Stable glycyl radical from pyruvate formate-lyase and ribonucleotide reductase (III)

Akhmanova, 1999, A hydrogenosome with pyruvate formate-lyase: anaerobic chytrid fungi use an alternative route for pyruvate metabolism, Mol. Microbiol., 32, 1103, 10.1046/j.1365-2958.1999.01434.x Andersson, 2000, Cysteines involved in radical generation and catalysis of class III anaerobic ribonucleotide reductase. A protein engineering study of bacteriophage T4 NrdD, J. Biol. Chem., 275, 19449, 10.1074/jbc.M001278200 Barone, 1995, Conformational behavior and magnetic properties of organic radicals derived from amino acid residues. The dipeptide analogue of glycine radical, J. Am. Chem. Soc., 117, 1083, 10.1021/ja00108a026 Becker, 1999, Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase, Nature Struct. Biol., 6, 969, 10.1038/13341 Bianchi, 1993, Flavodoxin is required for the activation of the anaerobic ribonucleotide reductase, Biochem. Biophys. Res. Commun., 197, 792, 10.1006/bbrc.1993.2548 Bianchi, 1993, Escherichia coli ferredoxin NADP+ reductase. Activation of E. coli anaerobic ribonucleotide reduction, cloning of the gene (fpr) and overexpression of the protein, J. Bacterial., 175, 1590, 10.1128/jb.175.6.1590-1595.1993 Blankenhorn, 1999, Acid- and base-induced proteins during aerobic and anaerobic growth of Escherichia coli revealed by two-dimensional gel electrophoresis, J. Bacterial., 181, 2209, 10.1128/JB.181.7.2209-2216.1999 Blaschkowski, 1982, Routes of flavodoxin and ferredoxin reduction in Escherichia coli. CoA-acetylating pyruvate:flavodoxin and NADP:flavodoxin oxidoreductases participating in the activation of pyruvate formate-lyase, Eur. J Biochem., 123, 563, 10.1111/j.1432-1033.1982.tb06569.x Broderick, 1997, Pyruvate formate-lyase activating enzyme is an iron-sulfur protein, J. Am. Chem. Soc., 119, 7396, 10.1021/ja9711425 Broderick, 2000, Pyruvate formatelyase activating enzyme: strictly anaerobic isolation yields active enzyme containing a [3Fe-4S]+ cluster, Biochem. Biophys. Res. Commun., 269, 451, 10.1006/bbrc.2000.2313 Conradt, 1984, Pyruvate formate-lyase (inactive form) and pyruvate formate-lyase activating enzyme of Escherichia coli: isolation and structural properties, Arch. Biochem. Biophys., 228, 133, 10.1016/0003-9861(84)90054-7 Coschigano, 1998, Identification and analysis of genes involved in anaerobic toluene metabolism by strain TI: putative role of a glycine free radical, Appl. Environ. Microbial., 64, 1650, 10.1128/AEM.64.5.1650-1656.1998 Dumont, 1993, Isolation and characterization of cDNA sequences controlled by inorganic phosphate in Chlamydomonas reinhardtii, Plant Science, 89, 55, 10.1016/0168-9452(93)90170-5 Eipper, 1993, Peptidylglycine alpha-amidating monooxygenase: a multifunctional protein with catalytic, processing, and routing domains, Protein Sci., 2, 489, 10.1002/pro.5560020401 Eklund, 1999, Glycyl radical enzymes: a conservative structural basis for radicals, Structure, 7, R257, 10.1016/S0969-2126(00)80019-2 Eliasson, 1990, The anaerobic ribonucleoside triphosphate reductase from Escherichia coli requires S-adenosylmethionine as a cofactor, 87, 3314 Eliasson, 1992, Characterization of components of the anaerobic ribonucleotide reductase system from Escherichia coli, J. Biol. Chem., 267, 25541, 10.1016/S0021-9258(19)74074-5 Eliasson, 1995, The mechanism of the anaerobic