the carboxy-terminus of the SoxY subunit. SoxYZ "as isolated" consisted mainly of the catalytically inactive SoxY-Y(Z)(2) heterotetramer linked by a Cys110(Y)-Cys110(Y) interprotein disulfide. Sulfide activated SoxYZ "as isolated" 456-fold, reduced the disulfide, and yielded an active SoxYZ heterodimer. The reductant tris(2-carboxyethyl)phosphine (TCEP) inactivated SoxYZ. This form was not re-activated by sulfide, which identified it as a different inactive form. In analytical gel filtration, the elution of "TCEP-treated" SoxYZ was retarded compared to active SoxYZ, indicating a conformational change. The possible enzymes involved in the re-activation of each inactive form of SoxYZ are discussed.


Subject(s)
Bacterial Proteins/chemistry , Oxidoreductases Acting on Sulfur Group Donors/chemistry , Paracoccus pantotrophus/enzymology , Bacterial Proteins/antagonists & inhibitors , Bacterial Proteins/isolation & purification , Catalysis , Enzyme Inhibitors/pharmacology , Isoenzymes/antagonists & inhibitors , Isoenzymes/chemistry , Isoenzymes/isolation & purification , Models, Molecular , Oxidoreductases Acting on Sulfur Group Donors/antagonists & inhibitors , Oxidoreductases Acting on Sulfur Group Donors/isolation & purification , Phosphines/pharmacology , Protein Subunits/chemistry , Protein Subunits/isolation & purification
17.
Microbiology (Reading) ; 154(Pt 7): 1980-1988, 2008 Jul.
Article in English | MEDLINE | ID: mdl-18599826

ABSTRACT

The periplasmic thiol-disulfide oxidoreductase SoxS is essential for chemotrophic growth of Paracoccus pantotrophus with thiosulfate. To trap its periplasmic partner, the cysteine residues of the CysXaaXaaCys motif of SoxS (11 kDa) were changed to alanine by site-directed mutagenesis. The disrupted soxS gene of the homogenote mutant G OmegaS was complemented with plasmids carrying the mutated soxS[C13A] or soxS[C16A] gene. Strain G OmegaS(pRD179.6[C16A](S)) displayed a marginal thiosulfate-oxidizing activity, suggesting that Cys13(S) binds the target protein. Evidence is presented that SoxS specifically binds SoxY. (i) Immunoblot analysis using non-reducing SDS gel electrophoresis and anti-SoxS and anti-SoxYZ antibodies identified the respective antigens of strain G OmegaS(pRD179.6[C16A](S)) at the 25 kDa position, suggesting an adduct of about 14 kDa, close to the value expected for SoxY migration. (ii) A mutant unable to produce SoxYZ, such as strain G OmegaX(pRD187.7[C16A](S)), did not form a SoxS(C16A) adduct, while addition of homogeneous SoxYZ resulted in the 25 kDa adduct. (iii) The SoxY and SoxZ subunits were distinguished by site-directed mutagenesis of the cysteine residue in SoxZ. SoxYZ(C53S) formed the 25 kDa adduct with SoxS(C16A). These results demonstrate that the target of SoxS is the sulfur-binding protein SoxY of the SoxYZ complex. As SoxYZ is reversibly inactivated, SoxS may activate SoxYZ as a crucial function for chemotrophy of P. pantotrophus.


Subject(s)
Bacterial Proteins/metabolism , Oxidoreductases Acting on Sulfur Group Donors/metabolism , Paracoccus pantotrophus/metabolism , Periplasmic Proteins/metabolism , Protein Disulfide Reductase (Glutathione)/metabolism , Thiosulfates/metabolism , Amino Acid Motifs , Amino Acid Substitution , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Gene Expression Regulation, Bacterial , Mutagenesis, Site-Directed , Mutation, Missense , Oxidation-Reduction , Oxidoreductases Acting on Sulfur Group Donors/chemistry , Oxidoreductases Acting on Sulfur Group Donors/genetics , Paracoccus pantotrophus/chemistry , Paracoccus pantotrophus/enzymology , Paracoccus pantotrophus/genetics , Periplasmic Proteins/chemistry , Periplasmic Proteins/genetics , Protein Binding , Protein Disulfide Reductase (Glutathione)/chemistry , Protein Disulfide Reductase (Glutathione)/genetics
18.
Biochem Biophys Res Commun ; 371(4): 719-23, 2008 Jul 11.
Article in English | MEDLINE | ID: mdl-18471989

ABSTRACT

A previous study of nitrite reduction by Paracoccus pantotrophus cytochrome cd(1) at pH 7.0 identified early reaction intermediates. The c-heme rapidly oxidised and nitrite was reduced to NO at the d(1)-heme. A slower equilibration of electrons followed, forming a stable complex assigned as 55% cFe(III)d(1)Fe(II)-NO and 45% cFe(II)d(1)Fe(II)-NO(+). No catalytically competent NO release was observed. Here we show that at pH 6.0, a significant proportion of the enzyme undergoes turnover and releases NO. An early intermediate, which was previously overlooked, is also identified; enzyme immediately following product release is a candidate. However, even at pH 6.0 a considerable fraction of the enzyme remains bound to NO so another component is required for full product release. The kinetically stable product formed at the end of the reaction differs significantly at pH 6.0 and 7.0, as does its rate of formation; thus the reaction is critically dependent on pH.


