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Structure of the oxidized long-chain flavodoxin from Anabaena 7120 at 2 A resolution.

Rao ST, Shaffie F, Yu C, Satyshur KA, Stockman BJ, Markley JL, Sundarlingam M
Protein Sci 1 1413-27 (1992)
Cited: 61 times
EuropePMC logo PMID: 1303762

Abstract

The structure of the long-chain flavodoxin from the photosynthetic cyanobacterium Anabaena 7120 has been determined at 2 A resolution by the molecular replacement method using the atomic coordinates of the long-chain flavodoxin from Anacystis nidulans. The structure of a third long-chain flavodoxin from Chondrus crispus has recently been reported. Crystals of oxidized A. 7120 flavodoxin belong to the monoclinic space group P2(1) with a = 48.0, b = 32.0, c = 51.6 A, and beta = 92 degrees, and one molecule in the asymmetric unit. The 2 A intensity data were collected with oscillation films at the CHESS synchrotron source and processed to yield 9,795 independent intensities with Rmerg of 0.07. Of these, 8,493 reflections had I > 2 sigma and were used in the analysis. The model obtained by molecular replacement was initially refined by simulated annealing using the XPLOR program. Repeated refitting into omit maps and several rounds of conjugate gradient refinement led to an R-value of 0.185 for a model containing atoms for protein residues 2-169, flavin mononucleotide (FMN), and 104 solvent molecules. The FMN shows many interactions with the protein with the isoalloxazine ring, ribityl sugar, and the 5'-phosphate. The flavin ring has its pyrimidine end buried into the protein, and the functional dimethyl benzene edge is accessible to solvent. The FMN interactions in all three long-chain structures are similar except for the O4' of the ribityl chain, which interacts with the hydroxyl group of Thr 88 side chain in A. 7120, while with a water molecule in the other two. The phosphate group interacts with the atoms of the 9-15 loop as well as with NE1 of Trp 57. The N5 atom of flavin interacts with the amide NH of Ile 59 in A. 7120, whereas in A. nidulans it interacts with the amide NH of Val 59 in a similar manner. In C. crispus flavodoxin, N5 forms a hydrogen bond with the side chain hydroxyl group of the equivalent Thr 58. The hydrogen bond distances to the backbone NH groups in the first two flavodoxins are 3.6 A and 3.5 A, respectively, whereas in the third flavodoxin the distance is 3.1 A, close to the normal value. Even though the hydrogen bond distances are long in the first two cases, still they might have significant energy because their microenvironment in the protein is not accessible to solvent.(ABSTRACT TRUNCATED AT 400 WORDS)

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  1. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Igumenova TI, Frederick KK, Wand AJ. Chem Rev 106 1672-1699 (2006)
  2. Overview of protein structural and functional folds. Sun PD, Foster CE, Boyington JC. Curr Protoc Protein Sci Chapter 17 Unit 17.1 (2004)

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  1. A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids. Devane R, Shinoda W, Moore PB, Klein ML. J Chem Theory Comput 5 2115-2124 (2009)
  2. Docking analysis of transient complexes: interaction of ferredoxin-NADP+ reductase with ferredoxin and flavodoxin. Medina M, Abagyan R, Gómez-Moreno C, Fernandez-Recio J. Proteins 72 848-862 (2008)
  3. Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers. Campbell IJ, Bennett GN, Silberg JJ. Front Energy Res 7 (2019)
  4. Magnetic susceptibility-induced alignment of proteins in reverse micelles. Valentine KG, Pometun MS, Kielec JM, Baigelman RE, Staub JK, Owens KL, Wand AJ. J Am Chem Soc 128 15930-15931 (2006)
  5. 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)
  6. High-resolution crystal structures reveal a mixture of conformers of the Gly61-Asp62 peptide bond in an oxidized flavodoxin from Bacillus cereus. Gudim I, Lofstad M, van Beek W, Hersleth HP. Protein Sci 27 1439-1449 (2018)
  7. Mechanistic and Crystallographic Studies of Azoreductase AzoA from Bacillus wakoensis A01. Romero E, Savino S, Fraaije MW, Lončar N. ACS Chem Biol 15 504-512 (2020)
  8. Crystallization of a flavodoxin involved in nitrogen fixation in Rhodobacter capsulatus. Pérez-Dorado I, Bortolotti A, Cortez N, Hermoso JA. Acta Crystallogr Sect F Struct Biol Cryst Commun 64 375-377 (2008)
  9. Protposer: The web server that readily proposes protein stabilizing mutations with high PPV. García-Cebollada H, López A, Sancho J. Comput Struct Biotechnol J 20 2415-2433 (2022)
  10. Structural insight into the high reduction potentials observed for Fusobacterium nucleatum flavodoxin. Mothersole RG, Macdonald M, Kolesnikov M, Murphy MEP, Wolthers KR. Protein Sci 28 1460-1472 (2019)
  11. Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations. Galano-Frutos JJ, Nerín-Fonz F, Sancho J. J Chem Inf Model 63 7791-7806 (2023)


