Crystal structure determination at 1.4 Å resolution of ferredoxin from the green alga Chlorella fusca

Structure

Volumn 7, Issue 10, 1999, Pages 1201-1211

  Bes, M Teresa ^a   Parisini, Emilio ^a,d   Inda, Luis A ^b   Saraiva, Lígia M ^c   Peleato, M Luisa ^b   Sheldrick, George M ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b UNIVERSITY OF ZARAGOZA   (Spain)

^c INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Chlorella fusca; Ferredoxin; Phosphoserine; Photosynthesis

Indexed keywords

FERREDOXIN;

ARTICLE; CHLORELLA; CRYSTAL STRUCTURE; GREEN ALGA; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

'CHLORELLA' FUSCA; ALGAE; CHLORELLA FUSCA; CHLOROPHYTA; EUKARYOTA;

EID: 0033570020     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(00)80054-4     Document Type: Article

References (60)

1. 1. Cammack, R., et al., & Rogers, P.J. (1977). Midpoint redox potentials of plant and algal ferredoxins. Biochem. J. 168, 205-209.
2. 2. Holden, H.M., et al., & Markley, J.L. (1994). Structure-function studies of (2Fe-2S) ferredoxins. J. Bioeng. Biomembr. 26, 67-88.
3. 3. Bairoch, A. & Apweiler, R. (1998). The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 16, 38-42.
4. 4. Knaff, D.B. (1996). Ferredoxin and ferredoxin dependent enzymes. In Oxygenic Photosynthesis: the Light Reactions. (Ort, D.R. & Vocum, C.F. eds), pp. 333-361, Kluwer Academic Publishers, The Netherlands.
5. 5. Huisman, J.R., Moorman, A.F.M. & Verkley, F.N. (1978). In vitro synthesis of chloroplast ferredoxin as a high molecular weight precursor in a cell-free protein synthesizing system from wheat germ. Biochem. Biophys. Res. Comm. 82, 1121-1131.
6. 6. Robinson, C. & Ellis, R.J. (1984). Transport of proteins into chloroplasts. Partial purification of a chloroplast protease involved in processing imported precursor proteins. Eur. J. Biochem. 142, 337-342.
7. 7. Li, H.M., Theg, S.M., Bauerle, C.M. & Keegstra, K. (1990). Metal-ion center assembly of ferredoxin and plastocyanin in isolated chloroplast. Plant Cell 1, 1223-1230.
8. 8. Zanetti, G. & Merati, G. (1987). Interaction between photosystem I and ferredoxin. Eur. J. Biochem. 169, 143-146.
9. 9. Weber, N. & Strotmann, H. (1993). On the function of subunit PsaE in chloroplast photosystem I. Biochim. Biophys. Acta 1143, 204-210.
10. 10. Yu, L., Zhao, J., Mühlenhoff, U., Bryan, D.A. & Golbeck, J.H. (1993). PsaE is required for in vivo cyclic electron flow around photosystem I in the cyanobacterium Synechococcus sp. PCC 7002. Plant Physiol. 103, 171-180.
11. + reductase for site specific ferredoxin mutants. Biochemistry 36, 11100-11117.
12. 12. Karplus, P.A. & Bruns, C.M. (1994). Structure-function relations for ferredoxin reductase. J. Bioenerg. Biomembr. 26, 89-99.
13. + reductase: the role of the carboxyl groups, electrostatic surface potential, and molecular dipole moment. Protein Sci. 2, 1126-1135.
14. 14. De Pascalis, A.R., Schurmann, P. & Bosshard, H.R. (1994). Comparison of the binding sites of plant ferredoxin for two ferredoxin-dependent enzymes. FEBS Lett. 337, 217-210.
15. 15. Tsukihara, T., et al., & Matsubara, H. (1981). X-ray analysis of a [2Fe-2S] ferredoxin from Spirulina platensis. Main chain fold and location of side chains at 2.5 Å resolution. J. Biochem. 90, 1763-1773.
16. 16. Fukuyama, K., Ueki, N., Nakamura, M., Tsukihara, T. & Matsubara, H. (1995). Tertiary structure of [2Fe-2S] ferredoxin from Spirulina platensis refined at 2.5 Å resolution: structural comparisons of plant-type ferredoxins and an electrostatic potential analysis. J. Biochem. 117, 1017-1023.
17. 17. Rypniewski, W.R., et al., & Holden, H.M. (1991). Crystallization and structure determination to 2.5 Å resolution of the oxidized [2Fe-2S] ferredoxin isolated from Anabaena 7120. Biochemistry 30, 4126-4131.
18. 18. Jacobson, B.L., Chae, Y.K., Markley, J.L., Rayment, I. & Holden, H.M. (1993). Molecular structure of the oxidized, recombinant, heterocyst [2Fe-2S] ferredoxin from Anabaena 7120 determined to 1.7 Å resolution. Biochemistry 32, 6788-6793.
19. 19. Tsukihara. T., et al., & Matsubara, H. (1990). Structure of the [2Fe-2S] ferredoxin I from the blue-green alga Aphanothece sacrum at 2.2 Å resolution. J. Mol. Biol. 216, 399-410.
20. 20. Frolow, F., Harel, M., Sussman, J.L., Mevarech, M. & Shoham, M. (1996). Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin. Nat. Struct. Biol. 3, 452-458.
21. 21. Ikemizu, S., et al., & Fukuyama, K. (1994). Structure of [2Fe-2S] ferredoxin from Equisetum arvense at 1.8 Å resolution. Acta Crystallogr. D 50, 167-174.
22. 22. Binda, C., Coda, A., Aliverti, A., Zanetti, G. & Maitevi. A. (1998). Structure of the mutant E92K of a [2Fe-2S] ferredoxin I from Spinacea oleracea at 1.7 Å resolution. Acta Crystallogr. D 54, 1353-1359.
23. 23. Kessler, E., Schäfer, M., Hümmer, C., Klobouck, A. & Huss, V.A.R. (1997). Physiological, biochemical and molecular characters for the taxonomy of the subgenera Scenedesmus (Chlorococcales, Chlorophyta). Bot. Acta 110, 244-250.
24. 24. Bold, H.C. & Wynne, M.J. (1985). Introduction to the Algae, 2nd edition. Prentice Hall, Englewood Cliffs, NJ.
25. 25. Graham, L.E. (1996). Green algae to land plants: an evolutionary transition. J. Plant Res. 109, 241-251.
26. 26. Morand, L.Z., Cheng, R.H., Krogmann, D.W. & Ho, K.K. (1994). Soluble electron transfer catalysts of cyanobacteria. In The Molecular Biology of Cyanobacteria. (Bryan, D.A. ed.), pp. 381-407, Kluwer Academic Publishers, The Netherlands.
27. 27. Zallen, D.T. (1993). The "light" organism for the job: green algae and photosynthesis research. J. History Biol. 26, 269-279.
28. 28. Böhme, H. & Schrautemeier, B. (1987). Comparative characterization of ferredoxins from heterocysts and vegetative cells of Anabaena variabilis. Biochim. Biophys. Acta 981, 1-7.
29. 29. Peleato, M.L., Ayora, S., Inda, L.A. & Gómez-Moreno, C. (1994). Isolation and characterization of two different flavodoxins from the eukaryote Chlorella fusca. Biochem. J. 302, 807-811.
30. 30. Chothia, C. & Lesk, A.M. (1986). The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823-826.
31. 31. Brese, N.E. & O'Keeffe, M.O. (1991). Bond-valence parameters for solids. Acta Crystallogr. B 47, 192-197.
32. 32. Bernstein, F.C., et al., & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
33. 33. Allen, F.H. & Kennard, O. (1993). 3D search and research using the Cambridge structural database. Chemical Design Automation News 8, 31-37.
34. 34. Stout, C.D., Stura, E.A. & McRee, D.E. (1998). Structure of Azotobacter vinelandii 7Fe ferredoxin at 1.35 Å resolution and determination of the [Fe-S] bonds with 0.01 Å accuracy. J. Mol. Biol. 278, 629-639.
35. 35. Dauter, Z., Wilson, K.S., Sieker, L.C., Meyer, J. & Moulis, J.M. (1997). Atomic resolution (0.94 Å) structure of Clostridium acidurici ferredoxin. Biochemistry 36, 16065-16073.
36. 36. Vidakovic, M., Fraczkiewicz, G., Dave, B.C., Czernuszewicz, R.S. & Germanas, J.P. (1995). The environment of [2Fe-2S] clusters in ferredoxins: the role of residue 45 probed by site-directed mutagenesis. Biochemistry 34, 13906-13913.
