Skip to main content
Biochemical Journal logoLink to Biochemical Journal
. 2002 Sep 15;366(Pt 3):883–888. doi: 10.1042/BJ20020795

A novel, kinetically stable, catalytically active, all-ferric, nitrite-bound complex of Paracoccus pantotrophus cytochrome cd1.

James W A Allen 1, Christopher W Higham 1, Richard S Zajicek 1, Nicholas J Watmough 1, Stuart J Ferguson 1
PMCID: PMC1222841  PMID: 12086580

Abstract

The oxidized form of Paracoccus pantotrophus cytochrome cd(1) nitrite reductase, as isolated, has bis-histidinyl co-ordination of the c haem and His/Tyr co-ordination of the d(1) haem. On reduction, the haem co-ordinations change to His/Met and His/vacant respectively. If the latter form of the enzyme is reoxidized, a conformer is generated in which the ferric c haem is His/Met co-ordinated; this can revert to the 'as isolated' state of the enzyme over approx. 20 min at room temperature. However, addition of nitrite to the enzyme after a cycle of reduction and reoxidation produces a kinetically stable, all-ferric complex with nitrite bound to the d(1) haem and His/Met co-ordination of the c haem. This complex is catalytically active with the physiological electron donor protein pseudoazurin. The effective dissociation constant for nitrite is 2 mM. Evidence is presented that d(1) haem is optimized to bind nitrite, as opposed to other anions that are commonly good ligands to ferric haem. The all-ferric nitrite bound state of the enzyme could not be generated stoichiometrically by mixing nitrite with the 'as isolated' conformer of cytochrome cd(1) without redox cycling.

