X-ray crystal structure of the Desulfovibrio vulgaris (Hildenborough) apoflavodoxin-riboflavin complex

European Journal of Biochemistry

Volumn 258, Issue 2, 1998, Pages 362-371

  Walsh, Martin A ^a,c   Mccarthy, Andrew ^a   O'Farrell, Paul A ^b   Mcardle, Patrick ^a   Cunningham, P Desmond ^a   Mayhew, Stephen G ^b   Higgins, Timothy M ^a  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^b UNIVERSITY COLLEGE DUBLIN   (Ireland)

^c ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

Desulfovibrio vulgaris; Electron transfer; Flavodoxin; Riboflavin; X ray crystal structure

Indexed keywords

APOFLAVODOXIN; FLAVINE MONONUCLEOTIDE; FLAVODOXIN; HYDROQUINONE; ISOLEUCINE; RIBOFLAVIN; SEMIQUINONE; SERINE; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; DESULFOVIBRIO VULGARIS; ELECTRON TRANSPORT; NONHUMAN; OXIDATION REDUCTION POTENTIAL; PRIORITY JOURNAL; PROTEIN EXPRESSION; X RAY CRYSTALLOGRAPHY;

BACTERIA (MICROORGANISMS); DESULFOVIBRIO VULGARIS;

EID: 0032403006     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1327.1998.2580362.x     Document Type: Article

References (42)