Escherichia coli ribonucleotide reductase investigated with nuclear magnetic resonance spectroscopy, Biochem. Biophys. Res. Commun., 214, 28, 10.1006/bbrc.1995.2252 Eriksson, 1997, Binding of allosteric effectors to ribonucleotide reductase protein RI: reduction of active-site cysteines promotes substrate binding, Structure, 5, 1077, 10.1016/S0969-2126(97)00259-1 Fontecave, 1989, Oxygen-sensitive ribonucleotide triphosphate reductase is present in anaerobic Escherichia coli, 86, 2147 Fontecave, 1992, The redox centers of ribonucleotide reductase of Escherichia coli, Adv. Enzymol Related Areas Mol. Biol., 65, 147 Freestone, 1998, Protein phosphorylation in Fscherichia coli L-form NC-7, Microbiology, 144, 3289, 10.1099/00221287-144-12-3289 Frey, 1994, Adenosylmethionine-dependent synthesis of the glycyl radical in pyruvate formate-lyase by abstraction of the glycine C-2 pro-S hydrogen atom. Studies of [2H] glycine-substituted enzyme and peptides homologous to the glycine 734 site, J. Biol. Chem., 269, 12432, 10.1016/S0021-9258(18)99892-3 Garrison, 1987, Reaction mechanisms in the radiolysis of peptides, polypeptides, and proteins, Chem. Rev., 87, 381, 10.1021/cr00078a006 Gauld, 2000, Oxidative degradation of pyruvate formatelyase, J. Am. Chem. Soc., 122, 2035, 10.1021/ja992862+ Green, 1997, HlyX, the FNR homologue of Actinobacillus pleuropneumoniae, is a [4Fe-4S] -containing oxygen-responsive transcription regulator that anaerobically activates FNR-dependent class I promoters via enhanced AR1 contact, Mol. Microbiol., 24, 593, 10.1046/j.1365-2958.1997.3801737.x Guex, 1997, SWISS-MODEL and the Swiss-Pdb Viewer: an environment for comparative protein modeling, Electrophoresis, 18, 2714, 10.1002/elps.1150181505 Harder, 1992, Activation of the anaerobic ribonucleotide reductase from Escherichin coli by S-adenosylmethionine, J. Biol. Chem., 267, 25548, 10.1016/S0021-9258(19)74075-7 Hayon, 1971, Pulse radiolysis study of cyclic peptides in aqueous solution. Absorption spectrum of the peptide radical -NHCHCO-, J. Am. Chem. Soc., 93, 6781, 10.1021/ja00754a013 Heblinger, 1998, Novel keto acid formate-lyase and propionate kinase enzymes are components of an anaerobic pathway in Escherichia coli that degrades L-threonine to propionate, Mol. Microbiol., 27, 477, 10.1046/j.1365-2958.1998.00696.x Himo, 1998, On the local structure of the glycyl radical in diferent enzymes, J. Chem. Soc. Perkin Trans., 2, 305, 10.1039/a706138b Himo, 1998, Catalytic mechanism of pyruvate formate-lyase (PFL). A theoretical study, J. Am. Chem. Soc., 120, 11449, 10.1021/ja9820947 Holm, 1996, Mapping the protein universe, Science, 273, 595, 10.1126/science.273.5275.595 Hoover, 1997, A flavodoxin that is required for enzyme activation: the structure of oxidized flavodoxin from Fsrherichia coli at 1.8 A resolution, Protein Sci., 6, 2525, 10.1002/pro.5560061205 Ingelman, 1997, The three-dimensional structure of flavodoxin reductase from Escherichia coli at 1.7 A resolution, J. Mol. Biol., 268, 147, 10.1006/jmbi.1997.0957 Jordan, 1998, Ribonucleotide reductases, Annu. Rev. Biochem., 67, 71, 10.1146/annurev.biochem.67.1.71 Kalnitsky, 1943, The anaerobic dissimilation of pyruvate by a cell-free extract of Escherichia coli, Arch. Biochem. Biophys., 2, 113 Kessler, 1991, Pyruvate-formate-lyase-deactivase and acetyl-CoA reductase activities of Escherichia