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  1. Structural and mechanistic aspects of flavoproteins: photosynthetic electron transfer from photosystem I to NADP+. Medina M. FEBS J 276 3942-3958 (2009)
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Articles citing this publication (46)

  1. Packing at the protein-water interface. Gerstein M, Chothia C. Proc Natl Acad Sci U S A 93 10167-10172 (1996)
  2. A novel main-chain anion-binding site in proteins: the nest. A particular combination of phi,psi values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions. Watson JD, Milner-White EJ. J Mol Biol 315 171-182 (2002)
  3. Crystal structure of chicken riboflavin-binding protein. Monaco HL. EMBO J 16 1475-1483 (1997)
  4. Crystal structure of the FMN-binding domain of human cytochrome P450 reductase at 1.93 A resolution. Zhao Q, Modi S, Smith G, Paine M, McDonagh PD, Wolf CR, Tew D, Lian LY, Roberts GC, Driessen HP. Protein Sci 8 298-306 (1999)
  5. Letter Closure of a tyrosine/tryptophan aromatic gate leads to a compact fold in apo flavodoxin. Genzor CG, Perales-Alcón A, Sancho J, Romero A. Nat Struct Biol 3 329-332 (1996)
  6. Conformational stability of apoflavodoxin. Genzor CG, Beldarraín A, Gómez-Moreno C, López-Lacomba JL, Cortijo M, Sancho J. Protein Sci 5 1376-1388 (1996)
  7. Crystal structure of the peptidyl-cysteine decarboxylase EpiD complexed with a pentapeptide substrate. Blaesse M, Kupke T, Huber R, Steinbacher S. EMBO J 19 6299-6310 (2000)
  8. Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method. Prabhu NV, Zhu P, Sharp KA. J Comput Chem 25 2049-2064 (2004)
  9. Crystal structure of oxidized flavodoxin, an essential protein in Helicobacter pylori. Freigang J, Diederichs K, Schäfer KP, Welte W, Paul R. Protein Sci 11 253-261 (2002)
  10. Interaction of Ferredoxin-NADP(+) Reductase with its Substrates: Optimal Interaction for Efficient Electron Transfer. Medina M, Gómez-Moreno C. Photosynth Res 79 113-131 (2004)
  11. Characterization of a redox active cross-linked complex between cyanobacterial photosystem I and soluble ferredoxin. Lelong C, Boekema EJ, Kruip J, Bottin H, Rögner M, Sétif P. EMBO J 15 2160-2168 (1996)
  12. Nitric-oxide synthase (NOS) reductase domain models suggest a new control element in endothelial NOS that attenuates calmodulin-dependent activity. Knudsen GM, Nishida CR, Mooney SD, Ortiz de Montellano PR. J Biol Chem 278 31814-31824 (2003)
  13. Six new candidate members of the alpha/beta twisted open-sheet family detected by sequence similarity to flavodoxin. Grandori R, Carey J. Protein Sci 3 2185-2193 (1994)
  14. 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)
  15. Comparisons of wild-type and mutant flavodoxins from Anacystis nidulans. Structural determinants of the redox potentials. Hoover DM, Drennan CL, Metzger AL, Osborne C, Weber CH, Pattridge KA, Ludwig ML. J Mol Biol 294 725-743 (1999)
  16. Energetics of a hydrogen bond (charged and neutral) and of a cation-pi interaction in apoflavodoxin. Fernández-Recio J, Romero A, Sancho J. J Mol Biol 290 319-330 (1999)
