Structural studies of flavodoxins

Last modified: Wed Apr 14 12:18:34 BST 2004

• Andersen, R.D., Apgar, P.A., Burnett, R.M., Darling, G.D., LeQuesne, M.E., Mayhew, S.G. and Ludwig, M.L. (1972) Structure of the radical form of clostridial flavodoxin: a new molecular model. Proc. Natl. Acad. Sci. USA 69, 3189-3191.
• Artali, R., Bombieri, G., Meneghetti, F., Gilardi, G., Sadeghi, S.J., Cavazzini, D. and Rossi, G.L. (2002) Comparison of the refined crystal structures of wild-type (1.34 Å) flavodoxin from Desulfovibrio vulgaris and the S35C mutant (1.44 Å) at 100 K. Acta Crystallogr. D58, 1787-1792.
• Barsukov, I., Modi, S., Lian, L.-Y., Sze, K.H., Paine, M.J.I., Wolf, C.R. and Roberts, G.C.K. (1997) ¹H, ¹⁵N and ¹³C NMR resonance assignment, secondary structure and global fold of the FMN-binding domain of human cytochrome P450 reductase. J. Biomol. NMR 10, 63-75.
• Blümel, M., Schmidt, J.M., Löhr, F. and Rüterjans, H. (1998) Quantitative f torsion angle analysis in Desulfovibrio vulgaris flavodoxin based on six f related ³J couplings. Eur. Biophys. J. 27, 321-334.
• Bradley, L.H. and Swenson, R.P. (1999) Role of glutamate-59 hydrogen bonded to N(3)H of the flavin mononucleotide cofactor in the modulation of the redox potentials of the Clostridium beijerinckii flavodoxin. Glutamate-59 is not responsible for the pH dependency but contributes to the stabilization of the flavin semiquinone. Biochemistry 38, 12377-12386.
• Bradley, L.H. and Swenson, R.P. (2001) Role of hydrogen bonding interactions to N(3)H of the flavin mononucleotide cofactor in the modulation of the redox potentials of the Clostridium beijerinckii flavodoxin. Biochemistry 38, 8686-8695.
• Burkhart, B.M., Ramakrishnan, B., Yan, H., Reedstrom, R.J., Markley, J.L., Straus, N.A. and 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.
• Burnett, R.M., Darling, G.D., Kendall, D.S., LeQuesne, M.E., Mayhew, S.G., Smith, W.W. and Ludwig, M.L. (1974) The structure of the oxidized form of clostridial flavodoxin at 1.9-Å resolution. J. Biol. Chem. 249, 4383-4392.
• Chang, F.-C. and Swenson, R.P. (1997) Regulation of oxidation-reduction potentials through redox-linked ionization in the Y98H mutant of the Desulfovibrio vulgaris [Hildenborough] flavodoxin: Direct proton nuclear magnetic resonance spectroscopic evidence for the redox-dependent shift in the pK_a of histidine-98. Biochemistry 36, 9013-9021.
• Chang, F.-C. and Swenson, R.P. (1999) The midpoint potentials for the oxidized-semiquinone couple for Gly57 mutants of the Clostridium beijerinckii flavodoxin correlate with changes in the hydrogen-bonding interaction with the proton on N(5) of the reduced flavin mononucleotide cofactor as measured by NMR chemical shift temperature dependencies. Biochemistry 38, 7168-7176.
• Clubb, R.T., Thanabal, V., Osborne, C. and Wagner, G. (1991) ¹H and ¹⁵N resonance assignments of oxidized flavodoxin from Anacystis nidulans with 3D NMR. Biochemistry 30, 7718-7730.
• Doherty, G.M., Mayhew, S.G. and Malthouse, J.P. (1993) ¹³C-n.m.r. of the cyanylated apoflavodoxin and flavodoxin from Clostridium pasteurianum. Biochem. J. 294, 215-218.
• Drennan, C.L., Pattridge, K.A., Weber, C.H., Metzger, A.L., Hoover, D.M. and Ludwig, M.L. (1999) Refined structures of oxidized flavodoxin from Anacystis nidulans. J. Mol. Biol. 294, 711-724.
