Structural and functional analyses of Mycobacterium tuberculosis Rv3315c-encoded metal-dependent homotetrameric cytidine deaminase

Journal of Structural Biology

Volumn 169, Issue 3, 2010, Pages 413-423

  Sánchez Quitian, Zilpa A ^a   Schneider, Cristopher Z ^a   Ducati, Rodrigo G ^a,b   de Azevedo Jr , Walter F ^a   Bloch Jr , Carlos ^c   Basso, Luiz A ^a   Santos, Diógenes S ^a  

^a PONTIFICAL CATHOLIC UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^b FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^c EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

Author keywords

Crystal structure; Cytidine deaminase; Enzyme kinetics; Metalloenzyme; Mycobacterium tuberculosis; Pyrimidine salvage pathway

Indexed keywords

CYTIDINE; CYTIDINE DEAMINASE; DEOXYCYTIDINE; ZINC ION;

AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL GENE; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME BINDING; ENZYME STRUCTURE; GEL FILTRATION CHROMATOGRAPHY; MASS SPECTROMETRY; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; STEADY STATE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; CYTIDINE DEAMINASE; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HYDROGEN-ION CONCENTRATION; KINETICS; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID; SPECTROPHOTOMETRY, ATOMIC; ZINC;

ESCHERICHIA COLI; MYCOBACTERIUM TUBERCULOSIS;

EID: 76749150421     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2009.12.019     Document Type: Article

References (48)

