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. 1996 Jun;5(6):1081–1092. doi: 10.1002/pro.5560050610

The heme redox center of chloroplast cytochrome f is linked to a buried five-water chain.

S E Martinez 1, D Huang 1, M Ponomarev 1, W A Cramer 1, J L Smith 1
PMCID: PMC2143431  PMID: 8762139

Abstract

The crystal structure of the 252-residue lumen-side domain of reduced cytochrome f, a subunit of the proton-pumping integral cytochrome b6f complex of oxygenic photosynthetic membranes, was determined to a resolution of 1.96 A from crystals cooled to -35 degrees. The model was refined to an R-factor of 15.8% with a 0.013-A RMS deviation of bond lengths from ideality. Compared to the structure of cytochrome f at 20 degrees, the structure at -35 degrees has a small change in relative orientation of the two folding domains and significantly lower isotropic temperature factors for protein atoms. The structure revealed an L-shaped array of five buried water molecules that extend in two directions from the N delta 1 of the heme ligand His 25. The longer branch extends 11 A within the large domain, toward Lys 66 in the prominent basic patch at the top of the large domain, which has been implicated in the interaction with the electron acceptor, plastocyanin. The water sites are highly occupied, and their temperature factors are comparable to those of protein atoms. Virtually all residues that form hydrogen bonds with the water chain are invariant among 13 known cytochrome f sequences. The water chain has many features that optimize it as a proton wire, including insulation from the protein medium. It is suggested that this chain may function as the lumen-side exit port for proton translocation by the cytochrome b6f complex.