Full Text

The Full Text of this article is available as a PDF (128.7 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Allen J. W., Cheesman M. R., Higham C. W., Ferguson S. J., Watmough N. J. A novel conformer of oxidized Paracoccus pantotrophus cytochrome cd(1) observed by freeze-quench NIR-MCD spectroscopy. Biochem Biophys Res Commun. 2000 Dec 20;279(2):674–677. doi: 10.1006/bbrc.2000.4009. [DOI] [PubMed] [Google Scholar]
  2. Allen J. W., Watmough N. J., Ferguson S. J. A switch in heme axial ligation prepares Paracoccus pantotrophus cytochrome cd1 for catalysis. Nat Struct Biol. 2000 Oct;7(10):885–888. doi: 10.1038/82821. [DOI] [PubMed] [Google Scholar]
  3. Averill Bruce A. Dissimilatory Nitrite and Nitric Oxide Reductases. Chem Rev. 1996 Nov 7;96(7):2951–2964. doi: 10.1021/cr950056p. [DOI] [PubMed] [Google Scholar]
  4. 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]
  5. Cheesman M. R., Ferguson S. J., Moir J. W., Richardson D. J., Zumft W. G., Thomson A. J. Two enzymes with a common function but different heme ligands in the forms as isolated. Optical and magnetic properties of the heme groups in the oxidized forms of nitrite reductase, cytochrome cd1, from Pseudomonas stutzeri and Thiosphaera pantotropha. Biochemistry. 1997 Dec 23;36(51):16267–16276. doi: 10.1021/bi971677a. [DOI] [PubMed] [Google Scholar]
  6. Crane B. R., Siegel L. M., Getzoff E. D. Structures of the siroheme- and Fe4S4-containing active center of sulfite reductase in different states of oxidation: heme activation via reduction-gated exogenous ligand exchange. Biochemistry. 1997 Oct 7;36(40):12101–12119. doi: 10.1021/bi971065q. [DOI] [PubMed] [Google Scholar]
  7. Cutruzzola F., Brown K., Wilson E. K., Bellelli A., Arese M., Tegoni M., Cambillau C., Brunori M. The nitrite reductase from Pseudomonas aeruginosa: essential role of two active-site histidines in the catalytic and structural properties. Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2232–2237. doi: 10.1073/pnas.041365298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cutruzzolà F. Bacterial nitric oxide synthesis. Biochim Biophys Acta. 1999 May 5;1411(2-3):231–249. doi: 10.1016/s0005-2728(99)00017-1. [DOI] [PubMed] [Google Scholar]
  9. Day E. P., Peterson J., Bonvoisin J. J., Young L. J., Wilkerson J. O., Siegel L. M. Magnetization of the sulfite and nitrite complexes of oxidized sulfite and nitrite reductases: EPR silent spin S = 1/2 states. Biochemistry. 1988 Mar 22;27(6):2126–2132. doi: 10.1021/bi00406a046. [DOI] [PubMed] [Google Scholar]
  10. Ferguson S. J. Nitrogen cycle enzymology. Curr Opin Chem Biol. 1998 Apr;2(2):182–193. doi: 10.1016/s1367-5931(98)80059-8. [DOI] [PubMed] [Google Scholar]
  11. Fülöp V., Moir J. W., Ferguson S. J., Hajdu J. The anatomy of a bifunctional enzyme: structural basis for reduction of oxygen to water and synthesis of nitric oxide by cytochrome cd1. Cell. 1995 May 5;81(3):369–377. doi: 10.1016/0092-8674(95)90390-9. [DOI] [PubMed] [Google Scholar]
  12. George S. J., Allen J. W., Ferguson S. J., Thorneley R. N. Time-resolved infrared spectroscopy reveals a stable ferric heme-NO intermediate in the reaction of Paracoccus pantotrophus cytochrome cd1 nitrite reductase with nitrite. J Biol Chem. 2000 Oct 27;275(43):33231–33237. doi: 10.1074/jbc.M005033200. [DOI] [PubMed] [Google Scholar]
  13. Jafferji A., Allen J. W., Ferguson S. J., Fulop V. X-ray crystallographic study of cyanide binding provides insights into the structure-function relationship for cytochrome cd1 nitrite reductase from Paracoccus pantotrophus. J Biol Chem. 2000 Aug 18;275(33):25089–25094. doi: 10.1074/jbc.M001377200. [DOI] [PubMed] [Google Scholar]
  14. Kobayashi K., Koppenhöfer A., Ferguson S. J., Tagawa S. Pulse radiolysis studies on cytochrome cd1 nitrite reductase from Thiosphaera pantotropha: evidence for a fast intramolecular electron transfer from c-heme to d1-heme. Biochemistry. 1997 Nov 4;36(44):13611–13616. doi: 10.1021/bi971045o. [DOI] [PubMed] [Google Scholar]
  15. Koppenhöfer A., Little R. H., Lowe D. J., Ferguson S. J., Watmough N. J. Oxidase reaction of cytochrome cd(1) from Paracoccus pantotrophus. Biochemistry. 2000 Apr 11;39(14):4028–4036. doi: 10.1021/bi991912k. [DOI] [PubMed] [Google Scholar]
