X-ray structure of the Ferredoxin:NADP+ reductase from the cyanobacterium Anabaena PCC 7119 at 1.8 Å resolution, and crystallographic studies of NADP+ binding at 2.25 Å resolution

Journal of Molecular Biology

Volumn 263, Issue 1, 1996, Pages 20-39

  Serre, Laurence ^a   Vellieux, Frédéric M D ^a   Medina, Milagros ^b   Gomez Moreno, Carlos ^b   Fontecilla Camps, Juan C ^a   Frey, Michel ^a  

^a INSTITUT DE BIOLOGIE STRUCTURALE   (France)

^b UNIVERSITY OF ZARAGOZA   (Spain)

Author keywords

Electron transferase; Ferredoxin reductase; Flavoprotein; NADP+ complex; Photosynthetic bacteria

Indexed keywords

ARGININE; FERREDOXIN NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE REDUCTASE; LYSINE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; WATER;

ALPHA HELIX; ANABAENA; ARTICLE; CARBOXY TERMINAL SEQUENCE; HYDROPHOBICITY; NONHUMAN; PHOTOTROPHIC BACTERIUM; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY;

ANABAENA; BACTERIA (MICROORGANISMS); NOSTOC SP. PCC 7119; PHOTOBACTERIA; SPINACIA OLERACEA;

EID: 0030592460     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0553     Document Type: Article

References (77)

