Three-dimensional structure and catalytic mechanism of cytosine deaminase

Biochemistry

Volumn 50, Issue 22, 2011, Pages 5077-5085

  Hall, Richard S ^a   Fedorov, Alexander A ^b   Xu, Chengfu ^a   Fedorov, Elena V ^b   Almo, Steven C ^b   Raushel, Frank M ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDOHYDROLASE SUPERFAMILY; CATALYTIC MECHANISMS; CHEMICAL MECHANISM; DIVALENT CATION; E. COLI; ISOCYTOSINE; LOW-BARRIER HYDROGEN BONDS; ORDERS OF MAGNITUDE; POTENTIAL SUBSTRATE; PROTON TRANSFER REACTIONS; SOLVENT ISOTOPE EFFECTS; STRUCTURAL DETERMINANTS; SUBSTRATE BINDING; THREE-DIMENSIONAL STRUCTURE; WATER MOLECULE;

AMINES; CHARGE TRANSFER; ENZYMES; ESCHERICHIA COLI; HYDROGEN; HYDROGEN BONDS; ISOTOPES; REACTION INTERMEDIATES; SUBSTRATES; ZINC;

CATALYST ACTIVITY;

CYTOSINE; CYTOSINE DEAMINASE; URACIL; WATER;

ARTICLE; CATALYSIS; DEAMINATION; ENZYME STRUCTURE; ESCHERICHIA COLI; HYDROGEN BOND; HYDROLYSIS; PH; PRIORITY JOURNAL; PROTON TRANSPORT; VISCOSITY;

CATALYSIS; CYTOSINE; CYTOSINE DEAMINASE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GLUTAMIC ACID; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; KINETICS; MODELS, MOLECULAR; ZINC;

EID: 79958058125     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi200483k     Document Type: Article

References (35)

