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Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic Archaea catalyzing the reduction of O2 to H2O.

Seedorf H, Hagemeier CH, Shima S, Thauer RK, Warkentin E, Ermler U
FEBS J 274 1588-99 (2007)
Related entries: 2ohh, 2ohj

Cited: 34 times
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Abstract

The di-iron flavoprotein F(420)H(2) oxidase found in methanogenic Archaea catalyzes the four-electron reduction of O(2) to 2H(2)O with 2 mol of reduced coenzyme F(420)(7,8-dimethyl-8-hydroxy-5-deazariboflavin). We report here on crystal structures of the homotetrameric F(420)H(2) oxidase from Methanothermobacter marburgensis at resolutions of 2.25 A, 2.25 A and 1.7 A, respectively, from which an active reduced state, an inactive oxidized state and an active oxidized state could be extracted. As found in structurally related A-type flavoproteins, the active site is formed at the dimer interface, where the di-iron center of one monomer is juxtaposed to FMN of the other. In the active reduced state [Fe(II)Fe(II)FMNH(2)], the two irons are surrounded by four histidines, one aspartate, one glutamate and one bridging aspartate. The so-called switch loop is in a closed conformation, thus preventing F(420) binding. In the inactive oxidized state [Fe(III)FMN], the iron nearest to FMN has moved to two remote binding sites, and the switch loop is changed to an open conformation. In the active oxidized state [Fe(III)Fe(III)FMN], both irons are positioned as in the reduced state but the switch loop is found in the open conformation as in the inactive oxidized state. It is proposed that the redox-dependent conformational change of the switch loop ensures alternate complete four-electron O(2) reduction and redox center re-reduction. On the basis of the known Si-Si stereospecific hydride transfer, F(420)H(2) was modeled into the solvent-accessible pocket in front of FMN. The inactive oxidized state might provide the molecular basis for enzyme inactivation by long-term O(2) exposure observed in some members of the FprA family.

Reviews - 2ohi mentioned but not cited (2)

  1. Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions. Greening C, Ahmed FH, Mohamed AE, Lee BM, Pandey G, Warden AC, Scott C, Oakeshott JG, Taylor MC, Jackson CJ. Microbiol Mol Biol Rev 80 451-493 (2016)
  2. Tunnel Architectures in Enzyme Systems that Transport Gaseous Substrates. Singh S, Anand R. ACS Omega 6 33274-33283 (2021)

Articles - 2ohi mentioned but not cited (1)

  1. Flavodiiron oxygen reductase from Entamoeba histolytica: modulation of substrate preference by tyrosine 271 and lysine 53. Gonçalves VL, Vicente JB, Pinto L, Romão CV, Frazão C, Sarti P, Giuffrè A, Teixeira M. J Biol Chem 289 28260-28270 (2014)


Reviews citing this publication (8)

  1. Cyanobacterial Oxygenic Photosynthesis is Protected by Flavodiiron Proteins. Allahverdiyeva Y, Isojärvi J, Zhang P, Aro EM. Life (Basel) 5 716-743 (2015)
  2. Essential prerequisites for successful bioprocess development of biological CH4 production from CO2 and H2. Rittmann S, Seifert A, Herwig C. Crit Rev Biotechnol 35 141-151 (2015)
  3. The dual function of flavodiiron proteins: oxygen and/or nitric oxide reductases. Romão CV, Vicente JB, Borges PT, Frazão C, Teixeira M, Teixeira M. J Biol Inorg Chem 21 39-52 (2016)
  4. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Chem Rev 120 5252-5307 (2020)
  5. Structure/function correlations over binuclear non-heme iron active sites. Solomon EI, Park K. J Biol Inorg Chem 21 575-588 (2016)
  6. Metalloproteins in the Biology of Heterocysts. Pernil R, Schleiff E. Life (Basel) 9 E32 (2019)
  7. Diversity and complexity of flavodiiron NO/O2 reductases. Folgosa F, Martins MC, Teixeira M. FEMS Microbiol Lett 365 (2018)
  8. Functional and protective hole hopping in metalloenzymes. Gray HB, Winkler JR. Chem Sci 12 13988-14003 (2021)

Articles citing this publication (23)

