Crystal structure of a glycyl radical enzyme from Archaeoglobus fulgidus

Journal of Molecular Biology

Volumn 357, Issue 1, 2006, Pages 221-235

  Lehtiö, Lari ^a,b   Gunter Grossmann J ^c   Kokona, Bashkim ^d   Fairman, Robert ^d   Goldman, Adrian ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b ÅBO AKADEMI UNIVERSITY   (Finland)

^c DARESBURY LABORATORY   (United Kingdom)

^d HAVERFORD COLLEGE   (United States)

Author keywords

Glycerol dehydratase; Glycyl radical; Hyperthermophile; PFL2; Pyruvate formate lyase

Indexed keywords

FORMATE ACETYLTRANSFERASE; GLYCEROL; GLYCEROL DEHYDRATASE; HYDROLYASE; LYASE; RIBONUCLEOTIDE REDUCTASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARCHAEOGLOBUS FULGIDUS; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA FINGERPRINTING; ENZYME STRUCTURE; NONHUMAN; PRIORITY JOURNAL; RADIATION SCATTERING; STRUCTURAL HOMOLOGY; THERMOPHILIC BACTERIUM; THERMOSTABILITY; ULTRACENTRIFUGATION;

ARCHAEOGLOBUS FULGIDUS; BACTERIA (MICROORGANISMS);

EID: 33644767163     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.12.049     Document Type: Article

References (48)