37. 1H NMR spectrocopy of serine-ligated [2Fe-2S] ferredoxins produced by site-directed mutagenesis of cysteine residues in recombinant Anabaena 7120 vegetative ferredoxin. Biochemistry 33, 3155-3164.
38. 38. Schmitter, J.M., et al., & Decottignies, P. (1988). Purification, properties and complete amino acid sequence of the ferredoxin from a green alga, Chlamidomonas reinhardtii. Eur. J. Biochem. 172, 405-412.
39. 39. Bairoch, A., Bucher, P. & Hofmann, K. (1997). The PROSITE database, its status in 1997. Nucleic Acids Res. 25, 217-221.
40. 40. Kanekatsu, M. (1995). Chloroplast ribonucleoproteins (RNPs) as phosphate acceptors for casein kinase II: purification by ssDNA-cellulose column chromatography. Plant Cell Physiol. 36, 1649-1656.
41. 41. Vener, A.V., Van Kann, P.J., Gal, A., Anderson, B. & Ohad, I. (1995). Activation/deactivation cycle of redox-controlled thylakoid protein phosphorylation. Role of plastoquinol bound to the reduced cytochrome bf complex. J. Biol. Chem. 270, 25225-25232.
42. 42. Koivuniemi, A., Aro, E.M. & Anderson, B. (1995). Degradation of de D1-and D2 proteins of photosystem II in higher plants is regulated by reversible phosphorylation. Biochemistry 49, 16022-16029.
43. 43. Monnier, N., Defaye, G. & Chambaz, E.M. (1987). Phosphorylation of bovine adrenodoxin. Structural study and enzymatic activity. Eur. J. Biochem. 169, 147-153.
44. 44. Nemani, R., et al., & Armbrech, J. (1989). Phosphorylation of ferredoxin and regulation of renal mitochondrial 25-hydroxyvitamin D-1α-hydroxylase activity in vitro. J. Biol. Chem. 264, 15361-15366.
45. 45. Kessler, E. & Czygan, F.C. (1970). Physiologische und biochemische beiträge für taxonomie der gattung Chlorella. Arch. Mikrobiol. 70, 211-216.
46. 46. Lowry, O.H., Rosebrough, N.J., Farr, A.L. & Randall, R.J. (1951). Protein measurement with the folin phenol reagent. J. Biol. Chem. 193, 265-275.
47. 47. Ouchterlony, O. (1949). Antigen-antibody reactions in gels. Acta Pathol. Microbiol. Scand. 26, 507-511.
48. 48. Ternynck, T. & Avrameas, S. (1989). Técnicas Inmunoenzimáticas. Grupo Editorial Iberoamericana, Mexico, pp. 68-69.
49. 49. Otwinowsky, Z. & Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
50. 50. Navaza, J. (1994). AMoRe: an automated package for molecular replacement. Acta Crystallogr. A 50, 157-163.
51. 51. Sheldrick, G.M. & Schneider, T.R. (1997). SHELXL: high resolution refinement. Methods Enzymol. 277, 319-343.
52. 52. Brünger, A.T. (1992). Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475.
53. 53. Engh, R.A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A 47, 392-400.
54. 54. Moews, P.C. & Kretsinger, R.H. (1975). Refinement of the structure of carp muscle calcium-binding parvalbumin by model building and difference Fourier analysis. J. Mol. Biol. 91, 201-228.
55. 55. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
56. 56. Esnouf, R.M. (1997). SUBSCRIPT. J. Mol. Graph. 15, 132-134.
57. 57. Merrit, E.A. & Murphy, M.E.P. (1994). RASTER-3D Version 2.0, a program for photorealistic molecular graphics. Acta Crystallogr. D 50, 869-873.
58. 58. Sheldrick, G.M. (1990). SHELXTL Software Package for the Determination of Crystal Structures, Release 5.10. Bruker AXS, Madison, WI, USA.
59. 59. McRee, D.E. (1992). A visual protein crystallographic software system for X11/Xview. J. Mol. Graph. 10, 44-46.
60. 60. Nicholls, A., Bharadwaj, R. & Honig, B. (1993). GRASP - graphical representation and analysis of surface properties. Biophys. J. 64, A166.