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Molecular mechanism of the redox-dependent interaction between NADH-dependent ferredoxin reductase and Rieske-type [2Fe-2S] ferredoxin.

Senda M, Kishigami S, Kimura S, Fukuda M, Ishida T, Senda T
J Mol Biol 373 382-400 (2007)
Related entries: 2e4p, 2e4q, 2gqw, 2gr0, 2yvg, 2yvj

Cited: 39 times
EuropePMC logo PMID: 17850818

Abstract

The electron transfer system of the biphenyl dioxygenase BphA, which is derived from Acidovorax sp. (formally Pseudomonas sp.) strain KKS102, is composed of an FAD-containing NADH-ferredoxin reductase (BphA4) and a Rieske-type [2Fe-2S] ferredoxin (BphA3). Biochemical studies have suggested that the whole electron transfer process from NADH to BphA3 comprises three consecutive elementary electron-transfer reactions, in which BphA3 and BphA4 interact transiently in a redox-dependent manner. Initially, BphA4 receives two electrons from NADH. The reduced BphA4 then delivers one electron each to the [2Fe-2S] cluster of the two BphA3 molecules through redox-dependent transient interactions. The reduced BphA3 transports the electron to BphA1A2, a terminal oxygenase, to support the activation of dioxygen for biphenyl dihydroxylation. In order to elucidate the molecular mechanisms of the sequential reaction and the redox-dependent interaction between BphA3 and BphA4, we determined the crystal structures of the productive BphA3-BphA4 complex, and of free BphA3 and BphA4 in all the redox states occurring in the catalytic cycle. The crystal structures of these reaction intermediates demonstrated that each elementary electron transfer induces a series of redox-dependent conformational changes in BphA3 and BphA4, which regulate the interaction between them. In addition, the conformational changes induced by the preceding electron transfer seem to induce the next electron transfer. The interplay of electron transfer and induced conformational changes seems to be critical to the sequential electron-transfer reaction from NADH to BphA3.

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  1. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. J Mol Biol 427 3031-3041 (2015)


Reviews citing this publication (9)

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  7. Crystal structure of the putidaredoxin reductase x putidaredoxin electron transfer complex. Sevrioukova IF, Poulos TL, Churbanova IY. J Biol Chem 285 13616-13620 (2010)
  8. Specific Interactions between the ferredoxin and terminal oxygenase components of a class IIB Rieske nonheme iron oxygenase, carbazole 1,9a-dioxygenase. Inoue K, Ashikawa Y, Umeda T, Abo M, Katsuki J, Usami Y, Noguchi H, Fujimoto Z, Terada T, Yamane H, Nojiri H. J Mol Biol 392 436-451 (2009)
  9. Asymmetric dimeric structure of ferredoxin-NAD(P)+ oxidoreductase from the green sulfur bacterium Chlorobaculum tepidum: implications for binding ferredoxin and NADP+. Muraki N, Seo D, Shiba T, Sakurai T, Kurisu G. J Mol Biol 401 403-414 (2010)
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  13. Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica. Park AK, Kim IS, Do H, Jeon BW, Lee CW, Roh SJ, Shin SC, Park H, Kim YS, Kim YH, Yoon HS, Lee JH, Kim HW. Sci Rep 6 33903 (2016)
  14. Crystal structure of the Leishmania major peroxidase-cytochrome c complex. Jasion VS, Doukov T, Pineda SH, Li H, Poulos TL. Proc Natl Acad Sci U S A 109 18390-18394 (2012)
  15. On the influence of crystal size and wavelength on native SAD phasing. Liebschner D, Yamada Y, Matsugaki N, Senda M, Senda T. Acta Crystallogr D Struct Biol 72 728-741 (2016)
  16. Suppression of electron transfer to dioxygen by charge transfer and electron transfer complexes in the FAD-dependent reductase component of toluene dioxygenase. Lin TY, Werther T, Jeoung JH, Dobbek H. J Biol Chem 287 38338-38346 (2012)
  17. Mutational and crystallographic analysis of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813: Interconversion between oxidase and monooxygenase activities. Matsui D, Im DH, Sugawara A, Fukuta Y, Fushinobu S, Isobe K, Asano Y. FEBS Open Bio 4 220-228 (2014)
  18. Structural basis of interprotein electron transfer in bacterial sulfite oxidation. McGrath AP, Laming EL, Casas Garcia GP, Kvansakul M, Guss JM, Trewhella J, Calmes B, Bernhardt PV, Hanson GR, Kappler U, Maher MJ. Elife 4 e09066 (2015)
  19. High-resolution structures of cholesterol oxidase in the reduced state provide insights into redox stabilization. Golden E, Karton A, Vrielink A. Acta Crystallogr D Biol Crystallogr 70 3155-3166 (2014)
  20. Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein-Protein Docking. Scafuri N, Soler MA, Spitaleri A, Rocchia W. J Chem Theory Comput 17 7271-7280 (2021)
  21. Development of a strain for efficient degradation of polychlorinated biphenyls by patchwork assembly of degradation pathways. Ohmori T, Morita H, Tanaka M, Miyauchi K, Kasai D, Furukawa K, Miyashita K, Ogawa N, Masai E, Fukuda M. J Biosci Bioeng 111 437-442 (2011)
  22. Expression in Escherichia coli of biphenyl 2,3-dioxygenase genes from a Gram-positive polychlorinated biphenyl degrader, Rhodococcus jostii RHA1. Ohmori T, Morita H, Tanaka M, Tomoi M, Miyauchi K, Kasai D, Furukawa K, Masai E, Fukuda M. Biosci Biotechnol Biochem 75 26-33 (2011)
  23. The α- and β-Subunit Boundary at the Stem of the Mushroom-Like α3β3-Type Oxygenase Component of Rieske Non-Heme Iron Oxygenases Is the Rieske-Type Ferredoxin-Binding Site. Tsai PC, Chakraborty J, Suzuki-Minakuchi C, Terada T, Kotake T, Matsuzawa J, Okada K, Nojiri H. Appl Environ Microbiol 88 e0083522 (2022)
  24. Cell-Free Protein Synthesis of Metalloproteins. Koo J. Adv Biochem Eng Biotechnol 185 47-58 (2023)
  25. Complete pyridine-nucleotide-specific conversion of an NADH-dependent ferredoxin reductase. Nishizawa A, Harada A, Senda M, Tachihara Y, Muramatsu D, Kishigami S, Mori S, Sugiyama K, Senda T, Kimura S. Biochem J 462 257-265 (2014)
  26. Crystal structure of the ferredoxin reductase component of carbazole 1,9a-dioxygenase from Janthinobacterium sp. J3. Ashikawa Y, Fujimoto Z, Inoue K, Yamane H, Nojiri H. Acta Crystallogr D Struct Biol 77 921-932 (2021)
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  28. Expression, purification and crystal structure determination of a ferredoxin reductase from the actinobacterium Thermobifida fusca. Rodriguez Buitrago JA, Klünemann T, Blankenfeldt W, Schallmey A. Acta Crystallogr F Struct Biol Commun 76 334-340 (2020)
  29. Relationship between the binding free energy and PCBs' migration, persistence, toxicity and bioaccumulation using a combination of the molecular docking method and 3D-QSAR. Zhao XH, Wang XL, Li Y. Chem Cent J 12 20 (2018)


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