Structure and characterization of amidase from Rhodococcus sp. N-771: Insight into the molecular mechanism of substrate recognition

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1804, Issue 1, 2010, Pages 184-192

  Ohtaki, Akashi ^a   Murata, Kensuke ^a   Sato, Yuichi ^a   Noguchi, Keiichi ^a   Miyatake, Hideyuki ^b   Dohmae, Naoshi ^b   Yamada, Kazuhiro ^a   Yohda, Masafumi ^a   Odaka, Masfumi ^a  

^a TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

^b RIKEN   (Japan)

Author keywords

Amidase; Amidase signature family; Crystal structure; Rhodococcus sp. N 771; Substrate specificity

Indexed keywords

ACETAMIDE; ACRYLAMIDE; AMIDASE; BENZAMIDE; PROPIONAMIDE DERIVATIVE;

ARTICLE; BACTERIAL STRAIN; CRYSTALLIZATION; ENZYME ANALYSIS; ENZYME STRUCTURE; GEL PERMEATION CHROMATOGRAPHY; HYDROLYSIS; LIGHT SCATTERING; MOLECULAR MECHANICS; NONHUMAN; PRIORITY JOURNAL; RHODOCOCCUS;

AMIDOHYDROLASES; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; PROTEIN MULTIMERIZATION; RHODOCOCCUS; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); RHODOCOCCUS SP. N-771;

EID: 71649107994     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2009.10.001     Document Type: Article

References (42)