• Druhan, L.J. and Swenson, R.P. (1998) Role of methionine 56 in the control of the oxidation-reduction potentials of the Clostridium beijerinckii flavodoxin: Effects of substitutions by aliphatic amino acids and evidence for a role of sulfur-flavin interactions. Biochemistry 37, 9668-9678.
• Feng, Y. and Swenson, R.P. (1997) Evaluation of the role of specific acidic amino acid residues in electron transfer between the flavodoxin and cytochrome c₃ from Desulfovibrio vulgaris [Hildenborough]. Biochemistry 36, 13617-13628.
• Fernández-Recio, J., Romero, A. and Sancho, J. (1999) Energetics of a hydrogen bond (charged and neutral) and of a cation- interaction in apoflavodoxin. J. Mol. Biol. 290, 319-330.
• Franken, H.D., Rüterjans, H. and Müller, F. (1984) Nuclear-magnetic-resonance investigation of ¹⁵N-labeled flavins, free and bound to Megasphaera elsdenii apoflavodoxin. Eur. J. Biochem. 138, 481-489.
• Freigang, J., Diederichs, K., Schäfer, K.P., Welte, W. and Paul, R. (2002) Crystal structure of oxidized flavodoxin, an essential protein in Helicobacter pylori. Protein Science 11, 253-261.
• Fukuyama, K., Wakabayashi, S., Matsubara, H. and Rogers, L.J. (1990) Tertiary structure of oxidized flavodoxin from an eukaryotic red alga Chondrus crispus at 2.35-Å resolution. Localization of charged residues and implication for interaction with electron transfer partners. J. Biol. Chem. 265, 15804-15812.
• Fukuyama, K., Matsubara, H. and 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.
• Genzor, C.G., Perales-Alcón, A., Sancho, J. and Romero, A. (1996a) Closure of a tyrosine/tryptophan aromatic gate leads to a compact fold in apo flavodoxin. Nature Struct. Biol. 3, 329-332.
• Genzor, C.G., Beldarraín, A., Gómez-Moreno, C., López-Lacomba, J.L., Cortijo, M. and Sancho, J. (1996b) Conformational stability of apoflavodoxin. Protein Science 5, 1376-1388.
• Hoover, D.M., Drennan, C.L., Metzger, A.L., Osborne, C., Weber, C.H., Pattridge, K.A. and Ludwig, M.L. (1999) Comparisons of wild-type and mutant flavodoxins from Anacystis nidulans. Structural determinants of the redox potentials. J. Mol. Biol. 294, 725-743.
• Hrovat, A., Blüel, M., Löhr, F., Mayhew, S.G. and Rüterjans, H. (1997) Backbone dynamics of oxidized and reduced D. vulgaris flavodoxin in solution. J. Biomol. NMR 10, 53-62.
• Irún, M.P., Maldonado, S. and Sancho, J. (2001) Stabilization of apoflavodoxin by replacing hydrogen-bonded charged Asp or Glu residues by the neutral isosteric Asn or Gln. Protein Engineering 14, 173-181.
• Knauf, M.A., Löhr, F., Curley, G.P., O'Farrell, P., Mayhew, S.G., Müller, F. and Rüterjans, H. (1993) Homonuclear and heteronuclear NMR studies of oxidized Desulfovibrio vulgaris flavodoxin. Sequential assignments and identification of secondary structure elements. Eur. J. Biochem. 213, 167-184.
• Knauf, M.A., Löhr, F., Blümel, Mayhew, S.G. and Rüterjans, H. (1996) NMR investigation of the solution conformation of oxidized flavodoxin from Desulfovibrio vulgaris. Determination of the tertiary structure and detection of protein-bound water molecules. Eur. J. Biochem. 238, 423-434.
• Langdon, G.M., Jiménez, M.A., Genzor, C.G., Maldonado, S., Sancho, J. and Rico, M. (2001) Anabaena apoflavodoxin hydrogen exchange: On the stable exchange core of the /ß(21345) flavodoxin-like family. Proteins 43, 476-488.