  17. Prediction of methyl-side chain dynamics in proteins. Ming D, Brüschweiler R. J Biomol NMR 29 363-368 (2004)
  18. Binding thermodynamics of ferredoxin:NADP+ reductase: two different protein substrates and one energetics. Martínez-Júlvez M, Medina M, Velázquez-Campoy A. Biophys J 96 4966-4975 (2009)
  19. Crystal structure of flavodoxin from Desulfovibrio desulfuricans ATCC 27774 in two oxidation states. Romero A, Caldeira J, Legall J, Moura I, Moura JJ, Romao MJ. Eur J Biochem 239 190-196 (1996)
  20. The flavodoxin from Helicobacter pylori: structural determinants of thermostability and FMN cofactor binding. Cremades N, Velazquez-Campoy A, Freire E, Sancho J. Biochemistry 47 627-639 (2008)
  21. Metal complexes of amino acids and amino acid side chain groups. Structures and properties. Shimazaki Y, Takani M, Yamauchi O. Dalton Trans 7854-7869 (2009)
  22. 1H, 15N and 13C NMR resonance assignment, secondary structure and global fold of the FMN-binding domain of human cytochrome P450 reductase. Barsukov I, Modi S, Lian LY, Sze KH, Paine MJ, Wolf CR, Roberts GC. J Biomol NMR 10 63-75 (1997)
  23. A double-deletion method to quantifying incremental binding energies in proteins from experiment: example of a destabilizing hydrogen bonding pair. Campos LA, Cuesta-López S, López-Llano J, Falo F, Sancho J. Biophys J 88 1311-1321 (2005)
  24. Anabaena apoflavodoxin hydrogen exchange: on the stable exchange core of the alpha/beta(21345) flavodoxin-like family. Langdon GM, Jiménez MA, Genzor CG, Maldonado S, Sancho J, Rico M. Proteins 43 476-488 (2001)
  25. Native-specific stabilization of flavodoxin by the FMN cofactor: structural and thermodynamical explanation. Campos LA, Sancho J. Proteins 63 581-594 (2006)
  26. Salt-induced stabilization of apoflavodoxin at neutral pH is mediated through cation-specific effects. Maldonado S, Irún MP, Campos LA, Rubio JA, Luquita A, Lostao A, Wang R, García-Moreno E B, Sancho J. Protein Sci 11 1260-1273 (2002)
  27. Common conformational changes in flavodoxins induced by FMN and anion binding: the structure of Helicobacter pylori apoflavodoxin. Martínez-Júlvez M, Cremades N, Bueno M, Pérez-Dorado I, Maya C, Cuesta-López S, Prada D, Falo F, Hermoso JA, Sancho J. Proteins 69 581-594 (2007)
  28. Refined structures of oxidized flavodoxin from Anacystis nidulans. Drennan CL, Pattridge KA, Weber CH, Metzger AL, Hoover DM, Ludwig ML. J Mol Biol 294 711-724 (1999)
  29. Structural analysis of interactions for complex formation between Ferredoxin-NADP+ reductase and its protein partners. Mayoral T, Martínez-Júlvez M, Pérez-Dorado I, Sanz-Aparicio J, Gómez-Moreno C, Medina M, Hermoso JA. Proteins 59 592-602 (2005)
  30. Apoflavodoxin: structure, stability, and FMN binding. Maldonado S, Lostao A, Irún MP, Férnandez-Recio J, Gustavo Genzor C, Begoña González E, Rubio JA, Luquita A, Daoudi F, Sancho J. Biochimie 80 813-820 (1998)
  31. 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)
