The fluorinase, the chlorinase and the duf-62 enzymes

Current Opinion in Chemical Biology

Volumn 12, Issue 5, 2008, Pages 582-592

  Deng, Hai ^a   O'Hagan, David ^a  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; BACTERIAL PROTEIN; CHLORINASE; FLUORINASE; PROTEIN DUF 62; S ADENOSYLMETHIONINE; S ADENOSYLMETHIONYLHYDROXIDE ADENOSYLTRANSFERASE; TRANSFERASE; UNCLASSIFIED DRUG;

ACTINOMYCES; AMINO ACID SEQUENCE; CATALYSIS; CHEMICAL BOND; CHEMICAL REACTION; CHLORINATION; CRYSTAL STRUCTURE; ELECTRICITY; ENZYME MECHANISM; ENZYME STRUCTURE; HYDROGEN BOND; HYDROLYSIS; NONHUMAN; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; PYROCOCCUS HORIKOSHII; REVIEW; SALINISPORA TROPICA; STREPTOMYCES; STREPTOMYCES CATTLEYA; SUBSTITUTION REACTION;

ALKYL AND ARYL TRANSFERASES; CATALYTIC DOMAIN; CHLORINE; FLUORINE; OXIDOREDUCTASES;

SALINISPORA TROPICA; STREPTOMYCES CATTLEYA;

EID: 53849101806     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2008.06.036     Document Type: Review

References (37)