• Leenders, R., Kooijman, M., van Hoek, A., Veeger, C. and Visser, A.J. (1993) Flavin dynamics in reduced flavodoxins. A time-resolved polarized fluorescence study. Eur. J. Biochem. 211, 37-45.
• Löhr, F., Blüel, M., Schmidt, J.M. and Rüterjans, H. (1997) Application of H(N)CA, CO-E.COSY experiments for calibrating the angular dependencies of vicinal couplings J(C´_i-1, H_i), J(C´_i-1, C^ß_i) and J(C´_i-1, C´_i) in proteins. J. Biomol. NMR 10, 107-118.
• Löhr, F., Mayhew, S.G. and Rüterjans, H. (2000) Detection of scalar couplings across NH···OP and OH···OP hydrogen bonds in a flavoprotein. J. Am. Chem. Soc. 122, 9289-9295.
• Ludwig, M.L., Schopfer, L.M., Metzger, A.L., Pattridge, K.A. and Massey, V. (1990) Structure and oxidation-reduction behavior of 1-deaza-FMN flavodoxins: modulation of redox potentials in flavodoxins. Biochemistry 29, 10364-10375.
• Ludwig, M.L., Pattridge, K.A., Metzger, A.L., Dixon, M.M., Eren, M., Feng, Y. and Swenson, R.P. (1997) Control of oxidation-reduction potentials in flavodoxin from Clostridium beijerinckii: the role of conformation changes. Biochemistry 36, 1259-1280.
• Maldonado, S., Jiménez, M.Á., Langdon, G.M. and Sancho, J. (1998) Cooperative stabilization of a molten globule apoflavodoxin fragment. Biochemistry 37, 10589-10596.
• Medina, M., Lostao, A., Sancho, J., Gómez-Moreno, C., Cammack, R., Alonso, P.J. and Martínez, J.I. (1999) Electron-nuclear double resonance and hyperfine sublevel correlation spectroscopic studies of flavodoxin mutants from Anabaena sp. PCC 7119. Biophys. J. 77, 1712-1720.
• Moonen, C.T. and Müller, F. (1982) Structural and dynamic information on the complex of Megasphaera elsdenii apoflavodoxin and riboflavin 5´-phosphate. A phosphorus-31 nuclear magnetic resonance study. Biochemistry 21, 408-414.
• Moonen, C.T., Scheek, R.M., Boelens, R. and Müller, F. (1984) The use of two-dimensional nuclear-magnetic-resonance spectroscopy and two-dimensional difference spectra in the elucidation of the active center of Megasphaera elsdenii flavodoxin. Eur. J. Biochem. 141, 323-330.
• O'Farrell, P.A., Walsh, M.A., McCarthy, A.A., Higgins, T.M., Voordouw, G. and Mayhew, S.G. (1998) Modulation of the redox potentials of FMN in Desulfovibrio vulgaris flavodoxin: Thermodynamic properties and crystal structures of glycine-61 mutants. Biochemistry 37, 8405-8416.
• Peelen, S. and Vervoort, J. (1994) Two-dimensional NMR studies of the flavin binding site of Desulfovibrio vulgaris flavodoxin in its three redox states. Arch. Biochem. Biophys. 314, 291-300.
• Peelen, S., Wijmenga, S.S., Erbel, P.J.A., Robson, R.L., Eady, R.R. and Vervoort, J. (1996) Possible role of a short extra loop of the long-chain flavodoxin from Azotobacter chroococcum in electron transfer to nitrogenase: Complete ¹H, ¹⁵N and ¹³C backbone assignments and secondary solution structure of the flavodoxin. J. Biomol. NMR 7, 315-330.
• Pollock, J.R., Swenson, R.P. and Stockman, B.J. (1996) ¹H and ¹⁵N resonance assignments and solution secondary structure of Desulfovibrio desulfuricans flavodoxin. J. Biomol. NMR 7, 225-235.