1. Ireton, G. C., McDermott, G., Black, M. E., and Stoddard, B. L. (2002) The structure of Escherichia coli cytosine deaminase J. Mol. Biol. 315, 687-697 (Pubitemid 34729319)
2. Seibert, C. M. and Raushel, F. M. (2005) Structural and catalytic diversity within the amidohydrolase superfamily Biochemistry 44, 6383-6391 (Pubitemid 40593789)
3. Holm, L. and Sander, C. (1997) An evolutionary treasure: unification of a broad set of amidohydrolases related to urease Proteins 28, 72-82 (Pubitemid 27194020)
4. Xiang, D. F., Patskovsky, Y., Xu, C., Fedorov, A. A., Fedorov, E. V., Sisco, A. A., Sauder, J. M., Burley, S. K., Almo, S. C., and Raushel, F. M. (2010) Functional identification and structure determination of two novel prolidases from cog1228 in the amidohydrolase superfamily Biochemistry 49, 6791-6803
5. Maynes, J. T., Yuan, R. G., and Snyder, F. F. (2000) Identification, expression, and characterization of Escherichia coli guanine deaminase J. Bacteriol. 182, 4658-4660 (Pubitemid 30599835)
6. Wilson, D. K., Rudolph, F. B., and Quiocho, F. A. (1991) Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations Science 252, 1278-1284 (Pubitemid 21917036)
7. Hermann, J. C., Marti-Arbona, R., Fedorov, A. A., Fedorov, E., Almo, S. C., Shoichet, B. K., and Raushel, F. M. (2007) Structure-based activity prediction for an enzyme of unknown function Nature 448, 775-779 (Pubitemid 47266333)
8. Marti-Arbona, R., Xu, C., Steele, S., Weeks, A., Kuty, G. F., Seibert, C. M., and Raushel, F. M. (2006) Annotating enzymes of unknown function: N-formimino-L-glutamate deiminase is a member of the amidohydrolase superfamily Biochemistry 45, 1997-2005 (Pubitemid 43271299)
9. Hall, R. S., Fedorov, A. A., Marti-Arbona, R., Fedorov, E. V., Kolb, P., Sauder, J. M., Burley, S. K., Shoichet, B. K., Almo, S. C., and Raushel, F. M. (2010) The hunt for 8-oxoguanine deaminase J. Am. Chem. Soc. 132, 1762-1763
10. Hall, R. S., Agarwal, R., Hitchcock, D., Sauder, J. M., Burley, S. K., Swaminathan, S., and Raushel, F. M. (2010) Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase Biochemistry 49, 4374-4382
11. Porter, D. J. and Austin, E. A. (1993) Cytosine deaminase. The roles of divalent metal ions in catalysis J. Biol. Chem. 268, 24005-24011 (Pubitemid 23335379)
12. 2+ holoenzyme are similar Biochim. Biophys. Acta, Protein Struct. Mol. Enzymol. 1476, 239-252 (Pubitemid 30089189)
13. Fuchita, M., Ardiani, A., Zhao, L., Serve, K., Stoddard, B. L., and Black, M. E. (2009) Bacterial cytosine deaminase mutants created by molecular engineering show improved 5-fluorocytosine-mediated cell killing in vitro and in vivo Cancer Res. 69, 4791-4799
14. Mahan, S. D., Ireton, G. C., Knoeber, C., Stoddard, B. L., and Black, M. E. (2004) Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy Protein Eng. Des. Sel. 17, 625-633 (Pubitemid 39665399)
15. Huber, B. E., Austin, E. A., Richards, C. A., Davis, S. T., and Good, S. S. (1994) Metabolism of 5-fluorocytosine to 5-fluorouracil in human colorectal tumor cells transduced with the cytosine deaminase gene: significant antitumor effects when only a small percentage of tumor cells express cytosine deaminase Proc. Natl. Acad. Sci. U.S.A. 91, 8302-8306
16. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., and Mori, H. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection Mol. Syst. Biol. 2, 2006.0008
17. Brookes, P. and Lawley, P. D. (1962) The methylation of cytosine and cytidine J. Chem. Soc. 1348-1351
18. Kaneko, K., Katayama, H., Wakabayashi, T., and Kumonaka, T. (1988) Pyrimidine-derivatives 0.1. The highly regioselective 4-thionation of pyrimidine-2,4(1h,3h)-dione derivatives with Lawesson reagent Synthesis (Stuttgart) 152-154 (Pubitemid 18033537)
19. Kazimier., Z., Shugar, D., and Lipski, M. (1972) Intermediates in the synthesis of purines and pteridines-Selective hydrolysis of chloropyrimidines Acta Biochim. Pol. 19, 359-&
20. Bartlett, P. A., Hunt, J. T., Adams, J. L., and Gehret, J. C. E. (1978) Phosphorus-containing purines and pyrimidines: a new class of transition-state analogs Bioorg. Chem. 7, 421-436
21. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276, 307-326 (Pubitemid 27085611)
22. Long, F., Vagin, A. A., Young, P., and Murshudov, G. N. (2008) BALBES: a molecular-replacement pipeline Acta Crystallogr., Sect. D: Biol. Crystallogr. 64, 125-132 (Pubitemid 350308686)
23. Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics Acta Crystallogr., Sect. D: Biol. Crystallogr. 60, 2126-2132 (Pubitemid 41742764)
24. Adams, P. D., Afonine, P. V., Bunkoczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L. W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C., and Zwart, P. H. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr., Sect. D: Biol. Crystallogr. 66, 213-221
25. Lamzin, V. S. and Wilson, K. S. (1993) Automated refinement of protein models Acta Crystallogr., Sect. D: Biol. Crystallogr. 49, 129-147
26. Porter, D. J. and Austin, E. A. (1993) Cytosine deaminase. The roles of divalent metal ions in catalysis J. Biol. Chem. 268, 24005-24011 (Pubitemid 23335379)
27. Ganguly, S. and Kundu, K. K. (1994) Protonation/deprotonation energetics of uracil, thymine and cytosine in water from e.m.f/spectrophotometric measurements Can. J. Chem. 72, 1120-1126 (Pubitemid 24212247)
28. Morrison, J. F. (1969) Kinetics of the reversible inhibition of enzyme-catalysed reactions by tight-binding inhibitors Biochim. Biophys. Acta 185, 269-286
29. Sculley, M. J., Morrison, J. F., and Cleland, W. W. (1996) Slow-binding inhibition: the general case Biochim. Biophys. Acta 1298, 78-86 (Pubitemid 26390921)
30. Wang, Z. and Quiocho, F. A. (1998) Complexes of adenosine deaminase with two potent inhibitors: X-ray structures in four independent molecules at pH of maximum activity Biochemistry 37, 8314-8324 (Pubitemid 28275450)
31. Brouwer, A. C. and Kirsch, J. F. (1982) Investigation of diffusion-limited rates of chymotrypsin reactions by viscosity variation Biochemistry 21, 1302-1307
32. St Maurice, M. and Bearne, S. L. (2002) Kinetics and thermodynamics of mandelate racemase catalysis Biochemistry 41, 4048-4058 (Pubitemid 34251044)
33. Merkler, D. J. and Schramm, V. L. (1993) Catalytic mechanism of yeast adenosine 5′-monophosphate deaminase. Zinc content, substrate specificity, pH studies, and solvent isotope effects Biochemistry 32, 5792-5799 (Pubitemid 23175681)
34. Weiss, P. M., Cook, P. F., Hermes, J. D., and Cleland, W. W. (1987) Evidence from nitrogen-15 and solvent deuterium isotope effects on the chemical mechanism of adenosine deaminase Biochemistry 26, 7378-7384
35. Cleland, W. W. (1992) Low-barrier hydrogen bonds and low fractionation factor bases in enzymatic reactions Biochemistry 31, 317-319