1. Thayer S.S., and Conn E.E. Subcellular Localization of Dhurrin beta-Glucosidase and Hydroxynitrile Lyase in the Mesophyll Cells of Sorghum Leaf Blades. Plant. Physiol. 67 (1981) 617-622
2. Gao M., Wang D.X., Zheng Q.Y., Huang Z.T., and Wang M.X. Remarkable electronic and steric effects in the nitrile biotransformations for the preparation of enantiopure functionalized carboxylic acids and amides: implication for an unsaturated carbon-carbon bond binding domain of the amidase. J. Org. Chem. 72 (2007) 6060-6066
3. Ma D.Y., Wang D.X., Pan J., Huang Z.T., and Wang M.X. Nitrile biotransformations for the synthesis of highly enantioenriched beta-hydroxy and beta-amino acid and amide derivatives: a general and simple but powerful and efficient benzyl protection strategy to increase enantioselectivity of the amidase. J. Org. Chem. 73 (2008) 4087-4091
4. Song L., Wang M., Shi J., Xue Z., Wang M.X., and Qian S. High resolution X-ray molecular structure of the nitrile hydratase from Rhodococcus erythropolis AJ270 reveals posttranslational oxidation of two cysteines into sulfinic acids and a novel biocatalytic nitrile hydration mechanism. Biochem. Biophys. Res. Commun. 362 (2007) 319-324
5. Wang J.Y., Wang D.X., Pan J., Huang Z.T., and Wang M.X. Nitrile and amide biotransformations for the synthesis of enantiomerically pure 3-arylaziridine-2-carboxamide derivatives and their stereospecific ring-opening reactions. J. Org. Chem. 72 (2007) 9391-9394
6. M.X. Wang, Enantioselective Biotransformations of Nitriles in Organic Synthesis Topics in Catalysis 35 (2005) 117-130.
7. M.X. Wang, Progress of Enantioselective Nitrile Biotransformations in Organic Synthesis Chimia 63 (2009) 331-333.
8. Endo I., Nojiri M., Tsujimura M., Nakasako M., Nagashima S., Yohda M., and Odaka M. Fe-type nitrile hydratase. J. Inorg. Biochem. 83 (2001) 247-253
9. Yamada H., and Kobayashi M. Nitrile hydratase and its application to industrial production of acrylamide. Biosci. Biotechnol. Biochem. 60 (1996) 1391-1400
10. Mayaux J.F., Cerbelaud E., Soubrier F., Yeh P., Blanche F., and Petre D. Purification, cloning, and primary structure of a new enantiomer-selective amidase from a Rhodococcus strain: structural evidence for a conserved genetic coupling with nitrile hydratase. J. Bacteriol. 173 (1991) 6694-6704
11. Chebrou H., Bigey F., Arnaud A., and Galzy P. Study of the amidase signature group. Biochim. Biophys. Acta 1298 (1996) 285-293
12. Fournand D., and Arnaud A. Aliphatic and enantioselective amidases: from hydrolysis to acyl transfer activity. J. Appl. Microbiol. 91 (2001) 381-393
13. Pace H.C., and Brenner C. The nitrilase superfamily: classification, structure and function. Genome. Biol. 2 (2002) REVIEWS0001.1-0001.9
14. Pertsovich S.I., Guranda D.T., Podchernyaev D.A., Yanenko A.S., and Svedas V.K. Aliphatic amidase from Rhodococcus rhodochrous M8 is related to the nitrilase/cyanide hydratase family. Biochemistry. (Mosc) 70 (2005) 1280-1287
15. Curnow A.W., Hong K., Yuan R., Kim S., Martins O., Winkler W., Henkin T.M., and Soll D. Glu-tRNAGln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 11819-11826
16. Nakamura A., Yao M., Chimnaronk S., Sakai N., and Tanaka I. Ammonia channel couples glutaminase with transamidase reactions in GatCAB. Science 312 (2006) 1954-1958
17. Schon A., Kannangara C.G., Gough S., and Soll D. Protein biosynthesis in organelles requires misaminoacylation of tRNA. Nature 331 (1988) 187-190
18. Cravatt B.F., Giang D.K., Mayfield S.P., Boger D.L., Lerner R.A., and Gilula N.B. Molecular characterization of an enzyme that degrades neuromodulatory fatty-acid amides. Nature 384 (1996) 83-87
19. Deutsch D.G., Ueda N., and Yamamoto S. The fatty acid amide hydrolase (FAAH). Prostaglandins, Leukot. Essent. Fat. Acids 66 (2002) 201-210
20. Koutek B., Prestwich G.D., Howlett A.C., Chin S.A., Salehani D., Akhavan N., and Deutsch D.G. Inhibitors of arachidonoyl ethanolamide hydrolysis. J. Biol. Chem. 269 (1994) 22937-22940
21. Omeir R.L., Arreaza G., and Deutsch D.G. Identification of two serine residues involved in catalysis by fatty acid amide hydrolase. Biochem. Biophys. Res. Commun. 264 (1999) 316-320
22. Gaffney T.D., da Costa e Silva O., Yamada T., and Kosuge T. Indoleacetic acid operon of Pseudomonas syringae subsp. savastanoi: transcription analysis and promoter identification. J. Bacteriol. 172 (1990) 5593-5601
23. Gomi K., Kitamoto K., and Kumagai C. Cloning and molecular characterization of the acetamidase-encoding gene (amdS) from Aspergillus oryzae. Gene 108 (1991) 91-98
24. Bracey M.H., Hanson M.A., Masuda K.R., Stevens R.C., and Cravatt B.F. Structural adaptations in a membrane enzyme that terminates endocannabinoid signaling. Science 298 (2002) 1793-1796
25. Labahn J., Neumann S., Buldt G., Kula M.R., and Granzin J. An alternative mechanism for amidase signature enzymes. J. Mol. Biol. 322 (2002) 1053-1064
26. Shin S., Lee T.H., Ha N.C., Koo H.M., Kim S.Y., Lee H.S., Kim Y.S., and Oh B.H. Structure of malonamidase E2 reveals a novel Ser-cisSer-Lys catalytic triad in a new serine hydrolase fold that is prevalent in nature. EMBO J. 21 (2002) 2509-2516
27. Shin S., Yun Y.S., Koo H.M., Kim Y.S., Choi K.Y., and Oh B.H. Characterization of a novel Ser-cisSer-Lys catalytic triad in comparison with the classical Ser-His-Asp triad. J. Biol. Chem. 278 (2003) 24937-24943
28. Hashimoto K., Suzuki H., Taniguchi K., Noguchi T., Yohda M., and Odaka M. Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile. J. Biol. Chem. 283 (2008) 36617-36623
29. Odaka M., Noguchi T., Nagashima S., Yohda M., Yabuki S., Hishino M., Inoue Y., and Endo I. Location of the non-heme iron center on the alpha subunit of photoreactive nitrile hydratase from Rhodococcus sp. N-771. Biochem. Biophys. Res. Commun. 221 (1996) 146-150
30. Taniguchi K., Murata K., Murakami Y., Takahashi S., Nakamura T., Hashimoto K., Koshino H., Dohmae N., Yohda M., Hirose T., Maeda M., and Odaka M. Novel catalytic activity of nitrile hydratase from Rhodococcus sp. N771. J. Biosci. Bioeng. 106 (2008) 174-179
31. Fournand D., Bigey F., and Arnaud A. Acyl transfer activity of an amidase from Rhodococcus sp. strain R312: formation of a wide range of hydroxamic acids. Appl. Environ. Microbiol. 64 (1998) 2844-2852
32. Hashimoto Y., Nishiyama M., Ikehata O., Horinouchi S., and Beppu T. Cloning and characterization of an amidase gene from Rhodococcus species N-774 and its expression in Escherichia coli. Biochim. Biophys. Acta 1088 (1991) 225-233
33. Otwinowski Z.A.M. Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods Enzymol Macromol. Crystallogr., part A 276 (1997) 307-326
34. N. Collaborative Computational Project. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D 50 (1994) 760-763
35. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28 (2000) 235-242
36. McRee D.E. XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125 (1999) 156-165
37. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., Read R.J., Rice L.M., Simonson T., and Warren G.L. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. 54 (1998) 905-921
38. Brunger A.T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355 (1992) 472-475
39. Laskowski M.M.W., R A M.D.S., and Thornton J.M. A program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26 (1993) 283-291
40. Kraulis P.J. MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures. J. Appl. Crystallogr. 24 (1991) 946-950
41. Merritt E.A., and Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277 (1997) 505-524
42. DeLano W.L. The PyMOL Molecular Graphics System (2002), DeLano Scientific, Palo Alto, CA, USA