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. 1996 Jul 15;317(Pt 2):557–563. doi: 10.1042/bj3170557

Structural investigation of the molybdenum site of the periplasmic nitrate reductase from Thiosphaera pantotropha by X-ray absorption spectroscopy.

B Bennett 1, J M Charnock 1, H J Sears 1, B C Berks 1, A J Thomson 1, S J Ferguson 1, C D Garner 1, D J Richardson 1
PMCID: PMC1217522  PMID: 8713085

Abstract

The molybdenum centre of the periplasmic respiratory nitrate reductase from the denitrifying bacterium Thiosphaera pantotropha has been probed using molybdenum K-edge X-ray absorption spectroscopy. The optimum fit of the Mo(VI) EXAFS suggests two ==O, three -S- and either a fourth -S- or an -O-/-N- as molybdenum ligands in the ferricyanide-oxidized enzyme. Three of the -S- ligands are proposed to be the two sulphur atoms of the molybdopterin dithiolene group and Cys-181. Comparison of the EXAFS of the ferricyanide-oxidized enzyme with that of a nitrate-treated sample containing 30% Mo(V) suggests that the Mo(VI)-->Mo(V) reduction is accompanied by conversion of one ==O to -O-. The best fit to the Mo(IV) EXAFS of dithionite-reduced enzyme was obtained using one ==O, one -O- and four -S-/-Cl ligands. The periplasmic nitrate reductase molybdenum co-ordination environment in both the Mo(VI) and Mo(IV) oxidation states is distinct from that found in the membrane-bound respiratory nitrate reductase.