coli reside on a polymeric protein particle encoded by adhE, FEBS Lett., 281, 59, 10.1016/0014-5793(91)80358-A Kessler, 1992, Ultrastructure and and pyruvate formatelyase radical quenching property of the multienzymic AdhE protein of Escherichia coli, J. Biol. Chem., 267, 18073, 10.1016/S0021-9258(19)37154-6 Kessler, 1996, Anaerobic dissimilation of pyruvate, 199 King, 1995, Mass spectrometric determination of the radical scission site in the anaerobic ribonucleotide reductase of Escherichia coli, Biochem. Biophys. Res. Commun., 206, 731, 10.1006/bbrc.1995.1103 Knappe, 1965, S-Adenosyl-L-methionine, a component of the clastic dissimilation of pyruvate in Escherichia coli, Biochim. Biophys. Acta, 107, 603, 10.1016/0304-4165(65)90205-9 Knappej Schacht, 1969, Pyruvate formate-lyase reaction in Escherichia coli. The enzymatic system converting an inactive form of the lyase into the catalytically active enzyme, Eur. J. Biochem., 11, 316, 10.1111/j.1432-1033.1969.tb00775.x Knappe, 1974, Pyruvate formatelyase of Escherichia coli: the acetyl-enzyme intermediate, Eur. J Biochem., 50, 253, 10.1111/j.1432-1033.1974.tb03894.x Knappe, 1976, A novel reaction of Sadenosyl-Irmethionine correlated with the activation of pyruvate formate4yase, Biochem. Biophys. Res. Commun., 71, 1110, 10.1016/0006-291X(76)90768-3 Knappe, 1984, Post-translational activation introduces a free radical into pyruvate formate-lyase, 81, 1332 Knappej Elbert, 1993, Pyruvate formate-lyase mechanism involving the protein-based glycyl radical, Biochem. Soc. Trans., 21, 731, 10.1042/bst0210731 Knappej, 1995, Glycyl free radical in pyruvate formate-lyase: synthesis, structure characteristics, and involvement in catalysis, Methods Enzymol., 258, 343, 10.1016/0076-6879(95)58055-7 Koradi, 1996, MOLMOL: a program for display and analysis of macromolecular structures, J. Mol. Graphics, 14, 51, 10.1016/0263-7855(96)00009-4 Kreuzberg, 1985, Pyruvate degradation via pyruvate formate4yase (EC 2.3.1.54) and the enzymes of for-mate fermentation in the green alga Chlorogonium elongatum, Planta, 163, 60, 10.1007/BF00395898 Kreuzberg, 1987, Subcellular distribution of pyruvate-degrading enzymes in Chlamydomonas reinhardtii studied by an improved protoplast fractionation procedure, Physiol. Plantarum, 69, 481, 10.1111/j.1399-3054.1987.tb09229.x Külzer, 1998, Reconstitution and characterization of the polynuclear iron-sulfur cluster in pyruvate formate-lyase-activating enzyme. Molecular properties of the holoenzyme form, J. Biol. Chem., 273, 4897, 10.1074/jbc.273.9.4897 Leppänen, 1999, Pyruvate formate lyase is structurally homologous to type I ribonucleotide reductase, Structure, 7, 733, 10.1016/S0969-2126(99)80098-7 Leuthner, 1998, Biochemical and generic characterization of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalyzing the first step in anaerobic toluene metabolism, Mol. Microbiol., 28, 615, 10.1046/j.1365-2958.1998.00826.x Lewisch, 1993, Pyruvate formate lyase: an investigation of formate and coenzyme A halfreactions, The FASEB J, 7 Licht, 1996, Thiyl radicals in ribonucleotide reductases, Science, 271, 477, 10.1126/science.271.5248.477 Liu, 2000, Electron paramagnetic resonance evidence for a novel interconversion of [3Fe-4S]+ and [4Fe-4S]+ clusters with endogenous iron and sulfide in anaerobic ribonucleotide reductase activase in vitro, J. Biol. Chem., 