Structural studies of thymidine kinases from Bacillus anthracis and Bacillus cereus provide insights into quaternary structure and conformational changes upon substrate binding

FEBS Journal

Volumn 274, Issue 3, 2007, Pages 727-737

  Kosinska, Urszula ^a   Carnrot, Cecilia ^a   Sandrini, Michael P B ^b   Clausen, Anders R ^b   Wang, Liya ^a   Piskur, Jure ^b   Eriksson, Staffan ^a   Eklund, Hans ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b LUND UNIVERSITY   (Sweden)

Author keywords

Deoxythymidine triphosphate; Dimer; Feedback inhibitor; Phosphate donor; Tetramer

Indexed keywords

BACTERIAL ENZYME; PHOSPHATE; PHOSPHATE BINDING PROTEIN; THYMIDINE; THYMIDINE KINASE; THYMIDINE TRIPHOSPHATE;

ARTICLE; BACILLUS ANTHRACIS; BACILLUS CEREUS; CONFORMATIONAL TRANSITION; ENZYME ANALYSIS; ENZYME CONFORMATION; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; HYDROGEN BOND; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; BACILLUS ANTHRACIS; BACILLUS CEREUS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; THYMIDINE KINASE;

BACILLUS ANTHRACIS; BACILLUS CEREUS; BACTERIA (MICROORGANISMS);

EID: 33846461153     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2006.05617.x     Document Type: Article

References (32)