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Selected References

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  1. Bell L. C., Page M. D., Berks B. C., Richardson D. J., Ferguson S. J. Insertion of transposon Tn5 into a structural gene of the membrane-bound nitrate reductase of Thiosphaera pantotropha results in anaerobic overexpression of periplasmic nitrate reductase activity. J Gen Microbiol. 1993 Dec;139(12):3205–3214. doi: 10.1099/00221287-139-12-3205. [DOI] [PubMed] [Google Scholar]
  2. Bennett B., Berks B. C., Ferguson S. J., Thomson A. J., Richardson D. J. Mo(V) electron paramagnetic resonance signals from the periplasmic nitrate reductase of Thiosphaera pantotropha. Eur J Biochem. 1994 Dec 15;226(3):789–798. doi: 10.1111/j.1432-1033.1994.00789.x. [DOI] [PubMed] [Google Scholar]
  3. Berks B. C., Ferguson S. J., Moir J. W., Richardson D. J. Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions. Biochim Biophys Acta. 1995 Dec 12;1232(3):97–173. doi: 10.1016/0005-2728(95)00092-5. [DOI] [PubMed] [Google Scholar]
  4. Berks B. C., Page M. D., Richardson D. J., Reilly A., Cavill A., Outen F., Ferguson S. J. Sequence analysis of subunits of the membrane-bound nitrate reductase from a denitrifying bacterium: the integral membrane subunit provides a prototype for the dihaem electron-carrying arm of a redox loop. Mol Microbiol. 1995 Jan;15(2):319–331. doi: 10.1111/j.1365-2958.1995.tb02246.x. [DOI] [PubMed] [Google Scholar]
  5. Berks B. C., Richardson D. J., Reilly A., Willis A. C., Ferguson S. J. The napEDABC gene cluster encoding the periplasmic nitrate reductase system of Thiosphaera pantotropha. Biochem J. 1995 Aug 1;309(Pt 3):983–992. doi: 10.1042/bj3090983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Berks B. C., Richardson D. J., Robinson C., Reilly A., Aplin R. T., Ferguson S. J. Purification and characterization of the periplasmic nitrate reductase from Thiosphaera pantotropha. Eur J Biochem. 1994 Feb 15;220(1):117–124. doi: 10.1111/j.1432-1033.1994.tb18605.x. [DOI] [PubMed] [Google Scholar]
  7. Blasco F., Iobbi C., Giordano G., Chippaux M., Bonnefoy V. Nitrate reductase of Escherichia coli: completion of the nucleotide sequence of the nar operon and reassessment of the role of the alpha and beta subunits in iron binding and electron transfer. Mol Gen Genet. 1989 Aug;218(2):249–256. doi: 10.1007/BF00331275. [DOI] [PubMed] [Google Scholar]
  8. Blasco F., Iobbi C., Ratouchniak J., Bonnefoy V., Chippaux M. Nitrate reductases of Escherichia coli: sequence of the second nitrate reductase and comparison with that encoded by the narGHJI operon. Mol Gen Genet. 1990 Jun;222(1):104–111. doi: 10.1007/BF00283030. [DOI] [PubMed] [Google Scholar]
  9. Bray R. C. The inorganic biochemistry of molybdoenzymes. Q Rev Biophys. 1988 Aug;21(3):299–329. doi: 10.1017/s0033583500004479. [DOI] [PubMed] [Google Scholar]
  10. Breton J., Berks B. C., Reilly A., Thomson A. J., Ferguson S. J., Richardson D. J. Characterization of the paramagnetic iron-containing redox centres of Thiosphaera pantotropha periplasmic nitrate reductase. FEBS Lett. 1994 May 23;345(1):76–80. doi: 10.1016/0014-5793(94)00445-5. [DOI] [PubMed] [Google Scholar]
  11. Chan M. K., Mukund S., Kletzin A., Adams M. W., Rees D. C. Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase. Science. 1995 Mar 10;267(5203):1463–1469. doi: 10.1126/science.7878465. [DOI] [PubMed] [Google Scholar]
  12. Cruz Ramos H., Boursier L., Moszer I., Kunst F., Danchin A., Glaser P. Anaerobic transcription activation in Bacillus subtilis: identification of distinct FNR-dependent and -independent regulatory mechanisms. EMBO J. 1995 Dec 1;14(23):5984–5994. doi: 10.1002/j.1460-2075.1995.tb00287.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R., Bult C. J., Tomb J. F., Dougherty B. A., Merrick J. M. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995 Jul 28;269(5223):496–512. doi: 10.1126/science.7542800. [DOI] [PubMed] [Google Scholar]
  14. Gangeswaran R., Lowe D. J., Eady R. R. Purification and characterization of the assimilatory nitrate reductase of Azotobacter vinelandii. Biochem J. 1993 Jan 15;289(Pt 2):335–342. doi: 10.1042/bj2890335. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. George G. N., Turner N. A., Bray R. C., Morpeth F. F., Boxer D. H., Cramer S. P. X-ray-absorption and electron-paramagnetic-resonance spectroscopic studies of the environment of molybdenum in high-pH and low-pH forms of Escherichia coli nitrate reductase. Biochem J. 1989 May 1;259(3):693–700. doi: 10.1042/bj2590693. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Gladyshev V. N., Khangulov S. V., Axley M. J., Stadtman T. C. Coordination of selenium to molybdenum in formate dehydrogenase H from Escherichia coli. Proc Natl Acad Sci U S A. 1994 Aug 2;91(16):7708–7711. doi: 10.1073/pnas.91.16.7708. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Guigliarelli B., Asso M., More C., Augier V., Blasco F., Pommier J., Giordano G., Bertrand P. EPR and redox characterization of iron-sulfur centers in nitrate reductases A and Z from Escherichia coli. Evidence for a high-potential and a low-potential class and their relevance in the electron-transfer mechanism. Eur J Biochem. 1992 Jul 1;207(1):61–68. doi: 10.1111/j.1432-1033.1992.tb17020.x. [DOI] [PubMed] [Google Scholar]
  18. Kim J., Rees D. C. Structural models for the metal centers in the nitrogenase molybdenum-iron protein. Science. 1992 Sep 18;257(5077):1677–1682. doi: 10.1126/science.1529354. [DOI] [PubMed] [Google Scholar]
  19. Lin J. T., Goldman B. S., Stewart V. Structures of genes nasA and nasB, encoding assimilatory nitrate and nitrite reductases in Klebsiella pneumoniae M5al. J Bacteriol. 1993 Apr;175(8):2370–2378. doi: 10.1128/jb.175.8.2370-2378.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Morpeth F. F., Boxer D. H. Kinetic analysis of respiratory nitrate reductase from Escherichia coli K12. Biochemistry. 1985 Jan 1;24(1):40–46. doi: 10.1021/bi00322a007. [DOI] [PubMed] [Google Scholar]
  21. Rajagopalan K. V., Johnson J. L. The pterin molybdenum cofactors. J Biol Chem. 1992 May 25;267(15):10199–10202. [PubMed] [Google Scholar]
  22. Reyes F., Roldán M. D., Klipp W., Castillo F., Moreno-Vivián C. Isolation of periplasmic nitrate reductase genes from Rhodobacter sphaeroides DSM 158: structural and functional differences among prokaryotic nitrate reductases. Mol Microbiol. 1996 Mar;19(6):1307–1318. doi: 10.1111/j.1365-2958.1996.tb02475.x. [DOI] [PubMed] [Google Scholar]
  23. Romão M. J., Archer M., Moura I., Moura J. J., LeGall J., Engh R., Schneider M., Hof P., Huber R. Crystal structure of the xanthine oxidase-related aldehyde oxido-reductase from D. gigas. Science. 1995 Nov 17;270(5239):1170–1176. doi: 10.1126/science.270.5239.1170. [DOI] [PubMed] [Google Scholar]
  24. Sears H. J., Bennett B., Spiro S., Thomson A. J., Richardson D. J. Identification of periplasmic nitrate reductase Mo(V) EPR signals in intact cells of Paracoccus denitrificans. Biochem J. 1995 Aug 15;310(Pt 1):311–314. doi: 10.1042/bj3100311. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Siddiqui R. A., Warnecke-Eberz U., Hengsberger A., Schneider B., Kostka S., Friedrich B. Structure and function of a periplasmic nitrate reductase in Alcaligenes eutrophus H16. J Bacteriol. 1993 Sep;175(18):5867–5876. doi: 10.1128/jb.175.18.5867-5876.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Turner N., Ballard A. L., Bray R. C., Ferguson S. Investigation by electron paramagnetic resonance spectroscopy of the molybdenum centre of respiratory nitrate reductase from Paracoccus denitrificans. Biochem J. 1988 Jun 15;252(3):925–926. doi: 10.1042/bj2520925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Vincent S. P., Bray R. C. Electron-paramagnetic-resonance studies on nitrate reductase from Escherichia coli K12. Biochem J. 1978 Jun 1;171(3):639–647. doi: 10.1042/bj1710639. [DOI] [PMC free article] [PubMed] [Google Scholar]

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