  16. Koppenhöfer A., Turner K. L., Allen J. W., Chapman S. K., Ferguson S. J. Cytochrome cd(1) from Paracoccus pantotrophus exhibits kinetically gated, conformationally dependent, highly cooperative two-electron redox behavior. Biochemistry. 2000 Apr 18;39(15):4243–4249. doi: 10.1021/bi000192a. [DOI] [PubMed] [Google Scholar]
  17. Leung Y. C., Chan C., Reader J. S., Willis A. C., van Spanning R. J., Ferguson S. J., Radford S. E. The pseudoazurin gene from Thiosphaera pantotropha: analysis of upstream putative regulatory sequences and overexpression in Escherichia coli. Biochem J. 1997 Feb 1;321(Pt 3):699–705. doi: 10.1042/bj3210699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Moir J. W., Baratta D., Richardson D. J., Ferguson S. J. The purification of a cd1-type nitrite reductase from, and the absence of a copper-type nitrite reductase from, the aerobic denitrifier Thiosphaera pantotropha; the role of pseudoazurin as an electron donor. Eur J Biochem. 1993 Mar 1;212(2):377–385. doi: 10.1111/j.1432-1033.1993.tb17672.x. [DOI] [PubMed] [Google Scholar]
  19. Muhoberac B. B., Wharton D. C. Electron paramagnetic resonance study of the interaction of some anionic ligands with oxidized Pseudomonas cytochrome oxidase. J Biol Chem. 1983 Mar 10;258(5):3019–3027. [PubMed] [Google Scholar]
  20. Nurizzo D., Silvestrini M. C., Mathieu M., Cutruzzolà F., Bourgeois D., Fülöp V., Hajdu J., Brunori M., Tegoni M., Cambillau C. N-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa. Structure. 1997 Sep 15;5(9):1157–1171. doi: 10.1016/s0969-2126(97)00267-0. [DOI] [PubMed] [Google Scholar]
  21. Richter Carsten D., Allen James W. A., Higham Christopher W., Koppenhofer Alrik, Zajicek Richard S., Watmough Nicholas J., Ferguson Stuart J. Cytochrome cd1, reductive activation and kinetic analysis of a multifunctional respiratory enzyme. J Biol Chem. 2001 Nov 14;277(5):3093–3100. doi: 10.1074/jbc.M108944200. [DOI] [PubMed] [Google Scholar]
  22. Shimada H., Orii Y. The nitric oxide compounds of Pseudomonas aeruginosa nitrite reductase and their probable participation in the nitrite reduction. FEBS Lett. 1975 Jun 15;54(2):237–240. doi: 10.1016/0014-5793(75)80082-2. [DOI] [PubMed] [Google Scholar]
  23. Silvestrini M. C., Colosimo A., Brunori M., Walsh T. A., Barber D., Greenwood C. A re-evaluation of some basic structural and functional properties of Pseudomonas cytochrome oxidase. Biochem J. 1979 Dec 1;183(3):701–709. doi: 10.1042/bj1830701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Silvestrini M. C., Tordi M. G., Musci G., Brunori M. The reaction of Pseudomonas nitrite reductase and nitrite. A stopped-flow and EPR study. J Biol Chem. 1990 Jul 15;265(20):11783–11787. [PubMed] [Google Scholar]
  25. Sjögren T., Hajdu J. The Structure of an alternative form of Paracoccus pantotrophus cytochrome cd(1) nitrite reductase. J Biol Chem. 2001 May 23;276(31):29450–29455. doi: 10.1074/jbc.M103657200. [DOI] [PubMed] [Google Scholar]
  26. Veselov A., Olesen K., Sienkiewicz A., Shapleigh J. P., Scholes C. P. Electronic structural information from Q-band ENDOR on the type 1 and type 2 copper liganding environment in wild-type and mutant forms of copper-containing nitrite reductase. Biochemistry. 1998 Apr 28;37(17):6095–6105. doi: 10.1021/bi971604r. [DOI] [PubMed] [Google Scholar]
  27. Walsh T. A., Johnson M. K., Thomson A. J., Barber D., Greenwood C. The characterization and magnetic properties of the azide and imidazole derivatives of Pseudomonas nitrite reductase. J Inorg Biochem. 1981 Feb;14(1):1–14. doi: 10.1016/s0162-0134(00)80010-0. [DOI] [PubMed] [Google Scholar]
  28. Williams P. A., Fülöp V., Garman E. F., Saunders N. F., Ferguson S. J., Hajdu J. Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme. Nature. 1997 Sep 25;389(6649):406–412. doi: 10.1038/38775. [DOI] [PubMed] [Google Scholar]
  29. Zumft W. G. Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev. 1997 Dec;61(4):533–616. doi: 10.1128/mmbr.61.4.533-616.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Biochemical Journal are provided here courtesy of The Biochemical Society

RESOURCES