1. H. Chantrenne, and F. Lipmann Coenzyme A dependence and acetyl donor function of the pyruvate-formate exchange system J. Biol. Chem. 187 1950 757 767
2. M.F. Utter, C.H. Werkman, and F. Lippman Reversibility of the phosphoroclastic split of pyruvate J. Biol. Chem. 154 1944 723 724
3. A.F. Wagner, M. Frey, F.A. Neugebauer, W. Schäfer, and J. Knappe The free radical in pyruvate formate-lyase is located on glycine-734 Proc. Natl Acad. Sci. USA 89 1992 996 1000
4. C. Heßlinger, S.A. Fairhurst, and G. Sawers 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 1998 477 492
5. C. Raynaud, P. Sarcabal, I. Meynial-Salles, C. Croux, and P. Soucaille Molecular characterization of the 1,3-propanediol (1,3-PD) operon of Clostridium butyricum Proc. Natl Acad. Sci. USA 100 2003 5010 5015
6. B. Leuthner, C. Leutwein, H. Schulz, P. Horth, W. Haehnel, and E. Schiltz Biochemical and genetic characterization of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalysing the first step in anaerobic toluene metabolism Mol. Microbiol. 28 1998 615 628
7. T. Selmer, and P.I. Andrei p-Hydroxyphenylacetate decarboxylase from Clostridium difficile. A novel glycyl radical enzyme catalysing the formation of p-cresol Eur. J. Biochem. 268 2001 1363 1372
8. L. Lehtiö, and A. Goldman The pyruvate formate lyase family: sequences, structures and activation Protein Eng. Des. Sel. 17 2004 545 552
9. V.M. Leppänen, M.C. Merckel, D.L. Ollis, K.K. Wong, J.W. Kozarich, and A. Goldman Pyruvate formate lyase is structurally homologous to type I ribonucleotide reductase Struct. Fold. Des. 7 1999 733 744
10. A. Becker, K. Fritz-Wolf, W. Kabsch, J. Knappe, S. Schultz, and A.F. Volker Wagner Structure and mechanism of the glycyl radical enzyme pyruvate formate-lyase Nature Struct. Biol. 6 1999 969 975
11. J.R. O'Brien, C. Raynaud, C. Croux, L. Girbal, P. Soucaille, and W.N. Lanzilotta Insight into the mechanism of the B12-independent glycerol dehydratase from Clostridium butyricum: preliminary biochemical and structural characterization Biochemistry 43 2004 4635 4645
12. D.T. Logan, J. Andersson, B.M. Sjöberg, and P. Nordlund A glycyl radical site in the crystal structure of a class III ribonucleotide reductase Science 283 1999 1499 1504
13. P. Young, J. Andersson, M. Sahlin, and B.M. Sjöberg Bacteriophage T4 anaerobic ribonucleotide reductase contains a stable glycyl radical at position 580 J. Biol. Chem. 271 1996 20770 20775
14. V. Unkrig, F.A. Neugebauer, and J. Knappe 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 1989 723 728
15. L. Lehtiö, V.M. Leppänen, J.W. Kozarich, and A. Goldman Structure of Escherichia coli pyruvate formate-lyase with pyruvate Acta Crystallog. sect. D 58 2002 2209 2212
16. H.J. Sofia, G. Chen, B.G. Hetzler, J.F. Reyes-Spindola, and N.E. Miller Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods Nucl. Acids Res. 29 2001 1097 1106
17. F. Berkovitch, Y. Nicolet, J.T. Wan, J.T. Jarrett, and C.L. Drennan Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme Science 303 2004 76 79
18. P. Hanzelmann, and H. Schindelin Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans Proc. Natl Acad. Sci. USA 101 2004 12870 12875
19. B.W. Lepore, F.J. Ruzicka, P.A. Frey, and D. Ringe The X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale Proc. Natl Acad. Sci. USA 102 2005 13819 13824
20. D.R. Tolan, B. Schuler, P.T. Beernink, and R. Jaenicke Thermodynamic analysis of the dissociation of the aldolase tetramer substituted at one or both of the subunit interfaces Biol. Chem. 384 2003 1463 1471
21. C. Vieille, and G.J. Zeikus Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability Microbiol. Mol. Biol. Rev. 65 2001 1 43
22. S.T. Farias, and M.C. Bonato Preferred amino acids and thermostability Genet. Mol. Res. 2 2003 383 393
23. T. Kajander, P.C. Kahn, S.H. Passila, D.C. Cohen, L. Lehtiö, and W. Adolfsen Buried charged surface in proteins Struct. Fold. Des. 8 2000 1203 1214
24. P.I. Andrei, A.J. Pierik, S. Zauner, L.C. Andrei-Selmer, and T. Selmer Subunit composition of the glycyl radical enzyme p-hydroxyphenylacetate decarboxylase. A small subunit, HpdC, is essential for catalytic activity Eur. J. Biochem. 271 2004 2225 2230
25. T. Fukui, H. Atomi, T. Kanai, R. Matsumi, S. Fujiwara, and T. Imanaka Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes Genome Res. 15 2005 352 363
26. B.A. Methe, K.E. Nelson, J.A. Eisen, I.T. Paulsen, W. Nelson, and J.F. Heidelberg Genome of Geobacter sulfurreducens: metal reduction in subsurface environments Science 302 2003 1967 1969
27. R. Rabus, A. Ruepp, T. Frickey, T. Rattei, B. Fartmann, and M. Stark The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments Environ. Microbiol. 6 2004 887 902
28. K.E. Nelson, R.A. Clayton, S.R. Gill, M.L. Gwinn, R.J. Dodson, and D.H. Haft Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima Nature 399 1999 323 329
29. C. Bräsen, C. Urbanke, and P. Schönheit A novel octameric AMP-forming acetyl-CoA synthetase from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum FEBS Letters 579 2005 477 482
30. H. Walden, G.L. Taylor, E. Lorentzen, E. Pohl, H. Lilie, and A. Schramm Structure and function of a regulated archaeal triosephosphate isomerase adapted to high temperature J. Mol. Biol. 342 2004 861 875
31. V.G. Eijsink, A. Bjørk, S. Gåseidnes, R. Sirevåg, B. Synstad, B. van den Burg, and G. Vriend Rational engineering of enzyme stability J. Biotechnol. 113 2004 105 120
32. R. Thoma, M. Hennig, R. Sterner, and K. Kirschner Structure and function of mutationally generated monomers of dimeric phosphoribosylanthranilate isomerase from Thermotoga maritima Struct. Fold. Des. 8 2000 265 276
33. K.E. Nordberg, M. Abou-Hachem, O. Holst, M.J. Danson, and D.W. Hough Rhodothermus marinus: a thermophilic bacterium producing dimeric and hexameric citrate synthase isoenzymes Extremophiles 6 2002 51 56
34. A.S. Thomas, and A.H. Elcock Molecular simulations suggest protein salt bridges are uniquely suited to life at high temperatures J. Am. Chem. Soc. 126 2004 2208 2214
35. G.S. Bell, R.J. Russell, H. Connaris, D.W. Hough, M.J. Danson, and G.L. Taylor Stepwise adaptations of citrate synthase to survival at life's extremes. From psychrophile to hyperthermophile Eur. J. Biochem. 269 2002 6250 6260
36. S. Majeed, G. Ofek, A. Belachew, C.C. Huang, T. Zhou, and P.D. Kwong Enhancing protein crystallization through precipitant synergy Structure (Camb) 11 2003 1061 1070
37. W. Kabsch Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants J. Appl. Crystallog. 26 1993 795 800
38. A.T. Brünger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, and R.W. Grosse-Kunstleve Crystallography & NMR system: a new software suite for macromolecular structure determination Acta Crystallog. sect. D 54 1998 905 921
39. J.V. Lehtonen, D.J. Still, V.V. Rantanen, J. Ekholm, D. Björklund, and Z. Iftikhar BODIL: a molecular modeling environment for structure-function analysis and drug design J. Comput. Aided Mol. Des. 18 2004 401 419
40. G.N. Murshudov Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallog. sect. D 53 1997 240 255
41. E. Towns-Andrews, A. Berry, J. Bordas, G.R. Mant, P.K. Murray, and K. Roberts Time-resolved X-ray diffraction station: X-ray optics, detectors, and data acquisition Intl. Conf. Synch. Rad. Instr. 60 1989 2346 2349
42. J.G. Grossmann, J.F. Hall, L.D. Kanbi, and S.S. Hasnain The N-terminal extension of rusticyanin is not responsible for its acid stability Biochemistry 41 2002 3613 3619
43. A.V. Semenyuk, and D.I. Svergun GNOM-a program package for small-angle scattering data processing J. Appl. Crystallog. 24 1991 537 540
44. D. Svergun, C. Barberato, and M.H.J. Koch CRYSOL-a program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates J. Appl. Crystallog. 28 1995 768 773
45. T. Laue, B.D. Shaw, T.M. Ridgeway, and S.L. Pelletier Analytical ultracentrifugation S.E. Harding A. Rowe J.C. Horton Biochemistry and Polymer Science 1992 Royal Society of Chemistry Cambridge, UK 90 125
46. G.J. Kleywegt, and T.A. Jones Detection, delineation, measurement and display of cavities in macromolecular structures Acta Crystallog. sect. D 50 1994 178 185
47. G. Vriend WHAT IF: a molecular modeling and drug design program J. Mol. Graph. 8 1990 52 56
48. T.A. Jones A graphics model building and refinement system for macromolecules J. Appl. Crystallog. 11 1974 268 272