275, 12367, 10.1074/jbc.275.17.12367 Logan, 1999, A glycyl radical site in the crystal structure of a class III ribonucleotide reductase, Science, 283, 1499, 10.1126/science.283.5407.1499 Marsh, 1995, A radical approach to enzyme catalysis, BioEssays, 17, 431, 10.1002/bies.950170511 Massey, 1978, Photoreduction of flavoproteins and other biological compounds catalyzed by deazaflavins, Biochemistry, 17, 9, 10.1021/bi00594a002 Mulliez, 1993, An iron-sulfur center and a free radical in the active anaerobic ribonucleotide reductase of Escherichia coli, J. Biol. Phem., 268, 2296 Mulliez, 1995, Formate is the hydrogen donor for the anaerobic ribonucleotide reductase from Escherichia roli, 92, 8759 Mulliez, 1999, Ribonucleotide reductases: metal and free radical interplay, Coordination Chemistry Reviews, 185–186, 775, 10.1016/S0010-8545(99)00044-2 Ollagnier, 1997, Activation of the anaerobic ribonucleotide reductase from Escherichia coli. The essential role of the iron-sulfur center for S-adenosylmethionine reduction, J. Biol. Chem., 272, 24216, 10.1074/jbc.272.39.24216 Ollagnier, 1999, Assembly of 2Fe-2S and 4Fe-4S clusters in the anaerobic ribonucleotide reductase from Escherichia roli, J. Am. Chem. Sor., 121, 6344, 10.1021/ja990073m Parast, 1995, Hydrogen exchange of the glycyl radical of pyruvate formate-lyase is catalyzed bv cysteine 419, Biochemistry, 34, 2393, 10.1021/bi00008a001 Pecher, 1982, Expression of pyruvate formate-lyase of Escherichia coli from the cloned structural gene, Arch. Mirrobiol., 132, 365, 10.1007/BF00413390 Plaga, 1988, Catalytic-site mapping ofpyruvate formate-lvase. Hypophosphite reaction on the acetyl-enzyme intermediate affords carbon-phosphorus bond synthesis (1-hydroxyethylphosphonate), Eur. J. Biochem., 178, 445, 10.1111/j.1432-1033.1988.tb14468.x Plaga, 2000, Modification of Cys-418 of pyruvate formate-lyase by methacrylic acid, based on its radical mechanism, FEBS Lell., 466, 45, 10.1016/S0014-5793(99)01752-4 Reddy, 1998, Dioxygen inactivation of pyruvate formate-lyase: EPR evidence for the formation of protein-based sulfinyl and peroxyl radicals, Biochemistry, 37, 558, 10.1021/bi972086n Reichard, 1983, Ribonucleotide reductase-a radical enzyme, Science, 221, 514, 10.1126/science.6306767 Reichard, 1993, The anaerobic ribonucleotide reductase from Escherichia coli, J. Biol. Chem., 268, 8383, 10.1016/S0021-9258(18)52882-9 Rödel, 1988, Primary structures of Escherchia coli pyruvate formate-lyase and pyruvate-formate-lyase-activating enzyme deduced from the DNA nucleotide sequences, Eur. J. Biochem., 177, 153, 10.1111/j.1432-1033.1988.tb14356.x Sauter, 1990, Transcriptional analysis of the gene encoding pyruvate formate4yase-activating enzyme of Escherichia coli, Mol. Microbiol., 4, 355, 10.1111/j.1365-2958.1990.tb00603.x Sawers, 1998, A glycyl radical solution: oxygen-dependent interconversion of pyruvate formate-lyase, Mol. Microbiol., 29, 945, 10.1046/j.1365-2958.1998.00941.x Sawers, 1999, Biochemistry, physiology and molecular biology of glycyl radical enzymes, FEMS Microbiol. Rev., 22, 543, 10.1111/j.1574-6976.1998.tb00386.x Stubbe, 1998, Protein radicals in enzyme catalysis, Chem. Rev., 98, 705, 10.1021/cr9400875 Sun, 1993, A possible glycine radical in anaerobic ribonucleotide reductase from Escherichia coli: nucleotide sequence of the cloned nrdD gene, 90, 577 