• Ponstingl, H. and Otting, G. (1997) NMR assignments, secondary structure and hydration of oxidized Escherichia coli flavodoxin. Eur. J. Biochem. 244, 384-399.
• Rao, S.T., Shaffie, F., Yu, C., Satyshur, K.A., Stockman, B.J., Markley, J.L. and Sundarlingam, M. (1992) Structure of the oxidized long-chain flavodoxin from Anabaena 7120 at 2 Å resolution. Protein Science 1, 1413-1427.
• Reynolds, R.A., Watt, W. and Watenpaugh, K.D. (2001) Structures and comparison of the Y98H (2.0 Å) and Y98W (1.5 Å) mutants of flavodoxin (Desulfovibrio vulgaris). Acta Crystallogr. D57, 527-535.
• Romero, A., Caldeira, J., LeGall, J., Moura, I., Moura, J.J.G. and Romão, M.J. (1996) Crystal structure of flavodoxin from Desulfovibrio desulfuricans ATCC 27774 in two oxidation states. Eur. J. Biochem. 239, 190-196.
• Schmidt, J.M., Löhr, F. and Rüterjans, H. (1996) Heteronuclear relayed E.COSY applied to the determination of accurate ³J(H^N, C´) and ³J(H^ß, C´) coupling constants in Desulfovibrio vulgaris flavodoxin. J. Biomol. NMR 7, 142-152.
• Smith, W.W., Pattridge, K.A., Ludwig, M.L., Petsko, G.A., Tsernoglou, D., Tanaka, M. and Yasunobu, K.T. (1983) Structure of oxidized flavodoxin from Anacystis nidulans. J. Mol. Biol. 165, 737-753.
• Steensma, E. and van Mierlo, C.P.M. (1998) Structural characterisation of apoflavodoxin shows that the location of the stable nucleus differs among proteins with a flavodoxin-like topology. J. Mol. Biol. 282, 653-666.
• Steensma, E., Nijman, M.J.M., Bollen, Y.J.M., de Jager, P.A., van den Berg, W.A.M., van Dongen, W.M.A.M. and van Mierlo, C.P.M. (1998) Apparent local stability of the secondary structure of Azotobacter vinelandii holoflavodoxin II as probed by hydrogen exchange: Implications for redox potential regulation and flavodoxin folding. Protein Science 7, 306-317.
• Stockman, B.J., Westler, W.M., Mooberry, E.S. and Markley, J.L. (1988) Flavodoxin from Anabaena 7120: uniform nitrogen-15 enrichment and hydrogen-1, nitrogen-15, and phosphorus-31 NMR investigations of the flavin mononucleotide binding site in the reduced and oxidized states. Biochemistry 27, 136-142.
• Stockman, B.J., Krezel, A.M., Markley, J.L., Leonhardt, K.G. and Straus, N.A. (1990) Hydrogen-1, carbon-13, and nitrogen-15 NMR spectroscopy of Anabaena 7120 flavodoxin: assignment of ß-sheet and flavin binding site resonances and analysis of protein-flavin interactions. Biochemistry 29, 9600-9609.
• Stockman, B.J., Euvrard, A., Kloosterman, D.A., Scahill, T.A. and Swenson, R.P. (1993) ¹H and ¹⁵N resonance assignments and solution secondary structure of oxidized Desulfovibrio vulgaris flavodoxin determined by heteronuclear three-dimensional NMR spectroscopy. J. Biomol. NMR 3, 133-149.
• Stockman, B.J., Richardson, T.E. and Swenson, R.P. (1994) Structural changes caused by site-directed mutagenesis of tyrosine-98 in Desulfovibrio vulgaris flavodoxin delineated by ¹H and ¹⁵N NMR spectroscopy: implications for redox potential modulation. Biochemistry 33, 15298-15308.
• Swenson, R.P. and Krey, G.D. (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 interactions. Biochemistry 33, 8505-8514.
• van Mierlo, C.P.M., Lijnzaad, P., Vervoort, J., Müller, F., Berendsen, H.J.C. and de Vlieg, J. (1990) Tertiary structure of two-electron reduced Megasphaera elsdenii flavodoxin and some implications, as determined by two-dimensional ¹H-NMR and restrained molecular dynamics. Eur. J. Biochem. 194, 185-198.