  1. Operon flv4-flv2 provides cyanobacterial photosystem II with flexibility of electron transfer. Zhang P, Eisenhut M, Brandt AM, Carmel D, Silén HM, Vass I, Allahverdiyeva Y, Salminen TA, Aro EM. Plant Cell 24 1952-1971 (2012)
  2. The O2-scavenging flavodiiron protein in the human parasite Giardia intestinalis. Di Matteo A, Scandurra FM, Testa F, Forte E, Sarti P, Brunori M, Giuffrè A. J Biol Chem 283 4061-4068 (2008)
  3. Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases. Safarian S, Rajendran C, Müller H, Preu J, Langer JD, Ovchinnikov S, Hirose T, Kusumoto T, Sakamoto J, Michel H. Science 352 583-586 (2016)
  4. More than 200 genes required for methane formation from H₂ and CO₂ and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus. Kaster AK, Goenrich M, Seedorf H, Liesegang H, Wollherr A, Gottschalk G, Thauer RK. Archaea 2011 973848 (2011)
  5. Metabolic traits of an uncultured archaeal lineage--MSBL1--from brine pools of the Red Sea. Mwirichia R, Alam I, Rashid M, Rashid M, Vinu M, Ba-Alawi W, Anthony Kamau A, Kamanda Ngugi D, Göker M, Klenk HP, Bajic V, Stingl U. Sci Rep 6 19181 (2016)
  6. Flavodiiron protein from Trichomonas vaginalis hydrogenosomes: the terminal oxygen reductase. Smutná T, Gonçalves VL, Saraiva LM, Tachezy J, Teixeira M, Hrdy I. Eukaryot Cell 8 47-55 (2009)
  7. Redox properties of the oxygen-detoxifying flavodiiron protein from the human parasite Giardia intestinalis. Vicente JB, Vicente JB, Testa F, Mastronicola D, Forte E, Sarti P, Teixeira M, Giuffrè A. Arch Biochem Biophys 488 9-13 (2009)
  8. Simultaneous methanogenesis and oxygen reduction by Methanobrevibacter cuticularis at low oxygen fluxes. Tholen A, Pester M, Brune A. FEMS Microbiol Ecol 62 303-312 (2007)
  9. The genome and transcriptome of a newly described psychrophilic archaeon, Methanolobus psychrophilus R15, reveal its cold adaptive characteristics. Chen Z, Yu H, Li L, Hu S, Dong X. Environ Microbiol Rep 4 633-641 (2012)
  10. Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments. Lyu Z, Lu Y. ISME J 12 411-423 (2018)
  11. A Novel F420-dependent Thioredoxin Reductase Gated by Low Potential FAD: A TOOL FOR REDOX REGULATION IN AN ANAEROBE. Susanti D, Loganathan U, Mukhopadhyay B. J Biol Chem 291 23084-23100 (2016)
  12. Histidine ligand variants of a flavo-diiron protein: effects on structure and activities. Fang H, Caranto JD, Mendoza R, Taylor AB, Hart PJ, Kurtz DM. J Biol Inorg Chem 17 1231-1239 (2012)
  13. Method for assessing the impact of emission gasses on physiology and productivity in biological methanogenesis. Seifert AH, Rittmann S, Bernacchi S, Herwig C. Bioresour Technol 136 747-751 (2013)
  14. Elongation of the Poly-γ-glutamate Tail of F420 Requires Both Domains of the F420:γ-Glutamyl Ligase (FbiB) of Mycobacterium tuberculosis. Bashiri G, Rehan AM, Sreebhavan S, Baker HM, Baker EN, Squire CJ. J Biol Chem 291 6882-6894 (2016)
  15. Structure of Escherichia coli Flavodiiron Nitric Oxide Reductase. Romão CV, Vicente JB, Borges PT, Victor BL, Lamosa P, Silva E, Pereira L, Bandeiras TM, Soares CM, Carrondo MA, Turner D, Teixeira M, Teixeira M, Frazão C. J Mol Biol 428 4686-4707 (2016)
  16. A Genetic System for Methanocaldococcus jannaschii: An Evolutionary Deeply Rooted Hyperthermophilic Methanarchaeon. Susanti D, Frazier MC, Mukhopadhyay B. Front Microbiol 10 1256 (2019)
  17. Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas. Victor BL, Baptista AM, Soares CM. J Biol Inorg Chem 14 853-862 (2009)
  18. Methanogenic Archaea dominate mature heartwood habitats of Eastern Cottonwood (Populus deltoides). Yip DZ, Veach AM, Yang ZK, Cregger MA, Schadt CW. New Phytol 222 115-121 (2019)
  19. Quaternary structure of flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering. Petoukhov MV, Vicente JB, Vicente JB, Crowley PB, Carrondo MA, Teixeira M, Svergun DI. Structure 16 1428-1436 (2008)
  20. The multidomain flavodiiron protein from Clostridium difficile 630 is an NADH:oxygen oxidoreductase. Folgosa F, Martins MC, Teixeira M. Sci Rep 8 10164 (2018)
  21. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. Grinter R, Greening C. FEMS Microbiol Rev 45 fuab021 (2021)
  22. On the diversity of F420 -dependent oxidoreductases: A sequence- and structure-based classification. Mascotti ML, Juri Ayub M, Fraaije MW. Proteins 89 1497-1507 (2021)
  23. The Draft Genome of the Non-Host-Associated Methanobrevibacter arboriphilus Strain DH1 Encodes a Large Repertoire of Adhesin-Like Proteins. Poehlein A, Daniel R, Seedorf H. Archaea 2017 4097425 (2017)


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