X-ray crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase: Catalytic mechanism and evolution of an enzyme responsible for nylon-6 byproduct degradation

Journal of Biological Chemistry

Volumn 285, Issue 2, 2010, Pages 1239-1248

  Yasuhira, Kengo ^a   Shibata, Naoki ^a,b   Mongami, Go ^a   Uedo, Yuki ^a   Atsumi, Yu ^a   Kawashima, Yasuyuki ^a   Hibino, Atsushi ^a   Tanaka, Yusuke ^a   Lee, Young Ho ^c   Kato, Dai Ichiro ^a   Takeo, Masahiro ^a   Higuchi, Yoshiki ^a,b   Negoro, Seiji ^a  

^a UNIVERSITY OF HYOGO   (Japan)

^b RIKEN HARIMA INSTITUTE   (Japan)

^c OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDASE; AMIDE BOND; ARTHROBACTER SP; CARBOXYLESTERASES; CATALYTIC CENTER; CATALYTIC MECHANISMS; CYCLIC DIMERS; ESTEROLYTIC ACTIVITY; HYDROLASES; HYDROLYTIC ACTIVITIES; INDUSTRY BYPRODUCT; MALONAMIDES; NYLON-6; OXYANIONS; SITE DIRECTED MUTAGENESIS; SPECIFIC ACTIVITY; STRUCTURAL SIMILARITY; X-RAY CRYSTALLOGRAPHIC ANALYSIS; Z-SCORES;

AMIDES; AMINO ACIDS; COMPLEXATION; ENZYMES; HYDROGEN BONDS; ORGANIC ACIDS; POLYAMIDES; QUANTUM CHEMISTRY; RAYON; STRUCTURAL ANALYSIS;

PHOTODEGRADATION;

6 AMINOHEXANOATE CYCLIC DIMER HYDROLASE; ALANINE; CYSTEINE; GLUTAMATE TRANSFER RNA LIGASE; GLUTAMINE; HYDROLASE; LYSINE; NITROGEN; NYLON; SERINE; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ARTHROBACTER; ARTICLE; CATALYSIS; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; HYDROGEN BOND; HYDROLYSIS; MUTANT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SITE DIRECTED MUTAGENESIS; X RAY CRYSTALLOGRAPHY;

AMIDOHYDROLASES; AMINO ACID SUBSTITUTION; ARTHROBACTER; BACTERIAL PROTEINS; BIODEGRADATION, ENVIRONMENTAL; CAPROLACTAM; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; MUTATION, MISSENSE; POLYMERS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; STRUCTURE-ACTIVITY RELATIONSHIP;

ARTHROBACTER SP.;

EID: 74049115832     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.041285     Document Type: Article

References (45)