• van Mierlo, C.P.M., Müller, F. and Vervoort, J. (1990) Secondary and tertiary structure characteristics of Megasphaera elsdenii flavodoxin in the reduced state as determined by two-dimensional ¹H NMR. Eur. J. Biochem. 189, 589-600.
• van Mierlo, C.P.M., van der Sanden, B.P., van Woensel, P., Müller, F. and Vervoort, J. (1990) A two-dimensional ¹H-NMR study on Megasphaera elsdenii flavodoxin in the oxidized state and some comparisons with the two-electron-reduced state. Eur. J. Biochem. 194, 199-216.
• van Mierlo, C.P.M., Vervoort, J., Müller, F. and Bacher, A. (1990) A two-dimensional ¹H-NMR study on Megasphaera elsdenii flavodoxin in the reduced state. Sequential assignments. Eur. J. Biochem. 187, 521-541.
• van Mierlo, C.P.M., van Dongen, W.M.A.M., Vergeldt, F., van Berkel, W.J.H. and Steensma, E. (1998) The equilibrium unfolding of Azotobacter vinelandii apoflavodoxin II occurs via a relatively stable folding intermediate. Protein Science 7, 2331-2344.
• van Mierlo, C.P.M., van den Oever, J.M.P. and Steensma, E. (2000) Apoflavodoxin (un)folding followed at the residue level by NMR. Protein Science 9, 145-157.
• Vervoort, J., Müller, F., LeGall, J., Bacher, A. and Sedlmaier, H. (1985) Carbon-13 and nitrogen-15 nuclear-magnetic-resonance investigation on Desulfovibrio vulgaris flavodoxin. Eur. J. Biochem. 151, 49-57.
• Vervoort, J., Müller, F., Mayhew, S.G., van den Berg, W.A., Moonen, C.T. and Bacher, A. (1986) A comparative carbon-13, nitrogen-15, and phosphorus-31 nuclear magnetic resonance study on the flavodoxins from Clostridium MP, Megasphaera elsdenii, and Azotobacter vinelandii. Biochemistry 25, 6789-6799.
• Visser, A.J., Vervoort, J., O'Kane, D.J., Lee, J. and Carreira, L.A. (1983) Raman spectra of flavin bound in flavodoxins and in other flavoproteins. Evidence for structural variations in the flavin-binding region. Eur. J. Biochem. 131, 639-645.
• Walsh, M.A., McCarthy, A., O'Farrell, P.A., McArdle, P., Cunningham, P.D., Mayhew, S.G. and Higgins, T.M. (1998) X-ray crystal structure of the Desulfovibrio vulgaris (Hildenborough) apoflavodoxin-riboflavin complex. Eur. J. Biochem. 258, 362-371.
• Watenpaugh, K.D., Sieker, L.C., Jensen, L.H., Legall, J. and Dubourdieu, M. (1972) Structure of the oxidized form of a flavodoxin at 2.5-Å resolution: resolution of the phase ambiguity by anomalous scattering. Proc. Natl. Acad. Sci. USA 69, 3185-3188.
• Watt, W., Tulinsky, A., Swenson, R.P. and 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.
• Wijmenga, S.S. and van Mierlo, C.P.M. (1991) Three-dimensional correlated NMR study of Megasphaera elsdenii flavodoxin in the oxidized state. Eur. J. Biochem. 195, 807-822.
• Yalloway, G.N., Mayhew, S.G., Malthouse, J.P.G., Gallagher, M.E. and Curley, G.P. (1999) pH-dependent spectroscopic changes associated with the hydroquinone of FMN in flavodoxins. Biochemistry 38, 3753-3762.
• Zhang, P., Dayie, K.T. and Wagner, G. (1997) Unusual lack of internal mobility and fast overall tumbling in oxidized flavodoxin from Anacystis nidulans. J. Mol. Biol. 272, 443-455.
• Zhou, Z. and 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 36, 12443-12454.

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