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A crystallographic study of Cys69Ala flavodoxin II from Azotobacter vinelandii: structural determinants of redox potential.

Alagaratnam S, van Pouderoyen G, Pijning T, Dijkstra BW, Cavazzini D, Rossi GL, Van Dongen WM, van Mierlo CP, van Berkel WJ, Canters GW
Protein Sci 14 2284-95 (2005)
Cited: 37 times
EuropePMC logo PMID: 16131657

Abstract

Flavodoxin II from Azotobacter vinelandii is a "long-chain" flavodoxin and has one of the lowest E1 midpoint potentials found within the flavodoxin family. To better understand the relationship between structural features and redox potentials, the oxidized form of the C69A mutant of this flavodoxin was crystallized and its three-dimensional structure determined to a resolution of 2.25 A by molecular replacement. Its overall fold is similar to that of other flavodoxins, with a central five-stranded parallel beta-sheet flanked on either side by alpha-helices. An eight-residue insertion, compared with other long-chain flavodoxins, forms a short 3(10) helix preceding the start of the alpha3 helix. The flavin mononucleotide (FMN) cofactor is flanked by a leucine on its re face instead of the more conserved tryptophan, resulting in a more solvent-accessible FMN binding site and stabilization of the hydroquinone (hq) state. In particular the absence of a hydrogen bond to the N5 atom of the oxidized FMN was identified, which destabilizes the ox form, as well as an exceptionally large patch of acidic residues in the vicinity of the FMN N1 atom, which destabilizes the hq form. It is also argued that the presence of a Gly at position 58 in the sequence stabilizes the semiquinone (sq) form, as a result, raising the E2 value in particular.

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  1. Electron Transfer in Nitrogenase. Rutledge HL, Tezcan FA. Chem Rev 120 5158-5193 (2020)
  2. What lessons can be learned from studying the folding of homologous proteins? Nickson AA, Clarke J. Methods 52 38-50 (2010)
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Articles - 1yob mentioned but not cited (13)

  1. A crystallographic study of Cys69Ala flavodoxin II from Azotobacter vinelandii: structural determinants of redox potential. Alagaratnam S, van Pouderoyen G, Pijning T, Dijkstra BW, Cavazzini D, Rossi GL, Van Dongen WM, van Mierlo CP, van Berkel WJ, Canters GW. Protein Sci 14 2284-2295 (2005)
  2. Distant residues mediate picomolar binding affinity of a protein cofactor. Bollen YJ, Westphal AH, Lindhoud S, van Berkel WJ, van Mierlo CP. Nat Commun 3 1010 (2012)
  3. Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase. Tomasiak TM, Archuleta TL, Andréll J, Luna-Chávez C, Davis TA, Sarwar M, Ham AJ, McDonald WH, Yankovskaya V, Stern HA, Johnston JN, Maklashina E, Cecchini G, Iverson TM. J Biol Chem 286 3047-3056 (2011)
  4. Interrupted hydrogen/deuterium exchange reveals the stable core of the remarkably helical molten globule of alpha-beta parallel protein flavodoxin. Nabuurs SM, van Mierlo CPM. J Biol Chem 285 4165-4172 (2010)
  5. Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers. Campbell IJ, Bennett GN, Silberg JJ. Front Energy Res 7 (2019)
  6. Electrochemical and structural characterization of Azotobacter vinelandii flavodoxin II. Segal HM, Spatzal T, Hill MG, Udit AK, Rees DC. Protein Sci 26 1984-1993 (2017)
  7. Structural and phylogenetic analysis of Rhodobacter capsulatus NifF: uncovering general features of nitrogen-fixation (nif)-flavodoxins. Pérez-Dorado I, Bortolotti A, Cortez N, Hermoso JA. Int J Mol Sci 14 1152-1163 (2013)
  8. Illuminating the off-pathway nature of the molten globule folding intermediate of an α-β parallel protein. Lindhoud S, Westphal AH, Borst JW, van Mierlo CP. PLoS One 7 e45746 (2012)
  9. Unraveling the interactions of the physiological reductant flavodoxin with the different conformations of the Fe protein in the nitrogenase cycle. Pence N, Tokmina-Lukaszewska M, Yang ZY, Ledbetter RN, Seefeldt LC, Bothner B, Peters JW. J Biol Chem 292 15661-15669 (2017)
  10. Fluorescence of Alexa fluor dye tracks protein folding. Lindhoud S, Westphal AH, Visser AJ, Borst JW, van Mierlo CP. PLoS One 7 e46838 (2012)
  11. Non-native hydrophobic interactions detected in unfolded apoflavodoxin by paramagnetic relaxation enhancement. Nabuurs SM, de Kort BJ, Westphal AH, van Mierlo CP. Eur Biophys J 39 689-698 (2010)
  12. Cofactor binding protects flavodoxin against oxidative stress. Lindhoud S, van den Berg WA, van den Heuvel RH, Heck AJ, van Mierlo CP, van Berkel WJ. PLoS One 7 e41363 (2012)
  13. The Ribosome Restrains Molten Globule Formation in Stalled Nascent Flavodoxin. Houwman JA, André E, Westphal AH, van Berkel WJ, van Mierlo CP. J Biol Chem 291 25911-25920 (2016)