1. Mayhew, S. G. & Tollin, G. (1992) General properties of flavodoxins, in Chemistry and biochemistry of flavoenzymes (Müller, F., ed.) vol. 3, pp. 389-426, CRC Press, Boca Raton.
2. Mayhew, S. G. & Ludwig, M. L. (1975) Flavodoxins and electron-transferring flavoproteins, In The Enzymes (Boyer, P. D., ed.) 3rd edn, vol. 12B, pp. 57-109, Academic Press, New York.
3. Mayhew, S. G. (1971) Studies on flavin binding in flavodoxins, Biochim. Biophys. Acta 235, 289-302.
4. Curley, G. P., Carr, M. C., Mayhew, S. G. & Voordouw, G. (1991) Redox and flavin-binding properties of recombinant flavodoxin from Desulfovibrio vulgaris (Hildenborough), Eur. J. Biochem. 302, 1091-1100.
5. D'Anna, J. A. & Tollin, G. (1972) Studies of flavin-protein interaction in flavoproteins using protein fluorescence and circular dichroism, Biochemistry 11, 1073-1080.
6. Burkhart, B., Ramakrishnan, B., Yan, H., Reedstrom, R., Markley, J., Straus, N. & Sundaralingam, M. (1995) Structure of the trigonal form of recombinant oxidized flavodoxin from Anabaena 7120 at 1.40 Å resolution, Acta Crystallogr. D51, 318-330.
7. Burnett, R. M., Darling, G. D., Kendall, D. S., LeQuensne, M. E., Mayhew, S. G., Smith, W. W. & Ludwig, M. L. (1974). The structure of the oxidized form of clostridial flavodoxin at 1.9 Å resolution. Description of the flavin mononucleotide binding site, J. Biol. Chem. 249, 4383-4392.
8. Smith, W. W., Pattridge, K. A., Ludwig, M. L., Petsko, G. A., Tsernoglou, D., Tanaka, M. & Yasunobu, K. T. (1983) The structure of oxidized flavodoxin from Anacystis nidulans, J. Mol. Biol. 165, 737-755.
9. Fukuyama, K., Matsubara, H. & Rogers, L. J. (1992) Crystal structure of oxidized flavodoxin from a red alga Chondrus crispus refined at 1.8 Å resolution. Description of the flavin mononucleotide binding site, J. Mol. Biol. 225, 775-789.
10. Watt, W., Tulinsky, A., Swenson, R. P. & Watenpaugh, K. D. (1991) Comparison of the crystal structures of a flavodoxin in its three oxidation states at cryogenic temperatures, J. Mol. Biol. 218, 195-208.
11. Walsh, M. A. (1994) Structural studies on a genetically engineered flavodoxin, Ph.D. Thesis, National University of Ireland.
12. Hoover, D. M. & Ludwig, M. L. (1997) A flavodoxin that is required for enzyme activation: The structure of oxidized flavodoxin from Escherichia coli at 1.8 Å resolution, Prot. Sci. 6, 2525-2537.
13. Genzor, C., Perales-Alcon, A., Sancho, J. & Romero, A. (1996). Closure of a tyrosine/tryptophan aromatic gate leads to a compact fold in apoflavodoxin, Nature Struct. Biol. 3, 329-332.
14. Moonen, C., Vervoort, J. & Müller, F. (1984) Some new ideas about the possible regulation of redox potentials in flavoproteins, with special reference to flavodoxins, in Flavins and flavoproteins (Bray, R. C., Engel, P. C. & Mayhew, S. G., eds) pp. 493-496, Walter de Gruyter, Berlin.
15. Vervoort, J., van Berkel, W. J. H., Mayhew, S. G., Müller, F., Bacher, A. & Nielsen, P. J. L. (1986) Properties of the complexes of riboflavin 3′,5′-bisphosphate and the apoflavodoxins from Megasphaera elsdenii and Desulfovibrio vulgaris (Hildenborough), Eur. J. Biochem. 161, 749-756.
16. Pueyo, J., Curley, G. P. & Mayhew, S. G. (1996) Kinetics and thermodynamics of the binding of riboflavin. riboflavin 5′-phosphate and riboflavin 3′5′-bisphosphate by apoflavodoxins, Biochem. J. 313, 855-861.
17. Zhou, Z. & Swenson, R. P. (1996) Evaluation of the electrostatic effect of the 5′-phosphate of the flavin mononucleotide cofactor on the oxidation-reduction potentials of the flavodoxin from Desulfovibrio vulgaris (Hildenborough), Biochemistry 35, 12443-12454.
18. Matthews, B. W. (1968) Solvent content of protein crystals, J. Mol. Biol. 215, 491-497.
19. Otwinowski, Z. & Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode, Methods Enzymol. 276, 307-326.
20. Navaza, J. (1994) AMoRe: an automated package for molecular replacement, Acta Crystallogr. D50, 157-163.
21. Collaborative Computing Project Number 4. (1994) The CCP4 suite: programs for protein crystallography collaborative computational project, number 4, Acta Crystallogr. D50, 760-763.
22. Jones, T., Zou, J., Cowan, S. & Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models, Acta Crystallogr. 47, 110-119.
23. Kleywegt, G. & Jones, T. (1994) Halloween...masks and bones, in From first map to final model in Daresbury, UK (Bailey, S., Hubbard, R. & Waller, D. eds) pp. 59-66, SERC Daresbury Laboratory, Warrington, UK.
24. Lamzin, V. S. & Wilson, K. S. (1997) Automatic refinement for protein crystallography, Methods Enzymol. 277, 269-305.
25. Read, R. J. (1986) Improved Fourier coefficients for maps using phases from partial structures with errors, Acta Crystallogr. A42, 140-149.
26. Ramachandran, G. & Sasisekharan, V. (1968) Conformation of polypeptides and proteins, Adv. Prot. Chem. 23, 283-437.
27. Watenpaugh, K. D., Sieker, L. C. & Jensen, L. H. (1973) Structure of Desulfovibrio vulgaris flavodoxin at 2 Å; description of the FMN binding site, Proc. Natl Acad. Sci. USA 70, 3857-3860.
28. + binding sites, J. Mol. Biol. 256, 228-234.
29. O'Farrell, P. A., Walsh, M. A., McCarthy, A. A., Voordouw, G., Higgins, T. & Mayhew, S. G. (1998) Modulation of redox potentials of FMN in Desulfovibrio vulgaris flavodoxin: thermodynamic properties and crystal structures of glycine-61 mutants, Biochemistry 37, 8405-8416.
30. Allen, F. & Kennard, O. (1993) 3D search and research using the Cambridge Structural Database, Chem. Des. Autom. News 8, 31-37.
31. Barman, B. & Tollin, G. (1972) Flavine-protein interactions in flavoenzymes. Temperature-jump and stopped-flow studies of flavine-analog binding to the apoprotein of Azotobacter flavodoxin, Biochemistry 11, 4746-4754.
32. Sharkey, C., Mayhew, S. G., Higgins, T. M. & Walsh, M. A. (1997) Crystallographic studies on flavodoxin from Megasphaera elsdenii, in Flavins and flavoproteins 1996 (Stevenson, K. J., Massey, V. & Williams, C. H. Jr, eds) pp. 445-448, University of Calgary Press, Calgary.
33. Ludwig, M. L. & Luschinsky, C. L. (1992) Structure and redox properties of clostridial flavodoxin, in Chemistry and biochemistry of flavoenzymes (Müller, F., ed.) vol. 3, pp. 427-466, CRC Press, Boca Raton.
34. O'Connell, D. P. (1995) Flavin-protein interactions: A study on flavodoxin from Desulfovibrio vulgaris using site-directed mutagenesis, PhD thesis, National University of Ireland.
35. Mayhew, S. G., O'Connell, D., O'Farrell, P. A., Yalloway, G. & Geoghegan, S. (1996) Regulation of the redox potentials of flavodoxins: modification of the flavin binding site, Biochem. Soc. Trans. 24, 122-127.
36. Swenson, R. P. & Krey, G. (1994) Site-directed mutagenesis of tyrosine-98 in the flavodoxin from Desulfovibrio vulgaris (Hildenborough): regulation of oxidation-reduction properties of the bound FMN cofactor by aromatic solvent and electrostatic interaction. Biochemistry 33, 8505-8514.
37. Zhou, Z. & Swenson, R. P. (1995) Electrostatic effects of surface amino acid residues on the oxidation-reduction potentials of the flavodoxin from Desulfovibrio vulgaris (Hildenborough), Biochemistry 34, 3183-3192.
38. Walsh, M. A., McCarthy, A., Higgins, T., O'Farrell, P. A. & Mayhew, S. G. (1995) Crystallographic analysis of the Y-98-S and D-95-A mutations at the FMN binding site of Desulfovibrio vulgaris flavodoxin. Twenty-first EMBO symposium, 'Structure and Function of Proteins', p. 218.
39. 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. Cryst. 26, 283-291.
40. Kraulis, P. J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures, 946-950.
41. Esnouf, R. M. (1997) An extensively modified version of molscript that includes generally enhanced colouring capabilities, J. Mol. Graph Model 15, 132-134.
42. Wallace, A. C., Laskowski, R. A. & Thornton, J. M. (1995) LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions, Prot. Eng. 8, 127-134.