1. Ashley G.W., and Bartlett P.A. Purification and properties of cytidine deaminase from Escherichia coli. J. Biol. Chem. 259 (1984) 13615-13620
2. Ashley G.W., and Bartlett P.A. Inhibition of Escherichia coli cytidine deaminase by a phosphapyrimidine nucleoside. J. Biol. Chem. 259 (1984) 13621-13627
3. Betts L., Xiang S., Short S.A., Wolfenden R., and Carter C.W. Cytidine deaminase. The 2.3 Å crystal structure of an enzyme: transition-state analog complex. J. Mol. Biol. 235 (1994) 635-656
4. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72 (1976) 248-254
5. Braibant M., Gilot P., and Content J. The ATP binding cassette (ABC) transport systems of Mycobacterium tuberculosis. FEMS Microbiol. Rev. 24 (2000) 449-467
6. Brand G.D., Krause F.C., Silva L.P., Leite J.R., Melo J.A., Prates M.V., Pesquero J.B., Santos E.L., Nakaie C.R., Costa-Neto C.M., and Bloch Jr. C. Bradykinin related peptides from Phyllomedusa hypochondrialis. Peptides 27 (2006) 2137-2146
7. Carlow D.C., Carter C.W., Mejhede N., and Wolfenden R. Cytidine deaminases from B. subtilis and E. coli: compensating effects of changing zinc coordination and quaternary structure. Biochemistry 38 (1999) 12258-12265
8. Carter C.W. The nucleoside deaminases for cytidine and adenosine: structure, transition state stabilization, mechanism, and evolution. Biochimie 77 (1995) 92-98
9. CCP4, Collaborative computational project number 4, Acta Cryst. D 50 (1994) 760-763.
10. Centers for Disease Control and Prevention (CDC). Emergence of Mycobacterium tuberculosis with extensive resistance to second-line drugs worldwide, 2000-2004. Morb. Mortal. Wkly. Rep. 55 (2006) 301-305
11. Chung S.J., Fromme J.C., and Verdine G.L. Structure of human cytidine deaminase bound to a potent inhibitor. J. Med. Chem. 48 (2005) 658-660
12. Cohen R.M., and Wolfenden R. Cytidine deaminase Escherichia coli. J. Biol. Chem. 246 (1971) 7561-7565
13. Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry III C.E., Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R., Devlin K., Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., and Barrell B.G. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393 (1998) 537-544
14. Cook P.F., and Cleland W.W. PH Dependence of kinetic parameters and isotope effects. In: Cook P.F., and Cleland W.W. (Eds). Enzyme Kinetics and Mechanisms (2007), Garland Science, London and New York 325-366
15. Dye C., Scheele S., Dolin P., Pathania V., and Raviglione M.C. Global burden of tuberculosis: Estimated incidence, prevalence, and mortality by country. WHO Global Surveillance and Monitoring Project. J. Am. Med. Ass. 282 (1999) 677-686
16. Englard S., and Seifter S. Precipitation techniques. Methods Enzymol. 182 (1990) 285-300
17. Grossman T.H., Kawasaki E.S., Punreddy S.R., and Osburne M.S. Spontaneous cAMP-dependent derepression of gene expression in stationary phase plays a role in recombinant expression instability. Gene 209 (1998) 95-103
18. Hingley-Wilson S.M., Sambandamurthy V.K., and Jacobs Jr. W.R. Survival perspectives from the world's most successful pathogen, Mycobacterium tuberculosis. Nat. Immunol. 4 (2003) 949-955
19. Hirel P.H., Schmitter M.J., Dessen P., Fayat G., and Blanquet S. Extent of N-terminal methionine excision from Escherichia coli proteins is governed by the side-chain length of the penultimate amino acid. Proc. Natl. Acad. Sci. USA 86 (1989) 8247-8251
20. Humphrey W., Dalke A., and Schulten K. VMD - visual molecular dynamics. J. Mol. Graph. 14 (1996) 33-38
21. Hyde J.E. Targeting purine and pyrimidine metabolism in human apicomplexan parasites. Curr. Drug Targets 8 (2007) 31-47
22. Itapa P.L., Cercignani G., and Balestreri E. Partial purification and properties of Cytidine deaminase from Baker's yeast. Biochemistry 9 (1970) 3390-3395
23. Jain A., and Mondal R. Extensively drug-resistant tuberculosis: current challenges and threats. FEMS Immunol. Med. Microbiol. 53 (2008) 145-150
24. Jancarik J., and Kim S.-H. Sparse matrix sampling: a screening method for crystallization of proteins. J. Appl. Cryst. 24 (1991) 409-411
25. Johansson E., Mejlhede N., and Larsen S. Crystal structure of the cytidine deaminase from Bacillus subtilis at 2.0 Å resolution. Biochemistry 41 (2002) 2563-2570
26. Johansson E., Neuhard J., Willemoe M., and Larsen S. Structural, kinetic, and mutational studies of the zinc ion environment in tetrameric cytidine deaminase. Biochemistry 43 (2004) 6020-6029
27. Kelley K.C., Huestis K.J., Austen D.A., Sanderson C.T., Donohue M.A., Stickel S.K., Kawasaki E.S., and Osburne M.S. Regulation of CD4-183 gene expression from phage-T7-based vectors in Escherichia coli. Gene 156 (1995) 33-36
28. Laemmli U.K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227 (1970) 680-685
29. Lesley S.A., Kuhn P., Godzik A., Deacon A.M., Mathews I., Kreusch A., Spraggon G., Klock H.E., McMullan D., Shin T., Vincent J., Robb A., Brinen L.S., Miller M.D., McPhillips T.M., Miller M.A., Scheibe D., Canaves J.M., Guda C., Jaroszewski L., Selby T.L., Elsliger M.A., Wooley J., Taylor S.S., Hodgson K.O., Wilson I.A., Schultz P.G., and Stevens R.C. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc. Natl. Acad. Aci. USA 99 (2002) 11664-11669
30. Mizrahi V., Buckstein M., and Rubin H. Nucleic acid metabolism. In: Cole S.T., Eisenach K.D., McMurray D.N., and Jacobs Jr. W.R. (Eds). Tuberculosis and the Tubercle Bacillus (2005), ASM Press, Washington, DC 369-378
31. Oliveira J.S., Pinto C.A., Basso L.A., and Santos D.S. Cloning and overexpression in soluble form of functional shikimate kinase and 5-enolpyruvylshikimate 3-phosphate synthase enzymes from Mycobacterium tuberculosis. Protein Expr. Purif. 22 (2001) 430-435
32. Rizzi C., Frazzon J., Ely F., Weber P.G., Fonseca I.O., Gallas M., Oliveira J.S., Mendes M.A., Souza B.M., Palma M.S., Santos D.S., and Basso L.A. DAHP synthase from Mycobacterium tuberculosis H37Rv: cloning, expression, and purification of functional enzyme. Protein Expr. Purif. 40 (2005) 23-30
33. Sambrook J., and Russell D.W. Molecular Cloning a Laboratory Manual (2001), Cold Spring Harbor Laboratory Press, New York
34. Shambaugh G.E. Pyrimidine biosynthesis. Am. J. Clin. Nutr. 32 (1979) 1290-1297
35. Silva R.G., Carvalho L.P., Oliveira J.S., Pinto C.A., Mendes M.A., Palma M.S., Basso L.A., and Santos D.S. Cloning, overespression, and purification of functional human purine nucleoside phosphorylase. Protein Exp. Purif. 27 (2003) 158-164
36. Song B.H., and Neuhard J. Chromosomal location, cloning and nucleotide sequence of the Bacillus subtilis cdd gene encoding cytidine/deoxycytidine deaminase. Mol. Gen. Genet. 216 (1989) 462-468
37. Studier F.W. Protein production by auto-induction in high-density shaking cultures. Protein Expr. Purif. 41 (2005) 207-234
38. Taylor Ringia E.A., Tyler P.C., Evans G.B., Furneaux R.H., Murkin A.S., and Schramm V.L. Transition state analogue discrimination by related purine nucleoside phosphorylases. J. Am. Chem. Soc. 128 (2006) 7126-7127
39. WHO/Stop TB Partnership. The Global Stop TB 2006-2015. WHO/HTM/STB/2006.35, World Health Organization. Available from: .
40. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
41. Thomsen R., and Christensen M.H. MolDock: a new technique for high-accuracy molecular docking. J. Med. Chem. 49 (2006) 3315-3321
42. Traut T.W. Physiological concentrations of purines and pyrimidines. Mol. Cell. Biochem. 140 (1994) 1-22
43. Trimble R.B., and Maley F. Metabolism of 4-N-hydroxy-cytidine in Escherichia coli. J. Bacteriol. 108 (1971) 145-153
44. Vicentelli R., Bignon C., Gruez A., Canaan S., Sulzenbacher G., Tegoni M., Campanacci V., and Cambillau C. Medium-scale structural genomics: strategies for protein expression and crystallization. Acc. Chem. Res. 36 (2003) 197-225
45. Vincenzetti S., Cambi A., Neuhard J., Garattini E., and Vita A. Recombinant human cytidine deaminase: expression, purification, and characterization. Prot. Protein Exp. Purif. 8 (1996) 247-253
46. Vita A., Cacciamani T., Natalini P., Puggieri S., and Magn G. Cytidine deaminase from human spleen. Adv. Exp. Med. Biol. 253 (1989) 71-77
47. Wentworth D.F., and Wolfenden R. On the interaction of 3,4,5,6-tetrahydrouridine with human liver cytidine deaminase. Biochemistry 14 (1975) 5099-5105
48. Wheeler P.R. Biosynthesis and scavenging of pyrimidines by pathogenic mycobacteria. J. Gen. Microbiol. 136 (1990) 189-201