1. Negoro, S. (2000) Appl. Microbiol. Biotechnol. 54, 461-466
2. Negoro, S. (2002) Biopolymers 9, 395-415
3. Kinoshita, S., Negoro, S., Muramatsu, M., Bisaria, V. S., Sawada, S., and Okada, H. (1977) Eur. J. Biochem. 80, 489-495
4. Kanagawa, K., Negoro, S., Takada, N., and Okada, H. (1989) J. Bacteriol. 171, 3181-3186
5. Tsuchiya, K., Fukuyama, S., Kanzaki, N., Kanagawa, K., Negoro, S., and Okada, H. (1989) J. Bacteriol. 171, 3187-3191
6. Yasuhira, K., Tanaka, Y., Shibata, H., Kawashima, Y., Ohara, A., Kato, D., Takeo, M., and Negoro, S. (2007) Appl. Environ. Microbiol. 73, 7099-7102
7. Kato, K., Ohtsuki, K., Koda, Y., Maekawa, T., Yomo, T., Negoro, S., and Urabe, I. (1995) Microbiology 141, 2585-2590
8. Schmitt, E., Panvert, M., Blanquet, S., and Mechulam, Y. (2005) Structure 13, 1421-1433
9. Nakamura, A., Yao, M., Chimnaronk, S., Sakai, N., and Tanaka, I. (2006) Science 312, 1954-1958
10. Neu, D., Lehmann, T., Elleuche, S., and Pollmann, S. (2007) FEBS J. 274, 3440-3451
11. Yamada, T., Palm, C. J., Brooks, B., and Kosuge, T. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 6522-6526
12. Shin, S., Lee, T. H., Ha, N. C., Koo, H. M., Kim, S. Y., Lee, H. S., Kim, Y. S., and Oh, B. H. (2002) EMBO J. 21, 2509-2516
13. Yun, Y. S., Lee, W., Shin, S., Oh, B. H., and Choi, K. Y. (2006) J. Biol. Chem. 281, 40057-40064
14. Bracey, M. H., Hanson, M. A., Masuda, K. R., Stevens, R. C., and Cravatt, B. F. (2002) Science 298, 1793-1796
15. Wei, B. Q., Mikkelsen, T. S., McKinney, M. K., Lander, E. S., and Cravatt, B. F. (2006) J. Biol. Chem. 281, 36569-36578
16. Labahn, J., Neumann, S., Büldt, G., Kula, M. R., and Granzin, J. (2002) J. Mol. Biol. 322, 1053-1064
17. Valiña, A. L., Mazumder-Shivakumar, D., and Bruice, T. C. (2004) Biochemistry 43, 15657-15672
18. Kobayashi, M., Goda, M., and Shimizu, S. (1998) FEBS Lett. 439, 325-328
19. Cilia, E., Fabbri, A., Uriani, M., Scialdone, G. G., and Ammendola, S. (2005) FEBS J. 272, 4716-4724
20. Asano, Y., Fukuta, Y., Yoshida, Y., and Komeda, H. (2008) Biosci. Biotechnol. Biochem. 72, 2141-2150
21. Heumann, S., Eberl, A., Fischer-Colbrie, G., Pobeheim, H., Kaufmann, F., Ribitsch, D., Cavaco-Paulo, A., and Guebitz, G. M. (2009) Biotechnol. Bioeng. 102, 1003-1011
22. Yasuhira, K., Uedo, Y., Shibata, N., Negoro, S., Takeo, M., and Higuchi, Y. (2006) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62, 1209-1211
23. Ito, W., Ishiguro, H., and Kurosawa, Y. (1991) Gene 102, 67-70
24. Otwinowski, Z., and Minor, W. (1997) Methods Enzymol. 276, 307-326
25. Weeks, C. M., Blessing, R. H., Miller, R., Mungee, R., Potter, S. A., Rappleye, J., Smith, G. D., Xu, H., and Furey, W. (2002) Z. Kristallogr. 217, 686-693
26. de La Fortelle, E., and Bricogne, G. (1997) Methods Enzymol. 276, 472-494
27. McRee, D. E. (1993) Practical Protein Crystallography, Academic Press, San Diego, CA
28. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, N., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Acta Crystallogr. D Biol. Crystallogr. 54, 905-921
29. Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., 3rd, Snoeyink, J., Richardson, J. S., and Richardson, D. C. (2007) Nucleic Acids Res. 35, W375-W383
30. Fersht, A. R. (1984) Enzyme Structure and Mechanism (2nd Ed), pp. 389-452, W. H. Freeman and Co., New York
31. Arpigny, J. L., and Jaeger, K. E. (1999) Biochem. J. 343, 177-183
32. Zawadzke, L. E., Chen, C. C., Banerjee, S., Li, Z., Wäsch, S., Kapadia, G., Moult, J., and Herzberg, O. (1996) Biochemistry 35, 16475-16482
33. Minasov, G., Wang, X., and Shoichet, B. K. (2002) J. Am. Chem. Soc. 124, 5333-5340
34. Hermann, J. C., Ridder, L., Mulholland, A. J., and Höltje, H. D. (2003) J. Am. Chem. Soc. 125, 9590-9591
35. Okada, H., Negoro, S., Kimura, H., and Nakamura, S. (1983) Nature 306, 203-206
36. Yasuhira, K., Uedo, Y., Takeo, M., Kato, D., and Negoro, S. (2007) J. Biosci. Bioeng. 104, 521-524
37. Negoro, S., Ohki, T., Shibata, N., Mizuno, N., Wakitani, Y., Tsurukame, J., Matsumoto, K., Kawamoto, I., Takeo, M., and Higuchi, Y. (2005) J. Biol. Chem. 280, 39644-39652
38. Negoro, S., Ohki, T., Shibata, N., Sasa, K., Hayashi, H., Nakano, H., Yasuhira, K., Kato, D., Takeo, M., and Higuchi, Y. (2007) J. Mol. Biol. 370, 142-156
39. Ohki, T., Wakitani, Y., Takeo, M., Yasuhira, K., Shibata, N., Higuchi, Y., and Negoro, S. (2006) FEBS Lett. 580, 5054-5058
40. Kawashima, Y., Ohki, T., Shibata, N., Higuchi, Y., Wakitani, Y., Matsuura, Y., Nakata, Y., Takeo, M., Kato, D., and Negoro, S. (2009) FEBS J. 276, 2547-2556
41. Ohki, T., Shibata, N., Higuchi, Y., Kawashima, Y., Takeo, M., Kato, D., and Negoro, S. (2009) Protein Sci. 18, 1662-1673
42. Wagner, U. G., Petersen, E. I., Schwab, H., and Kratky, C. (2002) Protein Sci. 11, 467-478
43. Silvaggi, N. R., Anderson, J. W., Brinsmade, S. R., Pratt, R. F., and Kelly, J. A. (2003) Biochemistry 42, 1199-1208
44. Nukaga, M., Kumar, S., Nukaga, K., Pratt, R. F., and Knox, J. R. (2004) J. Biol. Chem. 279, 9344-9352
45. Laskowski, R. A., McArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl. Crystallogr. 265, 283-291