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Selected References

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  1. Baciou L., Michel H. Interruption of the water chain in the reaction center from Rhodobacter sphaeroides reduces the rates of the proton uptake and of the second electron transfer to QB. Biochemistry. 1995 Jun 27;34(25):7967–7972. doi: 10.1021/bi00025a001. [DOI] [PubMed] [Google Scholar]
  2. Cao Y., Váró G., Chang M., Ni B. F., Needleman R., Lanyi J. K. Water is required for proton transfer from aspartate-96 to the bacteriorhodopsin Schiff base. Biochemistry. 1991 Nov 12;30(45):10972–10979. doi: 10.1021/bi00109a023. [DOI] [PubMed] [Google Scholar]
  3. Cramer W. A., Martinez S. E., Huang D., Tae G. S., Everly R. M., Heymann J. B., Cheng R. H., Baker T. S., Smith J. L. Structural aspects of the cytochrome b6f complex; structure of the lumen-side domain of cytochrome f. J Bioenerg Biomembr. 1994 Feb;26(1):31–47. doi: 10.1007/BF00763218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. DAVENPORT H. E., HILL R. The preparation and some properties of cytochrome f. Proc R Soc Lond B Biol Sci. 1952 Apr 24;139(896):327–345. doi: 10.1098/rspb.1952.0016. [DOI] [PubMed] [Google Scholar]
  5. Hartshorn R. T., Moore G. R. A denaturation-induced proton-uptake study of horse ferricytochrome c. Biochem J. 1989 Mar 1;258(2):595–598. doi: 10.1042/bj2580595. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Henderson R., Baldwin J. M., Ceska T. A., Zemlin F., Beckmann E., Downing K. H. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol. 1990 Jun 20;213(4):899–929. doi: 10.1016/S0022-2836(05)80271-2. [DOI] [PubMed] [Google Scholar]
  7. Kim K. H., Kwon B. M., Myers A. G., Rees D. C. Crystal structure of neocarzinostatin, an antitumor protein-chromophore complex. Science. 1993 Nov 12;262(5136):1042–1046. doi: 10.1126/science.8235619. [DOI] [PubMed] [Google Scholar]
  8. Ko K., Straus N. A. Sequence of the apocytochrome f gene encoded by the Vicia faba chloroplast genome. Nucleic Acids Res. 1987 Mar 11;15(5):2391–2391. doi: 10.1093/nar/15.5.2391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Lanyi J. K. Proton translocation mechanism and energetics in the light-driven pump bacteriorhodopsin. Biochim Biophys Acta. 1993 Dec 7;1183(2):241–261. doi: 10.1016/0005-2728(93)90226-6. [DOI] [PubMed] [Google Scholar]
  10. Link T. A., Haase U., Brandt U., von Jagow G. What information do inhibitors provide about the structure of the hydroquinone oxidation site of ubihydroquinone: cytochrome c oxidoreductase? J Bioenerg Biomembr. 1993 Jun;25(3):221–232. doi: 10.1007/BF00762584. [DOI] [PubMed] [Google Scholar]
  11. Link T. A., Hagen W. R., Pierik A. J., Assmann C., von Jagow G. Determination of the redox properties of the Rieske [2Fe-2S] cluster of bovine heart bc1 complex by direct electrochemistry of a water-soluble fragment. Eur J Biochem. 1992 Sep 15;208(3):685–691. doi: 10.1111/j.1432-1033.1992.tb17235.x. [DOI] [PubMed] [Google Scholar]
  12. Malkin R. Interaction of photosynthetic electron transport inhibitors and the Rieske Iron-Sulfur center in chloroplasts and the cytochrome b6-f complex. Biochemistry. 1982 Jun 8;21(12):2945–2950. doi: 10.1021/bi00541a022. [DOI] [PubMed] [Google Scholar]
  13. Martinez S. E., Huang D., Szczepaniak A., Cramer W. A., Smith J. L. Crystal structure of chloroplast cytochrome f reveals a novel cytochrome fold and unexpected heme ligation. Structure. 1994 Feb 15;2(2):95–105. doi: 10.1016/s0969-2126(00)00012-5. [DOI] [PubMed] [Google Scholar]
  14. Mohr P., Scheler W., Schumann H., Müller K. Ligand-protein interactions in imidazole and 1,2,4-triazole complexes of methaemoglobin from Chironomus plumosus. Eur J Biochem. 1967 Dec;3(2):158–163. doi: 10.1111/j.1432-1033.1967.tb19511.x. [DOI] [PubMed] [Google Scholar]
  15. Morishima I., Neya S., Yonezawa T. Proton NMR study of hemoproteins. Ionization and orientation of iron-bound imidazole in methemoglobin and metmyoblobin. Biochim Biophys Acta. 1980 Feb 27;621(2):218–226. doi: 10.1016/0005-2795(80)90173-7. [DOI] [PubMed] [Google Scholar]
  16. Mulkidjanian A. Y., Junge W. Calibration and time resolution of lumenal pH-transients in chromatophores of Rhodobacter capsulatus following a single turnover flash of light: proton release by the cytochrome bc1-complex is strongly electrogenic. FEBS Lett. 1994 Oct 17;353(2):189–193. doi: 10.1016/0014-5793(94)01031-5. [DOI] [PubMed] [Google Scholar]
  17. Nagle J. F., Morowitz H. J. Molecular mechanisms for proton transport in membranes. Proc Natl Acad Sci U S A. 1978 Jan;75(1):298–302. doi: 10.1073/pnas.75.1.298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Paddock M. L., Rongey S. H., Feher G., Okamura M. Y. Pathway of proton transfer in bacterial reaction centers: replacement of glutamic acid 212 in the L subunit by glutamine inhibits quinone (secondary acceptor) turnover. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6602–6606. doi: 10.1073/pnas.86.17.6602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Paddock M. L., Rongey S. H., McPherson P. H., Juth A., Feher G., Okamura M. Y. Pathway of proton transfer in bacterial reaction centers: role of aspartate-L213 in proton transfers associated with reduction of quinoneto dihydroquinone. Biochemistry. 1994 Jan 25;33(3):734–745. doi: 10.1021/bi00169a015. [DOI] [PubMed] [Google Scholar]
  20. Papadopoulos G., Dencher N. A., Zaccai G., Büldt G. Water molecules and exchangeable hydrogen ions at the active centre of bacteriorhodopsin localized by neutron diffraction. Elements of the proton pathway? J Mol Biol. 1990 Jul 5;214(1):15–19. doi: 10.1016/0022-2836(90)90140-h. [DOI] [PubMed] [Google Scholar]
  21. Qi P. X., Di Stefano D. L., Wand A. J. Solution structure of horse heart ferrocytochrome c determined by high-resolution NMR and restrained simulated annealing. Biochemistry. 1994 May 31;33(21):6408–6417. doi: 10.1021/bi00187a004. [DOI] [PubMed] [Google Scholar]
  22. Qi P. X., Urbauer J. L., Fuentes E. J., Leopold M. F., Wand A. J. Structural water in oxidized and reduced horse heart cytochrome c. Nat Struct Biol. 1994 Jun;1(6):378–382. doi: 10.1038/nsb0694-378. [DOI] [PubMed] [Google Scholar]
  23. Rasmussen B. F., Stock A. M., Ringe D., Petsko G. A. Crystalline ribonuclease A loses function below the dynamical transition at 220 K. Nature. 1992 Jun 4;357(6377):423–424. doi: 10.1038/357423a0. [DOI] [PubMed] [Google Scholar]
  24. Rich P. R., Bendall D. S. The redox potentials of the b-type cytochromes of higher plant chloroplasts. Biochim Biophys Acta. 1980 Jun 10;591(1):153–161. doi: 10.1016/0005-2728(80)90229-7. [DOI] [PubMed] [Google Scholar]
  25. Rongey S. H., Paddock M. L., Feher G., Okamura M. Y. Pathway of proton transfer in bacterial reaction centers: second-site mutation Asn-M44-->Asp restores electron and proton transfer in reaction centers from the photosynthetically deficient Asp-L213-->Asn mutant of Rhodobacter sphaeroides. Proc Natl Acad Sci U S A. 1993 Feb 15;90(4):1325–1329. doi: 10.1073/pnas.90.4.1325. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Rottenberg H., Grunwald T. Determination of pH in chloroplasts. 3. Ammonium uptake as a measure of pH in chloroplasts and sub-chloroplast particles. Eur J Biochem. 1972 Jan 31;25(1):71–74. doi: 10.1111/j.1432-1033.1972.tb01668.x. [DOI] [PubMed] [Google Scholar]
  27. Roux B., Prod'hom B., Karplus M. Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy. Biophys J. 1995 Mar;68(3):876–892. doi: 10.1016/S0006-3495(95)80264-X. [DOI] [PMC free article] [PubMed] [Google Scholar]

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