1. + reductase by site-directed mutagenesis. J. Biol. Chem. 266, 17760-17763.
2. + reductase as assessed by site-directed mutagenesis. Biochemistry, 32, 6374-6380.
3. + reductase: structure-function relationships as studied by site-directed mutagenesis and X-ray crystallography. Biochemistry, 34, 8371-8379.
4. + reductase complex in solution. Biochim. Biophys. Acta, 936, 269-279.
5. + and ferredoxin. J. Biol. Chem. 259, 8832-8839.
6. + reductase with NADP(H) specificity and oxidation-reduction properties. J. Biol. Chem. 261, 11214-11223.
7. Blow, D. M. & Crick, F. H. C. (1959). The treatment of errors in the isomorphous replacement method. Acta Crystallog. sect. A, 12, 794-802.
8. Brünger, A. T. (1988). Crystallographic refinement by simulated annealing. In Crystallographic Computing 4; Techniques and New Technologies (Isaacs, N. W. & Taylor, M. R. eds), pp. 126-140, Clarendon Press, Oxford.
9. Brünger, A. T. (1992a). X-PLOR Version 3.0. A System for Crystallography and NMR. The Howards Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, Newhaven, CT, USA.
10. Brünger, A.T. (1992b). The free R-value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, 472-474.
11. Bruns, C. M. & Karplus, P. A. (1995). Refined crystal structure of spinach ferredoxin reductase at 1.7 Å. resolution: oxidized, reduced and 2′-phospho-5′-AMP bound states. J. Mol. Biol. 247, 125-145.
12. + oxidoreductase. Biochemistry, 34, 12842-12848.
13. Canters, G. W. & van de Kamp, M. (1992). Protein mediated electron transfer. Curr. Opin. Struct. Biol. 2, 859-869.
14. + oxidoreductase. In Topics in Photosynthesis (Barber, J., ed.), vol. 8, pp. 527-560. Elsevier, Amsterdam.
15. Castellano, E., Oliva, G. & Navaza, J. (1992). Fast rigid-body for molecular-replacement techniques. J. Appl. Crystallog. 25, 281-284.
16. Correl, C. C., Batie, C. J., Ballou, D. P. & Ludwig, M. L. (1992). Phthalate dioxygenase reductase: a modular structure for electron transfer from pyridine nucleotides to [2Fe-2S]. Science, 258, 1604-1610.
17. Collaborative Computational Project, Number 4. (1994). The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D, 50, 760-763.
18. + oxidoreductase: The role of carboxyl groups, electrostatic surface potential and molecular dipole moment. Protein Sci. 2, 1126-1135.
19. Dodson, E. J. (1975). A comparison of different heavy-atom refinement procedures. In Crystallographic Computing Techniques. (Ahmed, F. R., ed.), Munskgaard.
20. Engh, R. A. & Huber, R. (1991). Accurate bond and angle parameters for X-ray protein structure refinement sufferers). Acta Crystallog. sect. A, 47, 392-400.
21. Evans, Ph. (1983). The refinement of heavy atom sites. In Information Quarterly for Protein Crystallography, vol. 11, pp. 15-27, Daresbury Laboratory, Daresbury Warrington WA4 4AD, UK.
22. Fillat, M. F., Sandman, G. & Gómez-Moreno, C. (1988). Flavodoxin from the nitrogen-fixing cyanobacterium Anabaena PCC7119. Arch. Microbiol. 150, 160-164.
23. + reductase gene from Anabaena PCC7119. Nucl. Acids Res. 18, 7161.
24. Howard, A. J., Gilliland, G. L., Finzel, B. C., Poulos, T. L., Ohlendorf, D. H. & Salemme, F. R. (1987). The use of an imaging proportional counter in macromolecular crystallography. J. Appl. Crystallog. 20, 383-387.
25. + reductase system from Anabaena. Biochimie, 77, 539-548.
26. + reductase from Anabaena. J. Am. Chem. Soc. 118, 5526-5531.
27. Jones, T. A. (1985). Interactive computer graphics: FRODO. In Methods in Enzymology (Wyckoff, H., Hirs, C. H. & Timasheff, S. N, eds), vol. 15, Academic Press, New York.
28. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A, 47, 110-119.
29. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structures. Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 257-2637.
30. Karplus, P. A. & Schulz, G. E. (1987). Refined structure of glutathione reductase at 1.5 Å resolution. J. Mol. Biol. 195, 701-729.
31. Karplus, P. A. & Schulz, G. E. (1989). Substrate binding and catalysis by glutathione reductase as derived from refined enzyme: substrate crystal structures at 2 Å resolution. J. Mol. Biol. 210, 163-180.
32. + oxidoreductase. Biochemistry, 23, 6576-6583.
33. + reductase: Prototype for a structurally novel flavoenzyme family. Science, 251, 60-66.
34. Kleywegt, G. J. (1995). Dictionaries for Heteros. Joint CCP4 and ESF-EABCM Newsletter on Protein Crystallography, vol. 31, pp. 45-50. The Daresbury Laboratory, Daresbury, Warrington WA4 4AD, UK.
35. Kleywegt, G. J. & Jones, A. T. (1994). Detection, delineation measurement and display of cavities in macromolecular structures. Acta Crystallog. sect. D, 50, 178-185.
36. Krakow, G., Ammeraal, R. N. & Vennesland, B. (1965). The stereospecificity of the Hill reaction with triphosphopyridine nucleotide. J. Biol. Chem. 249, 1820-1823.
37. Kraulis, P. J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24, 946-950.
38. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26, 293-291.
39. Leslie, A. G. W. (1987a). "Profile fitting", Computational aspects of protein data analysis. Proceeding of the Daresbury Study Weekend (Helliwell, J. R., Machin, P. A. & Papiz, M. Z, eds), Daresbury Laboratory, Daresbury, Warrington UK.
40. Leslie, A. G. W. (1987b). A reciprocal space method for calculating a molecular envelope using the algorithm of B. C. Wang. Acta Crystallog. sect. A, 43, 134-136.
