Abstract
Enzymes with homology to nitrogenase are essential for the reduction of chemically stable double bonds within the biosynthetic pathways of bacteriochlorophyll and coenzyme F430. These tetrapyrrole-based compounds are crucial for bacterial photosynthesis and the biogenesis of methane in methanogenic archaea. Formation of bacteriochlorophyll requires the unique ATP-dependent enzyme chlorophyllide oxidoreductase (COR) for the two-electron reduction of chlorophyllide to bacteriochlorophyllide. COR catalysis is based on the homodimeric protein subunit BchX2, which facilitates the transfer of electrons to the corresponding heterotetrameric catalytic subunit (BchY/BchZ)2. By analogy to the nitrogenase system, the dynamic switch protein BchX2 contains a [4Fe-4S] cluster that triggers the ATP-driven transfer of electrons onto a second [4Fe-4S] cluster located in (BchY/BchZ)2. The subsequent substrate reduction and protonation is unrelated to nitrogenase catalysis, with no further involvement of a molybdenum-containing cofactor. The biosynthesis of the nickel-containing coenzyme F430 includes the six-electron reduction of the tetrapyrrole macrocycle of Ni2+-sirohydrochlorin a,c-diamide to Ni2+-hexahydrosirohydrochlorin a,c-diamide catalyzed by CfbC/D. The homodimeric CfbC2 subunit carrying a [4Fe-4S] cluster shows close homology to BchX2. Accordingly, parallelism for the initial ATP-driven electron transfer steps of CfbC/D was proposed. Electrons are received by the dimeric catalytic subunit CfbD2, which contains a second [4Fe-4S] cluster and carries out the saturation of an overall of three double bonds in a highly orchestrated spatial and regioselective process. Following a short introduction to nitrogenase catalysis, this chapter will focus on the recent progress toward the understanding of the nitrogenase-like enzymes COR and CfbC/D, with special emphasis on the underlying enzymatic mechanism(s).
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References
Hu Y, Ribbe MW (2015) Nitrogenase and homologs. J Biol Inorg Chem 20:435–445
Thauer RK, Kaster AK, Seedorf H et al (2008) Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 6:579–591
Appl M (2000) Ammonia. In: Ullmann's encyclopedia of industrial chemistry. Wiley-VCH Verlag GmbH & Co, KGaA
Ertl G (2008) Reactions at surfaces: from atoms to complexity (Nobel lecture). Angew Chem Int Ed 47:3524–3535
Duval S, Danyal K, Shaw S et al (2013) Electron transfer precedes ATP hydrolysis during nitrogenase catalysis. Proc Natl Acad Sci U S A 110:16414–16419
Einsle O, Tezcan FA, Andrade SL et al (2002) Nitrogenase MoFe-protein at 1.16 Å resolution: a central ligand in the FeMo-cofactor. Science 297:1696–1700
Kim J, Rees DC (1992) Crystallographic structure and functional implications of the nitrogenase molybdenum-iron protein from Azotobacter vinelandii. Nature 360:553–560
Thorneley RN, Lowe DJ, Eday RR et al (1979) The coupling of electron transfer in nitrogenase to the hydrolysis of magnesium adenosine triphosphate. Biochem Soc Trans 7:633–636
Tezcan FA, Kaiser JT, Mustafi D et al (2005) Nitrogenase complexes: multiple docking sites for a nucleotide switch protein. Science 309:1377–1380
Hoffman BM, Lukoyanov D, Yang ZY et al (2014) Mechanism of nitrogen fixation by nitrogenase: the next stage. Chem Rev 114:4041–4062
Moser J, Brocker MJ (2011) Methods for nitrogenase-like dark operative protochlorophyllide oxidoreductase. Methods Mol Biol 766:129–143
Moser J, Brocker MJ (2011) Enzymatic systems with homology to nitrogenase. Methods Mol Biol 766:67–77
Layer G, Krausze J, Moser J (2017) Reduction of chemically stable multibonds: nitrogenase-like biosynthesis of tetrapyrroles. Adv Exp Med Biol 925:147–161
Reinbothe C, El Bakkouri M, Buhr F et al (2010) Chlorophyll biosynthesis: spotlight on protochlorophyllide reduction. Trends Plant Sci 15:614–624
Moser J, Schubert W-D (2011) Dark-operative protochlorophyllide oxidoreductase. In: Encyclopedia of inorganic and bioinorganic chemistry. John Wiley & Sons, Ltd, Hoboken, New Jersey