  32. Reverse micelles as a platform for dynamic nuclear polarization in solution NMR of proteins. Valentine KG, Mathies G, Bédard S, Nucci NV, Dodevski I, Stetz MA, Can TV, Griffin RG, Wand AJ. J Am Chem Soc 136 2800-2807 (2014)
  33. 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)
  34. WrpA Is an Atypical Flavodoxin Family Protein under Regulatory Control of the Brucella abortus General Stress Response System. Herrou J, Czyż DM, Willett JW, Kim HS, Chhor G, Babnigg G, Kim Y, Crosson S. J Bacteriol 198 1281-1293 (2016)
  35. Analysis of the interaction of a hybrid system consisting of bovine adrenodoxin reductase and flavodoxin from the cyanobacterium Anabaena PCC 7119. Zöllner A, Nogués I, Heinz A, Medina M, Gómez-Moreno C, Bernhardt R. Bioelectrochemistry 63 61-65 (2004)
  36. Electron-nuclear double resonance and hyperfine sublevel correlation spectroscopic studies of flavodoxin mutants from Anabaena sp. PCC 7119. Medina M, Lostao A, Sancho J, Gómez-Moreno C, Cammack R, Alonso PJ, Martínez JI. Biophys J 77 1712-1720 (1999)
  37. Protein-protein interaction in electron transfer reactions: the ferredoxin/flavodoxin/ferredoxin:NADP+ reductase system from Anabaena. Gómez-Moreno C, Martínez-Júlvez M, Medina M, Hurley JK, Tollin G. Biochimie 80 837-846 (1998)
  38. Underexposed polar residues and protein stabilization. Ayuso-Tejedor S, Abián O, Sancho J. Protein Eng Des Sel 24 171-177 (2011)
  39. Stability and structure of mixed-ligand metal ion complexes that contain Ni2+, Cu2+, or Zn2+, and Histamine, as well as adenosine 5'-triphosphate (ATP4-) or uridine 5'-triphosphate (UTP(4-): an intricate network of equilibria. Knobloch B, Mucha A, Operschall BP, Sigel H, Jeżowska-Bojczuk M, Kozłowski H, Sigel RK. Chemistry 17 5393-5403 (2011)
  40. NMR assignments, secondary structure and hydration of oxidized Escherichia coli flavodoxin. Ponstingl H, Otting G. Eur J Biochem 244 384-399 (1997)
  41. The Dimer-of-Trimers Assembly Prevents Catalysis at the Transferase Site of Prokaryotic FAD Synthase. Lans I, Seco J, Serrano A, Burbano R, Cossio P, Daza MC, Medina M. Biophys J 115 988-995 (2018)
  42. A laboratory demonstration illustrating bioseparations using colorful proteins. Cohen TM, Rohs AE, Lefebvre BG. Biochem Mol Biol Educ 36 287-291 (2008)
  43. Laser flash-induced photoreduction of photosynthetic ferredoxins and flavodoxin by 5-deazariboflavin and by a viologen analogue. Navarro JA, Hervás M, Pueyo JJ, Medina M, Gómez-Moreno C, De la Rosa MA, Tollin G. Photochem Photobiol 60 231-236 (1994)
  44. Cofactor-apoprotein hydrogen bonding in oxidized and fully reduced flavodoxin monitored by trans-hydrogen-bond scalar couplings. Löhr F, Yalloway GN, Mayhew SG, Rüterjans H. Chembiochem 5 1523-1534 (2004)
  45. Design of ligand binding to an engineered protein cavity using virtual screening and thermal up-shift evaluation. Machicado C, López-Llano J, Cuesta-López S, Bueno M, Sancho J. J Comput Aided Mol Des 19 421-443 (2005)
  46. Spin Densities in Flavin Analogs within a Flavoprotein. Martínez JI, Frago S, Lans I, Alonso PJ, García-Rubio I, Medina M. Biophys J 110 561-571 (2016)


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