An allylic ketyl radical intermediate in clostridial amino-acid fermentation

Nature

Volumn 452, Issue 7184, 2008, Pages 239-242

  Kim, Jihoe ^a   Darley, Daniel J ^a,b   Buckel, Wolfgang ^a   Pierik, Antonio J ^a  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

^b University of Bath   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

2 HYDROXY 4 METHYLPENTANOYL COA; 2 HYDROXYACYL COA DEHYDRATASE; 2 HYDROXYPENT4 ENOYL COA; AMINO ACID; BENZYL COA REDUCTASE; COBAMAMIDE; COENZYME A; HYDROLYASE; KETONE DERIVATIVE; OXIDOREDUCTASE; OXYGEN; RADICAL; S ADENOSYLMETHIONINE; UNCLASSIFIED DRUG;

AMINO ACID; BACTERIUM; ENZYME ACTIVITY; FERMENTATION; KINETICS; PATHOGEN; RADICAL;

ARTICLE; CLOSTRIDIUM DIFFICILE; CONTROLLED STUDY; ELECTRON SPIN RESONANCE; ENZYME MECHANISM; ENZYME SUBSTRATE; FERMENTATION; ISOTOPE LABELING; KINETICS; NONHUMAN; PRIORITY JOURNAL;

BACTERIA (MICROORGANISMS); CLOSTRIDIUM DIFFICILE;

EID: 40749108599     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature06637     Document Type: Article

References (26)

1. Buckel, W. in Biology of the Prokaryotes (eds Lengeler, J. W., Drews, G. & Schlegel, H. G.) 278-326 (Thieme, Stuttgart, 1999).
2. Buckel, W. & Keese, R. One electron redox reactions of CoASH esters in anaerobic bacteria. A mechanistic proposal. Angew. Chem. Int. Edn Engl. 34, 1502-1506 (1995).
3. Buckel, W., Hetzel, M. & Kim, J. ATP-driven electron transfer in enzymatic radical reactions. Curr. Opin. Chem. Biol. 8, 462-467 (2004).
4. Boll, M. & Fuchs, G. Unusual reactions involved in anaerobic metabolism of phenolic compounds. Biol. Chem. 386, 989-997 (2005).
5. Seebach, D. Methods of reactivity Umpolung. Angew. Chem. Int. Edn Engl. 18, 239-258 (1979).
6. Brückner, R. Reaktionsmechanismen (Spektrum Akademischer, Heidelberg, 2003).
7. Buckel, W. & Golding, B. T. Radical enzymes in anaerobes. Annu. Rev. Microbiol. 60, 27-49 (2006).
8. Smith, D. M., Buckel, W. & Zipse, H. Deprotonation of enoxy radicals: theoretical validation of a 50-year-old mechanistic proposal. Angew. Chem. Int. Edn Engl. 42, 1867-1870 (2003).
9. Sebaihia, M. & Thomson, N. R. Colonic irritation. Nature Rev. Microbiol. 4, 882-883 (2006).
10. Reineke, J. et al. Autocatalytic cleavage of Clostridium difficile toxin B. Nature 446, 415-419 (2007).
11. Selmer, T. & Andrei, P. I. p-Hydroxyphenylacetate decarboxylase from Clostridium difficile. A novel glycyl radical enzyme catalysing the formation of p-cresol. Eur. J. Biochem. 268, 1363-1372 (2001).
12. Sebaihia, M. et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nature Genet. 38, 779-786 (2006).
13. Barker, H. A. Amino acid degradation by anaerobic bacteria. Annu. Rev. Biochem. 50, 23-40 (1981).
14. Elsden, S. R. & Hilton, M. G. Volatile acid production from threonine, valine, leucine and isoleucine by clostridia. Arch. Microbiol. 117, 165-172 (1978).
15. Kim, J., Darley, D., Selmer, T. & Buckel, W. Characterization of (R)-2-hydroxyisocaproate dehydrogenase and a family III coenzyme A transferase involved in reduction of L-leucine to isocaproate by Clostridium difficile. Appl. Environ. Microbiol. 72, 6062-6069 (2006).
16. Kim, J., Darley, D. & Buckel, W. 2-Hydroxyisocaproyl-CoA dehydratase and its activator from Clostridium difficile. FEBS J. 272, 550-561 (2005).
17. Hans, M., Buckel, W. & Bill, E. The iron-sulfur clusters in 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Biochemical and spectroscopic investigations. Eur. J. Biochem. 267, 7082-7093 (2000).
18. Weil, J. A. & Bolton, J. R. Electron Paramagnetic Resonance: Elementary Theory and Practical Applications 2nd edn (Wiley, Bognor Regis, 2007).
19. Wu, W. et al. Lysine 2,3-aminomutase and trans-4,5-dehydrolysine: characterization of an allylic analogue of a substrate-based radical in the catalytic mechanism. Biochemistry 39, 9561-9570 (2000).
20. Magnusson, O. T., Reed, G. H. & Frey, P. A. Characterization of an allylic analogue of the 5′-deoxyadenosyl radical: an intermediate in the reaction of lysine 2,3-aminomutase. Biochemistry 40, 7773-7782 (2001).
21. Layer, G. et al. The substrate radical of Escherichia coli oxygen-independent coproporphyrinogen III oxidase HemN. J. Biol. Chem. 281, 15727-15734 (2006).
22. Stubbe, J. & Van der Donk, W. A. Protein radicals in enzyme catalysis. Chem. Rev. 98, 705-762 (1998).
23. Buckel, W. The reversible dehydration of (R)-2-hydroxyglutarate to (E)-glutaconate. Eur. J. Biochem. 106, 439-447 (1980).
24. Beinert, H. & Albracht, S. P. J. New insights, ideas and unanswered questions concerning iron-sulfur clusters in mitochondria. Biochim. Biophys. Acta 683, 245-277 (1982).
25. Tsai, A. L., Berka, V., Kulmacz, R. J., Wu, G. & Palmer, G. An improved sample packing device for rapid freeze-trap electron paramagnetic resonance spectroscopy kinetic measurements. Anal. Biochem. 264, 165-171 (1998).
26. Ballinger, M. D., Reed, G. H. & Frey, P. A. An organic radical in the lysine 2,3-aminomutase reaction. Biochemistry 31, 949-953 (1992).