Mechanism of Phosphoryl Transfer Catalyzed by Shikimate Kinase from Mycobacterium tuberculosis

Journal of Molecular Biology

Volumn 364, Issue 3, 2006, Pages 411-423

  Hartmann, Marcus D ^a   Bourenkov, Gleb P ^a   Oberschall, Attila ^a   Strizhov, Nicolai ^a   Bartunik, Hans D ^a  

^a MAX PLANCK UNIT FOR STRUCTURAL MOLECULAR BIOLOGY   (Germany)

Author keywords

in line associative phosphotransfer; kinetic crystallography; P loop kinase; transition state; X ray crystal structure

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; ENZYME; NUCLEOTIDE; SHIKIMATE KINASE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; CATALYSIS; CHEMICAL REACTION; COMPARATIVE STUDY; CRYSTAL STRUCTURE; ENZYME CHEMISTRY; ENZYME STRUCTURE; MYCOBACTERIUM TUBERCULOSIS; PRIORITY JOURNAL; REACTION ANALYSIS;

MYCOBACTERIUM TUBERCULOSIS;

EID: 33751246776     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.09.001     Document Type: Article

References (39)

1. Roberts F., Roberts C.W., Johnson J.J., Kyle D.E., Krell T., Coggins J.R., et al. Evidence for the shikimate pathway in apicomplexan parasites. Nature 393 (1998) 801-805
2. Campbell S.A., Richards T.A., Mui E.J., Samuel B.U., Coggins J.R., McLeod R., and Roberts C.W. A complete shikimate pathway in Toxoplasma gondii: an ancient eukaryotic innovation. Int. J. Parasitol. 34 (2004) 5-13
3. Haslam E. Shikimic Acid: Metabolism and Metabolites (1993), Wiley, Chichester
4. Parish T., and Stoker N.G. The common aromatic amino acid biosynthesis pathway is essential in Mycobacterium tuberculosis. Microbiology 148 (2002) 3069-3077
5. Whipp M.J., and Pittard A.J. A reassessment of the relationship between aroK- and aroL-encoded shikimate kinase enzymes of Escherichia coli. J. Bacteriol. 177 (1995) 1627-1629
6. De Feyter R. Shikimate kinases from Escherichia coli K12. Methods Enzymol. 142 (1987) 355-361
7. Romanowski M.J., and Burley S.K. Crystal structure of the Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam. Proteins: Struct. Funct. Genet. 47 (2002) 558-562
8. Badger J., Sauder J.M., Adams J.M., Antonysamy S., Bain K., Bergseid M.G., et al. Structural analysis of a set of proteins resulting from a bacterial genomics project. Proteins: Struct. Funct. Genet. 60 (2005) 787-796
9. Cheng W.C., Chang Y.N., and Wang W.C. Structural basis for shikimate-binding specificity of Helicobacter pylori shikimate kinase. J. Bacteriol. 187 (2005) 8156-8163
10. Gan J., Gu Y., Li Y., Yan H., and Ji X. Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimic acid and an ATP analogue. Biochemistry 45 (2006) 8539-8545
11. Gu Y., Reshetnikova L., Li Y., Wu Y., Yan H., Singh S., and Ji X. Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis. J. Mol. Biol. 319 (2002) 779-789
12. Dhaliwal B., Nichols C.E., Ren J., Lockyer M., Charles I., Hawkins A.R., and Stammers D.K. Crystallographic studies of shikimate binding and induced conformational changes in Mycobacterium tuberculosis shikimate kinase. FEBS Letters 574 (2004) 49-54
13. Pereira J.H., de Oliveira J.S., Canduri F., Dias M.V., Palma M.S., Basso L.A., et al. Structure of shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid. Acta Crystallog. sect. D 60 (2004) 2310-2319
14. Madhusudan, Akamine P., Xuong N.H., and Taylor S.S. Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase. Nature Struct. Biol. 9 (2002) 273-277
15. Yan H., and Tsai M.D. Nucleoside monophosphate kinases: structure, mechanism, and substrate specificity. Advan. Enzymol. Relat. Areas Mol. Biol. 73 (1999) 103-134
16. Miron S., Munier-Lehmann H., and Craescu C.T. Structural and dynamic studies on ligand-free adenylate kinase from Mycobacterium tuberculosis revealed a closed conformation that can be related to the reduced catalytic activity. Biochemistry 43 (2004) 67-77
17. Mao L., Wang Y., Liu Y., and Hu X. Molecular determinants for ATP-binding in proteins: a data mining and quantum chemical analysis. J. Mol. Biol. 336 (2004) 787-807
18. Ostermann N., Schlichting I., Brundiers R., Konrad M., Reinstein J., Veit T., et al. Insights into the phosphoryltransfer mechanism of human thymidylate kinase gained from crystal structures of enzyme complexes along the reaction coordinate. Structure 8 (2000) 629-642
19. Knowles J.R. Enyzme-catalyzed phosphoryl transfer reactions. Annu. Rev. Biochemistry 49 (1980) 877-919
20. Holmes R.R. Pentacoordinated Phosphorous vol. 1 (1980), ACS Monograph, Town, Washington, DC 175
21. Abele U., and Schulz G.E. High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer. Protein Sci. 4 (1995) 1262-1271
22. Schlichting I., and Reinstein J. Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative. Biochemistry 36 (1997) 9290-9296
23. Fioravanti E., Haouz A., Ursby T., Munier-Lehmann H., Delarue M., and Bourgeois D. Mycobacterium tuberculosis thymidylate kinase: structural studies of intermediates along the reaction pathway. J. Mol. Biol. 327 (2003) 1077-1092
24. Krell T., Maclean J., Boam D.J., Cooper A., Resmini M., Brocklehurst K., et al. Biochemical and X-ray crystallographic studies on shikimate kinase: the important structural role of the P-loop lysine. Protein Sci. 10 (2001) 1137-1149
25. WHO Report. Global Tuberculosis Control. WHO/HTM/TB/2006.362 (2006)
26. Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393 (1998) 537-544
27. Popov A.N., and Bourenkov G.P. Choice of data-collection parameters based on statistic modelling. Acta Crystallog. sect. D 59 (2003) 1145-1153
28. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
29. Vagin A., and Teplyakov A. An approach to multi-copy search in molecular replacement. Acta Crystallog. sect. D 56 (2000) 1622-1624
30. Perrakis A., Morris R., and Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6 (1999) 458-463
31. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallog. sect. D 60 (2004) 2126-2132
32. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255
33. Laskowski R.A., McArthur M.W., Moss D.S., and Thornton J.M. PROCHECK, a programm to asses the validity of crystallographic models. J. Appl. Crystallog. 26 (1993) 283-291
34. Hooft R.W., Vriend G., Sander C., and Abola E.E. Errors in protein structures. Nature 381 (1996) 272
35. Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallog. sect. B 32 (1976) 922-923
36. Schneider T.R. A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta Crystallog. sect. D 58 (2002) 195-208
37. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24 (1991) 946-950
38. Esnouf R.M. Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallog. sect. D 55 (1999) 938-940
39. Merritt E.A., and Bacon D.J. Raster3D: Photorealistic Molecular Graphics. Methods Enzymol. 277 (1997) 505-524