Subject(s)
Cytochromes/chemistry , Nitric Oxide/chemistry , Nitrite Reductases/chemistry , Paracoccus pantotrophus/enzymology , Cytochrome c Group , Hydrogen-Ion Concentration , Kinetics , Nitrites/chemistry , Oxidation-Reduction , Spectrum Analysis
19.
Biochemistry ; 47(21): 5841-50, 2008 May 27.
Article in English | MEDLINE | ID: mdl-18442258

ABSTRACT

This work reports for the first time a resonance Raman study of the mixed-valence and fully reduced forms of Paracoccus pantotrophus bacterial cytochrome c peroxidase. The spectra of the active mixed-valence enzyme show changes in the structure of the ferric peroxidatic heme compared to the fully oxidized enzyme; these differences are observed upon reduction of the electron-transferring heme and upon full occupancy of the calcium site. For the mixed-valence form in the absence of Ca(2+), the peroxidatic heme is six-coordinate and low-spin on the basis of the frequencies of the structure-sensitive Raman lines: the enzyme is inactive. With added Ca(2+), the peroxidatic heme is five-coordinate high-spin and active. The calcium-dependent spectral differences indicate little change in the conformation of the ferrous electron-transferring heme, but substantial changes in the conformation of the ferric peroxidatic heme. Structural changes associated with Ca(2+) binding are indicated by spectral differences in the structure-sensitive marker lines, the out-of-plane low-frequency macrocyclic modes, and the vibrations associated with the heme substituents of that heme. The Ca(2+)-dependent appearance of a strong gamma 15 saddling-symmetry mode for the mixed-valence form is consistent with a strong saddling deformation in the active peroxidatic heme, a feature seen in the Raman spectra of other peroxidases. For the fully reduced form in the presence of Ca(2+), the resonance Raman spectra show that the peroxidatic heme remains high-spin.


Subject(s)
Calcium/chemistry , Cytochrome-c Peroxidase/metabolism , Heme/chemistry , Paracoccus pantotrophus/enzymology , Biochemistry/methods , Calcium/metabolism , Cations , Enzyme Activation , Ions , Magnesium/chemistry , Models, Chemical , Molecular Conformation , Oxygen/chemistry , Protein Conformation , Spectrum Analysis, Raman/methods
20.
J Biol Inorg Chem ; 13(5): 779-87, 2008 Jun.
Article in English | MEDLINE | ID: mdl-18365258

ABSTRACT

A comparative study of direct and mediated electrochemistry of metalloproteins in bulk and membrane-entrapped solutions is presented. This work reports the first electrochemical study of the electron transfer between a bacterial cytochrome c peroxidase and horse heart cytochrome c. The mediated catalysis of the peroxidase was analysed both using the membrane electrode configuration and with all proteins in solution. An apparent Michaelis constant of 66 +/- 4 and 42 +/- 5 microM was determined at pH 7.0 and 0 M NaCl for membrane and bulk solutions, respectively. The data revealed that maximum activity occurs at 50 mM NaCl, pH 7.0, with intermolecular rate constants of (4.4 +/- 0.5) x 10(6) and (1.0 +/- 0.5) x 10(6) M(-1) s(-1) for membrane-entrapped and bulk solutions, respectively. The influence of parameters such as pH or ionic strength on the mediated catalytic activity was analysed using this approach, drawing attention to the fact that careful analysis of the results is needed to ensure that no artefacts are introduced by the use of the membrane configuration and/or promoters, and therefore the dependence truly reflects the influence of these parameters on the (mediated) catalysis. From the pH dependence, a pK of 7.5 was estimated for the mediated enzymatic catalysis.


Subject(s)
Cytochrome-c Peroxidase/chemistry , Cytochromes c/chemistry , Metalloproteins/chemistry , Paracoccus pantotrophus/enzymology , Animals , Catalysis , Electrochemistry , Electrodes , Electron Transport , Horses , Hydrogen Peroxide/chemistry , Hydrogen-Ion Concentration , Membranes, Artificial , Myocardium/enzymology , Potentiometry
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