Crystallographic analysis of a thermoactive nitrilase

Journal of Structural Biology

Volumn 173, Issue 2, 2011, Pages 294-302

  Raczynska, Joanna E ^a   Vorgias, Constantinos E ^b   Antranikian, Garabed ^c   Rypniewski, Wojciech ^a  

^a INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^b UNIVERSITY OF ATHENS   (Greece)

^c HAMBURG UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Carboxylate group binding; Nitrilase; Thermophilic enzyme; X ray structure

Indexed keywords

ACETIC ACID; BROMIDE ION; DICARBOXYLIC ACID; GLUTAMINE; HYDROLASE; LYSINE; MALONONITRILE; NITRILASE; NUCLEOPHILE;

ARTICLE; BINDING AFFINITY; BINDING SITE; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME MECHANISM; PRIORITY JOURNAL; PYROCOCCUS ABYSSI;

AMINOHYDROLASES; CRYSTALLOGRAPHY, X-RAY; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PYROCOCCUS ABYSSI;

PYROCOCCUS ABYSSI;

EID: 78751567922     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2010.11.017     Document Type: Article

References (27)

1. Andrade J., Karmali A., Carrondo M.A., Frazão C. Structure of amidase from Pseudomonas aeruginosa showing a trapped acyl transfer reaction intermediate state. J. Biol. Chem. 2007, 282:19598-19605.
2. Baker N.A., Sept D., Joseph S., Holst M.J., McCammon J.A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 2001, 98:10037-10041.
3. Barglow K.T., Saikatendu K.S., Bracey M.H., Huey R., Morris G.M., Olson A.J., Stevens R.C., Cravatt B.F. Functional proteomic and structural insights into molecular recognition in the nitrilase family enzymes. Biochemistry 2008, 47:13514-13523.
4. Brenner C. Catalysis in the nitrilase superfamily. Curr. Opin. Struct. Biol. 2002, 12:775-782.
5. Chin K., Tsai Y., Chan N., Huang K., Wang A.H., Chou S. The crystal structure of XC1258 from Xanthomonas campestris: a putative procaryotic Nit protein with an arsenic adduct in the active site. Proteins 2007, 69:665-671.
6. Collaborative Computational Project, Number 4 The CCP4 suite: programs for protein crystallography. D Biol. Crystallogr. 1994, 50:760-763.
7. Dauter Z., Dauter M., Rajashankar K.R. Novel approach to phasing proteins: derivatization by short cryo-soaking with halides. Acta Crystallogr. D Biol. Crystallogr. 2000, 56:232-237.
8. Davis I.W., Leaver-Fay A., Chen V.B., Block J.N., Kapral G.J., Wang X., Murray L.W., Arendall W.B., Snoeyink J., Richardson J.S., Richardson D.C. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 2007, 35:W375-83.
9. DeLano, W.L. The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, CA, USA. http://www.pymol.org.
10. Dolinsky T.J., Nielsen J.E., McCammon J.A., Baker N.A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 2004, 32:W665-7.
11. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 2004, 60:2126-2232.
12. Goodsell D.S., Morris G.M., Olson A.J. Automated docking of flexible ligands: applications of AutoDock. J. Mol. Recognit. 1996, 9:1-5.
13. Hung C., Liu J., Chiu W., Huang S., Hwang J., Wang W. Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad. J. Biol. Chem. 2007, 282:12220-12229.
14. Kimani S.W., Agarkar V.B., Cowan D.A., Sayed M.F.R., Sewell B.T. Structure of an aliphatic amidase from Geobacillus pallidus RAPc8. Acta Crystallogr. D Biol. Crystallogr. 2007, 63:1048-1058.
15. Kumaran D., Eswaramoorthy S., Gerchman S.E., Kycia H., Studier F.W., Swaminathan S. Crystal structure of a putative CN hydrolase from yeast. Proteins 2003, 52:283-291.
16. Lundgren S., Lohkamp B., Andersen B., Piskur J., Dobritzsch D. The crystal structure of beta-alanine synthase from Drosophila melanogaster reveals a homooctameric helical turn-like assembly. J. Mol. Biol. 2008, 377:1544-1559.
17. McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., Read R.J. Phaser crystallographic software. J. Appl. Cryst. 2007, 40:658-674.
18. Mueller P., Egorova K., Vorgias C.E., Boutou E., Trauthwein H., Verseck S., Antranikian G. Cloning, overexpression, and characterization of a thermoactive nitrilase from the hyperthermophilic archaeon Pyrococcus abyssi. Protein Expr. Purif. 2006, 47:672-681.
19. Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 1997, 53:240-255.
20. Nakai T., Hasegawa T., Yamashita E., Yamamoto M., Kumasaka T., Ueki T., Nanba H., Ikenaka Y., Takahashi S., Sato M., Tsukihara T. Crystal structure of N-carbamyl-d-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases. Structure 2000, 8:729-737.
21. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997, 276:307-326.
22. Pace, H.C., Brenner, C. The nitrilase superfamily: classification, structure and function. Genome Biol. 2 (2001) REVIEWS0001.
23. Pace H.C., Hodawadekar S.C., Draganescu A., Huang J., Bieganowski P., Pekarsky Y., Croce C.M., Brenner C. Crystal structure of the worm NitFhit Rosetta stone protein reveals a Nit tetramer binding two Fhit dimers. Curr. Biol. 2000, 10:907-917.
24. Sakai N., Tajika Y., Yao M., Watanabe N., Tanaka I. Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6Å resolution. Proteins 2004, 57:869-873.
25. Thuku R.N., Weber B.W., Varsani A., Sewell B.T. Post-translational cleavage of recombinantly expressed nitrilase from Rhodococcus rhodochrous J1 yields a stable active helical form. FEBS J. 2007, 274:2099-2108.
26. Thuku R.N., Brady D., Benedik M.J., Sewell B.T. Microbial nitrilases: versatile, spiral forming, industrial enzymes. J. Appl. Microbiol. 2009, 106:703-727.
27. Yeates T.O. Detecting and overcoming crystal twinning. Methods Enzymol. 1997, 276:344-358.