Sun, 1995, Generation of the glycyl radical of the anaerobic Escherichia coli ribonucleotide reductase requires a specific activating enzyme, J. Biol. Chem., 270, 2443, 10.1074/jbc.270.6.2443 Sun, 1996, The free radical of the anaerobic ribonucleotide reductase from Escherichia coli is at glycine 681, J. Biol. Chem., 271, 6827, 10.1074/jbc.271.12.6827 Sustmann, 1990, The captodative effect, Adv. Phys. Organic Chem., 26, 131, 10.1016/S0065-3160(08)60045-3 Tamarit, 1999, The anaerobic ribonucleotide reductase from Escherichia coli. The small protein is an activating enzyme containing a [4Fe-4S]2+ center, J. Biol. Chem., 274, 31291, 10.1074/jbc.274.44.31291 Tamarit, 2000, The activating component of the anaerobic ribonucleotide reductase from Escherichia coli. An iron-sulfur center with only three cysteines, J. Biol. Chem., 275, 15669, 10.1074/jbc.275.21.15669 Taniguchi, 1977, An ESR study of the acid dissociation of NH protons. 2. Cyclic peptide radicals and related radicals, J. Am. Chem. Soc., 99, 3625, 10.1021/ja00453a019 Torrents, 2000, The anaerobic (class III) ribonucleotide reductase from Lactococcus lactis. Catalytic properties and allosteric regulation of the pure enzyme system, J. Biol. Chem., 275, 2463, 10.1074/jbc.275.4.2463 Uhlin, 1994, Structure of ribonucleotide reductase protein RI, Nature, 370, 533, 10.1038/370533a0 Unkrig, 1989, The free radical of pyruvate formate-lyase. Characterization by EPR spectroscopy and involvement in catalysis as studied with the substrate-analogue hypophosphite, Eur.j Biochem, 184, 723, 10.1111/j.1432-1033.1989.tb15072.x Utter, 1944, Reversibility of the phosphoroclastic split of pyruvate, J. Biol. Chem., 154, 723, 10.1016/S0021-9258(18)71909-1 Vetter, 1971, Flavodoxin and ferredoxin of Escherichia coli, HoppeSeyler's Z. Physiol. Chem., 352, 433, 10.1515/bchm2.1971.352.1.433 Viehe, 1985, The captodative effect, Acc. Chem. Res., 18, 148, 10.1021/ar00113a004 Wagner, 1992, The free radical in pyruvate formate-lyase is located on glycine 734, 89, 996 Wagner, 1999, A dehydroalanyl residue can capture the 5'-deoxyadenosyl radical generated from Sadenosylmethionine by pyruvate formate-lyase-activating enzyme, Biochem. Biophys. Res. Commun., 254, 306, 10.1006/bbrc.1998.9931 Weidner, 1996, Molecular characterization of the genes encoding pyruvate formate-lyase and its activating enzyme of Clostridium pasteurianum, J. Bacteriol., 178, 2440, 10.1128/jb.178.8.2440-2444.1996 Wong, 1993, Molecular properties of pyruvate formate-lvase activating enzyme, Biochemistry, 32, 14102, 10.1021/bi00214a005 Wong, 1994, S-Adenosylmethionine-dependent radical formation in anaerobic systems, Metal Ions in Biological Systems, 30, 279 Yamamoto, 1996, Cloning and sequence analysis of the pfl gene encoding pyruvate formate-lyase from Streptococcus mutans, Infect. Immun., 64, 385, 10.1128/IAI.64.2.385-391.1996 Young, 1994, Intron-containing T4 bacteriophage gene sunYencodes an anerobic ribonucleotide reductase, J. Biol. Chem., 269, 20229, 10.1016/S0021-9258(17)31980-4 Young, 1994, Bacteriophage T4 gene 55.9 encodes an activity required for anaerobic ribonucleotide reduction, J. Biol. Chem., 269, 27815, 10.1016/S0021-9258(18)46858-5 Young, 1996, Bacteriophage T4 anaerobic ribonucleotide reductase contains a stable glycyl radical at position 580./, J. Biol. Chem., 271, 20770, 10.1074/jbc.271.34.20770