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  1. Methanogenic archaea: ecologically relevant differences in energy conservation. Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R. Nat Rev Microbiol 6 579-591 (2008)
  2. Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD+ (Rnf) as Electron Acceptors: A Historical Review. Buckel W, Thauer RK. Front Microbiol 9 401 (2018)
  3. Structural and mechanistic aspects of flavoproteins: photosynthetic electron transfer from photosystem I to NADP+. Medina M. FEBS J 276 3942-3958 (2009)
  4. Flavodoxins as Novel Therapeutic Targets against Helicobacter pylori and Other Gastric Pathogens. Salillas S, Sancho J. Int J Mol Sci 21 E1881 (2020)
  5. Folding of proteins with a flavodoxin-like architecture. Houwman JA, van Mierlo CPM. FEBS J 284 3145-3167 (2017)

Articles citing this publication (16)

  1. Clostridium acidurici electron-bifurcating formate dehydrogenase. Wang S, Huang H, Kahnt J, Thauer RK. Appl Environ Microbiol 79 6176-6179 (2013)
  2. The folding energy landscape of apoflavodoxin is rugged: hydrogen exchange reveals nonproductive misfolded intermediates. Bollen YJ, Kamphuis MB, van Mierlo CP. Proc Natl Acad Sci U S A 103 4095-4100 (2006)
  3. A Förster-resonance-energy transfer-based method for fluorescence detection of the protein redox state. Kuznetsova S, Zauner G, Schmauder R, Mayboroda OA, Deelder AM, Aartsma TJ, Canters GW. Anal Biochem 350 52-60 (2006)
  4. Tryptophan-tryptophan energy migration as a tool to follow apoflavodoxin folding. Visser NV, Westphal AH, van Hoek A, van Mierlo CP, Visser AJ, van Amerongen H. Biophys J 95 2462-2469 (2008)
  5. Solution structures and backbone dynamics of a flavodoxin MioC from Escherichia coli in both Apo- and Holo-forms: implications for cofactor binding and electron transfer. Hu Y, Li Y, Zhang X, Guo X, Xia B, Jin C. J Biol Chem 281 35454-35466 (2006)
  6. Gradual Folding of an Off-Pathway Molten Globule Detected at the Single-Molecule Level. Lindhoud S, Pirchi M, Westphal AH, Haran G, van Mierlo CP. J Mol Biol 427 3148-3157 (2015)
  7. Tuning of the FMN binding and oxido-reduction properties by neighboring side chains in Anabaena flavodoxin. Frago S, Goñi G, Herguedas B, Peregrina JR, Serrano A, Perez-Dorado I, Molina R, Gómez-Moreno C, Hermoso JA, Martínez-Júlvez M, Mayhew SG, Medina M. Arch Biochem Biophys 467 206-217 (2007)
  8. 5-fluorotryptophan as dual probe for ground-state heterogeneity and excited-state dynamics in apoflavodoxin. Visser NV, Westphal AH, Nabuurs SM, van Hoek A, van Mierlo CP, Visser AJ, Broos J, van Amerongen H. FEBS Lett 583 2785-2788 (2009)
  9. Concurrent presence of on- and off-pathway folding intermediates of apoflavodoxin at physiological ionic strength. Houwman JA, Westphal AH, Visser AJWG, Borst JW, van Mierlo CPM. Phys Chem Chem Phys 20 7059-7072 (2018)
  10. Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors. Willistein M, Bechtel DF, Müller CS, Demmer U, Heimann L, Kayastha K, Schünemann V, Pierik AJ, Ullmann GM, Ermler U, Boll M. Nat Commun 10 2074 (2019)
  11. Streptococcus pneumoniae TIGR4 Flavodoxin: Structural and Biophysical Characterization of a Novel Drug Target. Rodríguez-Cárdenas Á, Rojas AL, Conde-Giménez M, Velázquez-Campoy A, Hurtado-Guerrero R, Sancho J. PLoS One 11 e0161020 (2016)
  12. Reconstructing a flavodoxin oxidoreductase with early amino acids. Lu MF, Ji HF, Li TX, Kang SK, Zhang YJ, Zheng JF, Tian T, Jia XS, Lin XM, Zhang HY. Int J Mol Sci 14 12843-12852 (2013)
  13. Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case. Galuzzi BG, Mirarchi A, Viganò EL, De Gioia L, Damiani C, Arrigoni F. J Chem Inf Model 62 4748-4759 (2022)
  14. Flavodoxin relaxes in microseconds upon excitation of the flavin chromophore: detection of a UV-visible silent intermediate by laser photocalorimetry. Martínez-Junza V, Rizzi AC, Alagaratnam S, Bell TD, Canters GW, Braslavsky SE. Photochem Photobiol 85 107-110 (2009)
  15. Long-chain flavodoxin FldB from Escherichia coli. Ye Q, Fu W, Hu Y, Jin C. J Biomol NMR 60 283-288 (2014)
  16. The conserved crown bridge loop at the catalytic centre of enzymes of the haloacid dehalogenase superfamily. Leader DP, Milner-White EJ. Curr Res Struct Biol 6 100105 (2023)


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