41. Li, R., Bianchet, M. A., Talalay, P. & Amzel, M. (1995). The three-dimensional structure of NAD(P)H: quinone reductase, a flavoprotein involved in cancer chemoprotection and chemotherapy: mechanism of the two-electron reduction. Proc. Natl Acad. Sci. USA, 92, 8846-8850.
42. Lu, G., Campbell, W. H., Schneider, G. & Lindqvist, Y. (1994). Crystal structure of the FAD-containing fragment of corn nitrate reductase at 2.5 Å resolution: relationships to other flavoprotein reductases. Structure, 2, 809-821.
43. Lu, G., Lindqvist, Y., Schneider, G., Dwivedi, U. & Campbell, W. H. (1995). Structural studies on corn nitrate reductase: refined structure of the cytochrome b reductase fragment at 2.5 Å, its ADP complex and an active-site mutant and modeling of the cytochrome b domain. J. Mol. Biol. 248, 931-948.
44. Luzzatti, V. (1952). Traitement statistique des erreurs dans la détermination des structures cristallines. Acta Crystallog. sect. A, 5, 802-810.
45. Machin, P. A., Wonacott, A. J. & Moss, D. (1984). Daresbury Lab. News, 13, 17-19. Daresbury Laboratory, Daresbury, Warrington UK.
46. Matthews, B. W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491-497.
47. McDonald, I. K., Naylor, D. N., Jones, D. T. & Thornton, J. M. (1993). HBPLUS (computer program), Department of Biochemistry and Molecular Biology, University College, London, UK.
48. + reductase from Anabaena sp. PCC 7119 involved in substrate binding. FEBS Letters, 298, 25-28.
49. + reductase from Anabaena sp. PCC 7119 to its substrates. Arch. Biochim Biophys. 299, 281-286.
50. + reductase on the kinetics of interprotein electron transfer reactions. Eur. J. Biochem. 210, 577-583.
51. Navaza, J. (1987). On the fast rotation function. Acta Crystallog. sect. A, 43, 645-653.
52. Navaza, J. (1994). AMoRE: an automated package for molecular replacement. Acta Crystallog. sect. A, 50, 157-163.
53. 5 reductase from pig liver at 2.4 Å resolution. Biochemistry, 34, 2763-2767.
54. + reductase by site-directed mutagenesis and deletion analysis. J. Biol. Chem. 268, 19267-19273.
55. Pai, E. F., Karplus, P. A. & Schulz, G. E. (1988). Crystallographic analysis of the binding of NADPH, NADPH fragments and NADPH analogues to glutathione reductase. Biochemistry, 27, 4465-4474.
56. Pelletier, H. & Kraut, J. (1992). Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c. Science, 258, 1748-1755.
57. + reductase, flavodoxin and ferredoxin from a single batch of the cyanobacterium Anabaena PCC 7119. Prep. Biochem. 21, 191-204.
58. Ramakrishman, C., Ramachandran, G. N. & Sasisekharan, V. (1965). Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units. Biophys. J. 5, 909-933.
59. Read, R. J. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallog. sect. A, 42, 140-149.
60. Rogers, L. J. (1987). The Cyanobacteria (Fagy, P. & van Baalen, C., eds), Elsevier Science Publishers, The Netherlands.
61. Rossmann, M. G. (1972). The Molecular Replacement Method, Gordon & Breach, New York.
62. Rossmann, M., Moras, D. & Olsen, K. (1974). Chemical and biological evolution of a nucleotide-binding protein. Nature, 250, 194-199.
63. + reductase from Anabaena with its substrates. Arch. Biochem. Biophys. 288, 231-233.
64. + oxidoreductase from the nitrogen-fixing cyanobacteria Anabaena variabilis. Arch. Biochim. Biophys. 260, 200-207.
65. Satow, Y., Cohen, G. W., Padlan, E. & Davies, D. R. (1986). Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 Å. J. Mol. Biol. 190, 593-604.
66. Schreuder, H.A., Mattevi, A., Obmolova, G., Kalk, K. H., Hol, W. G. J., van der Bolt, F. J T. & van Berkel, W. S. (1994). Crystal structures of wild-type p-hydroxybenzoate hydroxylase complexed with 4-aminobenzoate, 2,4-dihydroxybenzoate, and 2-hydroxy-4-aminobenzoate and of the Tyr222Ala mutant complexed with 2-hydroxy-4-aminobenzoate. Evidence for a proton channel and a new binding mode of the flavin ring. Biochemistry, 33, 10161-10170.
67. Scrutton, N. S., Berry, A. & Perham, R. N. (1990). Redesign of the coenzyme specificity of a dehydrogenase by protein engineering. Nature, 343, 38-43.
68. Sem, D. & Kasper, C. B. (1992). Geometric relationships between the nicotinamide and isoalloxazine rings in NADPH-cytochrome P-450 oxidoreductase: implications for the classification of evolutionarily and functionally related flavoproteins. Biochemistry, 31, 3391-3398.
69. + oxidoreductase from Anabaena, FEBS Letters, 170, 85-88.
70. + reductase. J. Mol. Biol. 218, 271-272.
71. + reductase in cyclic electron transport in chloroplasts. Biochim. Biophys. Acta, 636, 234-243.
72. Vrielink, A., Lloyd, L. F. & Blow, D. (1991). Crystal structure of cholesterol oxidase from Brevibacterium sterolicum refined at 1.8 Å resolution. J. Mol. Biol. 219, 553-554.
73. + reductase from Anabaena PCC 7119 and spinach: electrostatic effects on intracomplex electron transfer. Arch. Biochem. Biophys. 287, 351-358.
74. Wallace, A. C., Laskowski, R. A. & Thornton, J. M. (1995). LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8, 127-134.
75. Wang, B. C. (1985). Resolution of phase ambiguity in macromolecular crystallography. In Methods in Enzymology (Wyckoff, H., Hirs, C. H. & Timasheff, S. N., eds), vol. 115, Academic Press, New York.
76. + reductase. J. Biol. Chem. 259, 6153-6157.
77. + reductase. Biochemistry, 27, 3753-3759.