1. Dixon TC, Meselson M, Guillemin J & Hanna PC (1999) Anthrax. N Engl J Med 341, 815-826.
2. Kotiranta A, Lounatmaa K & Haapasalo M (2000) Epidemiology and pathogenesis of Bacillus cereus infections. Microbes Infect 2, 189-198.
3. Okinaka R, Cloud K, Hampton O, Hoffmaster A, Hill K, Keim P, Koehler T, Lamke G, Kumano S, Manter D, et al. (1999) Sequence, assembly and analysis of pX01 and pX02. J Appl Microbiol 87, 261-262.
4. Okinaka RT, Cloud K, Hampton O, Hoffmaster AR, Hill KK, Keim P, Koehler TM, Lamke G, Kumano S, Mahillon J, et al. (1999) Sequence and organization of pXO1, the large Bacillus anthracis plasmid harboring the anthrax toxin genes. J Bacteriol 181, 6509-6515.
5. Sandrini MP, Clausen AR, Munch-Petersen B & Piskur J (2006) Thymidine kinase diversity in bacteria. Nucleosides Nucleotides Nucleic Acids 25, 1153-1158.
6. Johansson K, Ramaswamy S, Ljungcrantz C, Knecht W, Piskur J, Munch-Petersen B, Eriksson S & Eklund H (2001) Structural basis for substrate specificities of cellular deoxyribonucleoside kinases. Nat Struct Biol 8, 616-620.
7. Sabini E, Ort S, Monnerjahn C, Konrad M & Lavie A (2003) Structure of human dCK suggests strategies to improve anticancer and antiviral therapy. Nat Struct Biol 10, 513-519.
8. Birringer MS, Claus MT, Folkers G, Kloer DP, Schulz GE & Scapozza L (2005) Structure of a type II thymidine kinase with bound dTTP. FEBS Lett 579, 1376-1382.
9. Welin M, Kosinska U, Mikkelsen NE, Carnrot C, Zhu C, Wang L, Eriksson S, Munch-Petersen B & Eklund H (2004) Structures of thymidine kinase 1 of human and mycoplasmic origin. Proc Natl Acad Sci USA A101, 17970-17975.
10. Knecht W, Sandrini MP, Johansson K, Eklund H, Munch-Petersen B & Piskur J (2002) A few amino acid substitutions can convert deoxyribonucleoside kinase specificity from pyrimidines to purines. EMBO J 21, 1873-1880.
11. Eriksson S, Munch-Petersen B, Johansson K & Eklund H (2002) Structure and function of cellular deoxyribonucleoside kinases. Cell Mol Life Sci 59, 1327-1346.
12. Sandrini MP & Piskur J (2005) Deoxyribonucleoside kinases: two enzyme families catalyze the same reaction. Trends Biochem Sci 30, 225-228.
13. El Omari K, Solaroli N, Karlsson A, Balzarini J & Stammers DK (2006) Structure of vaccinia virus thymidine kinase in complex with dTTP: insights for drug design. BMC Struct Biol 6, 22.
14. Kosinska U, Carnrot C, Eriksson S, Wang L & Eklund H (2005) Structure of the substrate complex of thymidine kinase from Ureaplasma urealyticum and investigations of possible drug targets for the enzyme. FEBS J 272, 6365-6372.
15. Carnrot C, Vogel SR, Byun Y, Wang L, Tjarks W, Eriksson S & Phipps AJ (2006) Evaluation of Bacillus anthracis thymidine kinase as a potential target for the development of antibacterial nucleoside analogs. Biol Chem 387, 1575-1581.
16. Welin M, Wang J, Eriksson S & Eklund H. (2006) Structure-function analysis of a bacterial deoxyadenosine kinase reveals the basis for substrate specificity. J Mol Biol, doi: 10.1016/j.jmb.2006.12.010.
17. Kuzin AP, Abashidze M, Forouhar F, Vorobiev SM, Acton TB, Ma LC, Xiao R, Montelione GT, Tong L & Hunt JF. (2006) X-ray structure of Clostridium acetobutylicum thymidine kinase with ADP. Northeast Structural Genomics Target Car26, PDB code: 1XXX6.
18. Krissinel E & Henrick K (2005) Detection of protein assemblies in crystals. Lecture Notes in Computer Science: Computational Life Sciences: Proceedings of the First International Symposium, Complife2005, Konstanz, Germany, September 25-27, 2005 3695, 163-174.
19. Birringer MS, Perozzo R, Kut E, Stillhart C, Surber W, Scapozza L & Folkers G (2006) High-level expression and purification of human thymidine kinase 1: quaternary structure, stability, and kinetics. Protein Expr Purif 47, 506-515.
20. Black ME & Hruby DE (1990) Quaternary structure of vaccinia virus thymidine kinase. Biochem Biophys Res Commun 169, 1080-1086.
21. Carnrot C, Wehelie R, Eriksson S, Bolske G & Wang L (2003) Molecular characterization of thymidine kinase from Ureaplasma urealyticum: nucleoside analogues as potent inhibitors of mycoplasma growth. Mol Microbiol 50, 771-780.
22. Munch-Petersen B, Tyrsted G & Cloos L (1993) Reversible ATP-dependent transition between two forms of human cytosolic thymidine kinase with different enzymatic properties. J Biol Chem 268, 15621-15625.
23. Sherley JL & Kelly TJ (1988) Human cytosolic thymidine kinase. Purification and physical characterization of the enzyme from HeLa cells. J Biol Chem 263, 375-382.
24. Igarashi K, Hiraga S & Yura T (1967) A deoxythymidine kinase deficient mutant of Escherichia coli. II. Mapping and transduction studies with phage phi 80. Genetics 57, 643-654.
25. Collaborative Computational Project, number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50, 760-763.
26. Vagin A & Teplyakov A (1997) MOLREP: an automated program for molecular replacement. J Appl Crystallogr 30, 1022-1025.
27. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, et al. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54, 905-921.
28. Murshudov GN, Vagin AA & Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53, 240-255.
29. Jones TA, Zou JY, Cowan SW & Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr 47, 110-119.
30. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG & Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31, 3497-3500.
31. Barton GJ (1993) ALSCRIPT: a tool to format multiple sequence alignments. Protein Eng 6, 37-40.
32. DeLano WL (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA.