A new approach to possible substrate binding mechanisms for nitrile hydratase

Biochemical and Biophysical Research Communications

Volumn 343, Issue 1, 2006, Pages 319-325

  Taştan Bishop, A Özlem ^a,b   Sewell, Trevor ^c  

^a UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^b UNIVERSITY OF PRETORIA   (South Africa)

^c UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

Breathing; Cavity; Flip flop; NHase; Normal mode; Substrate binding mechanism

Indexed keywords

BUTYRIC ACID; NITRILE HYDRATASE;

AMINO TERMINAL SEQUENCE; ARTICLE; BREATHING; CRYSTAL STRUCTURE; ENZYME SUBSTRATE COMPLEX; PRIORITY JOURNAL; PSEUDONOCARDIACEAE;

ACTINOMYCETALES; BACTERIAL PROTEINS; BINDING SITES; HYDRO-LYASES; PROTEIN CONFORMATION; SUBSTRATE SPECIFICITY;

PSEUDONOCARDIA THERMOPHILA; PSEUDONOCARDIACEAE;

EID: 33645104306     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2006.02.150     Document Type: Article

References (19)

1. H. Yamada, and M. Kobayashi Nitrile hydratase and its application to industrial production of acrylamide Biosci. Biotechnol. Biochem. 60 1996 1391 1400
2. J.M. Wyatt, and C.J. Knowles Microbial degradation of acrylonitrile waste effluents: the degradation of effluents and condensates from the manufacture of acrylonitrile Int. Biodeter. Biodegrad. 35 1995 227 248
3. M. Kobayashi, T. Nagasawa, and H. Yamada Enzymatic synthesis of acrylamide: a successful story not over yet Trends Biotechnol. 10 1992 402 408
4. Y. Asano, K. Fujishiro, Y. Tani, and H. Yamada Aliphatic nitrile hydratase from Arthrobacter sp. J-1. Purification and characterization Agric. Biol. Chem. 46 1982 1165 1174
5. W. Huang, J. Jia, J. Cummings, M. Nelson, G. Schneider, and Y. Lindqvist Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold Structure 5 1997 691 699
6. S. Nagashima, M. Nakasako, N. Dohmae, M. Tsujimura, K. Takio, M. Odaka, M. Yohda, N. Kamiya, and I. Endo Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms Nat. Struct. Biol. 5 1998 347 351
7. A. Miyanaga, S. Fushinobu, K. Ito, and T. Wakagi Crystal structure of cobalt-containing nitrile hydratase Biochem. Biophys. Res. Commun. 288 2001 1169 1174
8. S. Hourai, M. Miki, Y. Takashima, S. Mitsuda, and K. Yanagi Crystal structure of nitrile hydratase from a thermophilic Bacillus smithii Biochem. Biophys. Res. Commun. 312 2003 340 345
9. A. Miyanaga, S. Fushinobu, K. Ito, H. Shoun, and T. Wakagi Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding Eur. J. Biochem. 271 2004 429 438
10. V.L. Desai, and M. Zimmer Substrate selectivity and conformational space available to bromoxynil and acrylonitrile in iron hydratase Dalton Trans. 8 2004 72 877
11. G.E. Cohen ALIGN: a program to superimpose protein coordinates, accounting for insertions and deletions J. Appl. Cryst. 30 1997 1160 1161
12. W.L. DeLano, The PyMOL Molecular Graphics System on World Wide Web, 〈http://www.pymol.org/〉 (2002).
13. K. Suhre, and Y. Sanejouand ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement Nucleic Acids Res. 32 2004 W610 W614
14. J. Liang, H. Edelsbrunner, and C. Woodward Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design Protein Sci. 7 1998 1884 1897
15. G.J. Kleywegt, and T.A. Jones Detection, delineation, measurement and display of activities in macromolecular structures Acta Crystallogr. D 50 1994 178 185
16. A.T.R. Laurie, and R.M. Jackson Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites Bioinformatics 21 2005 1908 1916
17. M. Nakasako, M. Odaka, M. Yohda, N. Dohmae, K. Takio, N. Kamiya, and I. Endo Tertiary and quaternary structures of photoreactive Fe-type nitrile hydratase from Rhodococcus sp. N-771: roles of hydration water molecules in stabilizing the structures and the structural origin of the substrate specificity of the enzyme Biochemistry 38 1999 9887 9898
18. S. Chakravarty, A. Bhinge, and R. Varadarajan A procedure for detection and quantitation of cavity volumes in proteins J. Biol. Chem. 277 2002 31345 31353
19. Y. Takashima, Y. Yamaga, and S. Mitsuda Nitrile hydratase from a thermophilic Bacillus smithii J. Ind. Microbiol. Biotechnol. 20 1998 220 226