Nomata J, Mizoguchi T, Tamiaki H et al (2006) A second nitrogenase-like enzyme for bacteriochlorophyll biosynthesis: reconstitution of chlorophyllide a reductase with purified X-protein (BchX) and YZ-protein (BchY-BchZ) from Rhodobacter capsulatus. J Biol Chem 281:15021–15028
Moore SJ, Sowa ST, Schuchardt C et al (2017) Elucidation of the biosynthesis of the methane catalyst coenzyme F430. Nature 543:78–82
Zheng K, Ngo PD, Owens VL et al (2016) The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Science 354:339–342
Cavalier-Smith T (2003) Molecular mechanisms of photosynthesis. Q Rev Biol 78:234–235
Watzlich D, Brocker MJ, Uliczka F et al (2009) Chimeric nitrogenase-like enzymes of (bacterio)chlorophyll biosynthesis. J Biol Chem 284:15530–15540
Burke DH, Hearst JE, Sidow A (1993) Early evolution of photosynthesis: clues from nitrogenase and chlorophyll iron proteins. Proc Natl Acad Sci U S A 90:7134–7138
Kiesel S, Watzlich D, Lange C et al (2015) Iron-sulfur cluster-dependent catalysis of chlorophyllide a oxidoreductase from Roseobacter denitrificans. J Biol Chem 290:1141–1154
Kim EJ, Kim JS, Lee IH et al (2008) Superoxide generation by chlorophyllide a reductase of Rhodobacter sphaeroides. J Biol Chem 283:3718–3730
Schindelin H, Kisker C, Schlessman JL et al (1997) Structure of ADP•AlF4−-stabilized nitrogenase complex and its implications for signal transduction. Nature 387:370–376
Moser J, Lange C, Krausze J et al (2013) Structure of ADP-aluminium fluoride-stabilized protochlorophyllide oxidoreductase complex. Proc Natl Acad Sci U S A 110:2094–2098
Tsukatani Y, Yamamoto H, Harada J et al (2013) An unexpectedly branched biosynthetic pathway for bacteriochlorophyll b capable of absorbing near-infrared light. Sci Rep 3:1217
Harada J, Mizoguchi T, Tsukatani Y et al (2014) Chlorophyllide a oxidoreductase works as one of the divinyl reductases specifically involved in bacteriochlorophyll a biosynthesis. J Biol Chem 289:12716–12726
Tsukatani Y, Yamamoto H, Mizoguchi T et al (2013) Completion of biosynthetic pathways for bacteriochlorophyll g in Heliobacterium modesticaldum: the C8-ethylidene group formation. Biochim Biophys Acta 1827:1200–1204
Ellefson WL, Whitman WB, Wolfe RS (1982) Nickel-containing factor F430: chromophore of the methylreductase of Methanobacterium. Proc Natl Acad Sci U S A 79:3707–3710
Friedmann HC, Klein A, Thauer RK (1990) Structure and function of the nickel porphinoid, coenzyme F430 and of its enzyme, methyl coenzyme M reductase. FEMS Microbiol Rev 7:339–348
Färber G, Keller W, Kratky C et al (1991) Coenzyme F430 from methanogenic bacteria: complete assignment of configuration based on an x-ray analysis of 12,13-diepi-F430 pentamethyl ester and on NMR spectroscopy. Helv Chim Acta 74:697–716
Mayr S, Latkoczy C, Kruger M et al (2008) Structure of an F430 variant from archaea associated with anaerobic oxidation of methane. J Am Chem Soc 130:10758–10767
Ermler U, Grabarse W, Shima S et al (1997) Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Science 278:1457–1462
Shima S, Krueger M, Weinert T et al (2011) Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically. Nature 481:98–101
Moore SJ, Sowa ST, Schuchardt C et al (2017) Corrigendum: elucidation of the biosynthesis of the methane catalyst coenzyme F430. Nature 545:116
Boyd ES, Peters JW (2013) New insights into the evolutionary history of biological nitrogen fixation. Front Microbiol 4:201
Staples CR, Lahiri S, Raymond J et al (2007) Expression and association of group IV nitrogenase NifD and NifH homologs in the non-nitrogen-fixing archaeon Methanocaldococcus jannaschii. J Bacteriol 189:7392–7398
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Moser, J., Layer, G. (2019). Enzymatic Systems with Homology to Nitrogenase: Biosynthesis of Bacteriochlorophyll and Coenzyme F430. In: Hu, Y. (eds) Metalloproteins. Methods in Molecular Biology, vol 1876. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8864-8_2
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DOI: https://doi.org/10.1007/978-1-4939-8864-8_2
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