1. Dewar M.J.S. Alternative view of enzyme reactions. Proc Natl Acad Sci U S A 82 (1985) 2225-2229
2. Fontecave M., Atta M., and Mulliez E. S-adenosylmethionine: nothing goes to waste. Trends Biochem Res 29 (2004) 243-249
3. Loenen W.A.M. S-adenosylmethionine: jack of all trades and master of everything?. Biochem Soc Trans 34 (2006) 330-333
4. Nardi-Dei V., Kurihara T., Park C., Miyagi M., Tsunasawa S., Soda K., and Esaki N. dl-2-Haloacid dehalogenase from Pseudomonas sp. 113 is a new class of dehalogenase catalyzing hydrolytic dehalogenation not involving enzyme-substrate ester intermediate. J Biol Chem 274 (1999) 20977-20981
5. Ichiyama S., Kurihara T., Kogure Y., Tsunasawa S., Kawasaki H., and Esaki N. Reactivity of asparagine residue at the active site of the D105N mutant of fluoroacetate dehalogenase from Moraxella sp. B. Biochim Biophys Acta-Proteins Proteomics 1698 (2004) 27-36
6. de Jong R.M., and Dijkstra B.W. Structure and mechanism of bacterial dehalogenases: different ways to cleave a carbon-halogen bond. Curr Opin Struct Biol 13 (2003) 722-730
7. Schmidberger J.W., Wilce J.A., Weightman A.J., Whisstock J.C., and Wilce M.C.J. The crystal structure of Dehl reveals a new alpha-haloacid dehalogenase fold and active-site mechanism. J Mol Biol 378 (2008) 284-294
8. Arand M., Hallberg B.M., Zou J., Bergfors T., Oesch F., van der Werf M., deBont J.A.M., Jones T.A., and Mowbray S.L. Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site. EMBO J 22 (2003) 2583-2592
9. Johansson P., Unge T., Cronin A., Arand M., Bergfors T., Jones T.A., and Mowbray S.L. Structure of an atypical epoxide hydrolase from Mycobacterium tuberculosis gives insights into its function. J Mol Biol 351 (2005) 1048-1056
10. Sanada M., Miyano T., Iwadare S., Williamson J., Arison B., Smith J., Douglas A., Liesch J., and Inamine E. Biosynthesis of fluorothreonine and fluoroacetic acid by the thienamycin producer, Streptomyces cattleya. J Antibiot 39 (1984) 259-265
11. Deng H., O'Hagan D., and Schaffrath C. Fluorometabolite biosynthesis and the fluorinase from Streptomyces cattleya. Nat Prod Rep 21 (2004) 773-784
12. Schaffrath C., Cobb S.L., and O'Hagan D. Cell-Free Biosynthesis of Fluoroacetate and 4-Fluorothreonine in Streptomyces cattleya. Angew Chem Int Ed 41 (2002) 3913-3915
13. Cobb S.L., Deng H., John Hamilton T.G., McGlinchey R.P., and O'Hagan D. Identification of 5-fluoro-5-deoxy-d-ribose-1-phosphate as an intermediate in fluorometabolite biosynthesis in Streptomyces cattleya. Chem Commun (2004) 592-593
14. Onega M., McGlinchey R.P., Deng H., John Hamilton T.G., and O'Hagan D. The identification of (3R,4S)-5-fluoro-5-deoxy-d-ribulose-1-phosphate as an intermediate in fluorometabolite biosynthesis in Streptomyces cattleya. Bioorg Chem 35 (2007) 375-385
15. Murphy C., Schaffrath C., and O'Hagan D. Fluorinated natural products: the biosynthesis of fluoroacetate and 4-fluorothreonine in Streptomyces cattleya. Chemosphere 52 (2003) 455-461
16. O'Hagan D., Schaffrath C., Cobb S.L., Hamilton J.T.G., and Murphy C.D. Biosynthesis of an organofluorine molecule. Nature 416 (2002) 279
17. Dong C., Huang F.L., Deng H., Schaffrath C., Spencer J.B., O'Hagan D., and Naismith J.H. Crystal structure and mechanism of a bacterial fluorinating enzyme. Nature 427 (2004) 561-565. Crystallography studies shed light on the mechanism of the fluorinase. The studies revealed separate structures with SAM bound and 5′-FDA bound to the active site of the enzyme. Ser-158 of the fluorinase emerged as a key residue for a putative binding site for fluoride ion binding immediately before nucleophilic attack.
18. Deng H., Cobb S.L., McEwan A.R., McGlinchey R.P., Naismith J.H., O'Hagan D., Robinson D.A., and Spencer J.B. The fluorinase from Streptomyces cattleya is also a chlorinase. Angew Chem Int Ed Engl 45 (2006) 759-762
19. -.
20. - as substrates. Instead it utilises water/hydroxide as a nucleophile to generate adenosine. Oxygen-18 labelling studies support this hydrolytic reaction. The amino acid triad Asp-Arg-His is highly conserved across the Duf-62 protein superfamily but is not found in the halogenases.
21. N2 reaction mechanism. ChemBioChem 5 (2004) 685-690
22. Senn H.M., O'Hagan D., and Thiel W. Insight into enzymatic C{single bond}F bond formation from QM and QM/MM calculations. J Am Chem Soc 127 (2005) 13643-13655
23. Zhu X.F., Robinson D.A., McEwan A.R., O'Hagan D., and Naismith J.H. The mechanism of the enzymatic fluorination in Streptomyces cattleya. J Am Chem Soc 129 (2007) 14597-14604. The order of binding/debinding of substrates and products and mechanism of the fluorinase was explored using a combination of crystallography, site-directed mutagenesis and kinetic analysis.
24. Vincent M.A., and Hillier I.H. The solvated fluoride anion can be a good nucleophile. Chem Commun (2005) 5902-5903
25. Udwary D.W., Zeigler L., Asolkar R.N., Singan V., Lapidus A., Fenical W., Jensen P.R., and Moore B.S. Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci U S A 104 (2007) 10376-10381
26. Feling R.H., Buchanan G.O., Mincer T.J., Kauffman C.A., Jensen P.R., and Fenical W. Salinosporamide A: A highly cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus Salinospora. Angew Chem Int Ed Engl 42 (2003) 355-357
27. Williams P.G., Buchanan G.O., Feling R.H., Kauffman C.A., Jensen P.R., and Fenical W. New cytotoxic salinosporamides from the marine actinomycete Salinispora tropica. J Org Chem 70 (2005) 6196-6203
28. Eustáquio A., and Moore B.S. Mutasynthesis of fluorosalinosporamide, a potent and reversible inhibitor of the proteasome. Angew Chem Int Ed 47 (2008) 3936-3938
29. There is no primary literature on these structures however the co-ordinates of four Duf-62 X-ray structures have been deposited by various structural proteomics groups in the Protein Structure Data Bank. The structures have the following PDB codes. Methanococcus Jannaschii DSM 2661, PDB 2f4n; Pyrococcus horikoshii OT3, PDB 1WU8; Thermus Thermophilus Hb8, PDB 2CW5; Thermotoga maritima, PDB 2ZBU.
30. Gonzalez J.M., Masuchi Y., Robb F.T., Ammerman J.W., Maeder D.L., Yanagibayashi M., Tamaoka J., and Kato C. Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at Okinawa Trough. Extremophiles 2 (1998) 123-130
31. Valentine D.L. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nature 446 (2007) 316-323
32. Hopmann K.H., Hallberg B.M., and Himo F. Catalytic mechanism of limonene epoxide hydrolase, a theoretical study. J Am Chem Soc 127 (2005) 14339-14347
33. Schmuck C., and Wienland W. Highly stable self-assembly in water: ion pair driven dimerization of a guanidiniocarbonyl pyrrole carboxylate zwitterion. J Am Chem Soc 125 (2003) 452-459
34. Schmuck C. How to improve guanidinium cations for oxoanion binding in aqueous solution?: the design of artificial peptide receptors. Coordin Chem Rev 250 (2006) 3053-3067
35. Palmer J.L., and Abeles R.H. The mechanism of action of S-adenosylhomocysteinase. J Biol Chem 254 (1979) 1217-1226
36. Kimoto H., Fujii Y., Hirano S., Yokota Y., and Taketo A. Genetic and biochemical properties of Streptococcal NAD-glycohydrolase inhibitor. J Biol Chem 281 (2006) 9181-9189
37. Kimoto H., Fujii Y., Yokota Y., and Taketo A. Molecular characterization of NADase-streptolysin O operon of hemolytic streptococci. Biochim Biophys Acta-Gene Struct Expr 1681 (2005) 134-149