A novel structure of an antikinase and its inhibitor

Journal of Molecular Biology

Volumn 405, Issue 1, 2011, Pages 214-226

  Jacques, David A ^a   Langley, David B ^a   Hynson, Robert M G ^a   Whitten, Andrew E ^b   Kwan, Ann ^a   Guss, J Mitchell ^a   Trewhella, Jill ^a  

^a UNIVERSITY OF SYDNEY   (Australia)

^b AUSTRALIAN NUCLEAR SCIENCE AND TECHNOLOGY ORGANISATION   (Australia)

Author keywords

allophanate hydrolase; cyclophilin; histidine kinase inhibitor; KipA; KipI; protein structure

Indexed keywords

CYCLOPHILIN; INHIBITOR PROTEIN; KIPA PROTEIN; KIPI PROTEIN; PROTEIN HISTIDINE KINASE; TTHA0988; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS SUBTILIS; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; ENZYME INACTIVATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SMALL ANGLE SCATTERING; SPOROGENESIS; THERMUS THERMOPHILUS;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); THERMUS THERMOPHILUS;

EID: 78650419881     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.10.047     Document Type: Article

References (44)

1. Piggot P.J., and Hilbert D.W. Sporulation of Bacillus subtilis Curr. Opin. Microbiol. 7 2004 579 586
2. Burbulys D., Trach K.A., and Hoch J.A. Initiation of sporulation in B. subtilis is controlled by a multicomponent phosphorelay Cell 64 1991 545 552
3. Burkholder W.F., Kurtser I., and Grossman A.D. Replication initiation proteins regulate a developmental checkpoint in Bacillus subtilis Cell 104 2001 269 279
4. Veening J.W., Murray H., and Errington J. A mechanism for cell cycle regulation of sporulation initiation in Bacillus subtilis Genes Dev. 23 2009 1959 1970
5. Wang L., Grau R., Perego M., and Hoch J.A. A novel histidine kinase inhibitor regulating development in Bacillus subtilis Genes Dev. 11 1997 2569 2579
6. Yoshida K., Yamaguchi H., Kinehara M., Ohki Y.H., Nakaura Y., and Fujita Y. Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box Mol. Microbiol. 49 2003 157 165
7. Whitten A.E., Jacques D.A., Hammouda B., Hanley T., King G.F., and Guss J.M. The structure of the KinA-Sda complex suggests an allosteric mechanism of histidine kinase inhibition J. Mol. Biol. 368 2007 407 420
8. Jacques D.A., Langley D.B., Jeffries C.M., Cunningham K.A., Burkholder W.F., Guss J.M., and Trewhella J. histidine kinase regulation by a cyclophilin-like inhibitor J. Mol. Biol. 384 2008 422 435
9. Bick M.J., Lamour V., Rajashankar K.R., Gordiyenko Y., Robinson C.V., and Darst S.A. How to switch off a histidine kinase: crystal structure of Geobacillus stearothermophilus KinB with the inhibitor Sda J. Mol. Biol. 386 2009 163 177
10. Rowland S.L., Burkholder W.F., Cunningham K.A., Maciejewski M.W., Grossman A.D., and King G.F. Structure and mechanism of action of Sda, an inhibitor of the histidine kinases that regulate initiation of sporulation in Bacillus subtilis Mol. Cell 13 2004 689 701
11. Wang P., and Heitman J. The cyclophilins Genome Biol. 6 2005 226
12. Marina A., Waldburger C.D., and Hendrickson W.A. Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein EMBO J. 24 2005 4247 4259
13. Jacques D.A., and Trewhella J. Small-angle scattering for structural biology-expanding the frontier while avoiding the pitfalls Protein Sci. 19 2010 642 657
14. Guinier A. The diffusion of x-rays under the extremely weak angles applied to the study of fine particles and colloidal suspension C. R. Hebd. Seances Acad. Sci. 206 1938 1374 1376
15. Moore P.B. Small-angle scattering-information-content and error analysis J. Appl. Crystallogr. 13 1980 168 175
16. Chen L., Oughtred R., Berman H.M., and Westbrook J. TargetDB: a target registration database for structural genomics projects Bioinformatics 20 2004 2860 2862
17. Petoukhov M.V., and Svergun D.I. Global rigid body modeling of macromolecular complexes against small-angle scattering data Biophys. J. 89 2005 1237 1250
18. Holm L., and Rosenstrom P. Dali server: conservation mapping in 3D Nucleic Acids Res. 38 Suppl 2010 W545 W549
19. Van Duyne G.D., Ghosh G., Maas W.K., and Sigler P.B. Structure of the oligomerization and l-arginine binding domain of the arginine repressor of Escherichia coli J. Mol. Biol. 256 1996 377 391
20. Lombardia E., Rovetto A.J., Arabolaza A.L., and Grau R.R. A LuxS-dependent cell-to-cell language regulates social behavior and development in Bacillus subtilis J. Bacteriol. 188 2006 4442 4452
21. Montanier C., Money V.A., Pires V.M., Flint J.E., Pinheiro B.A., and Goyal A. The active site of a carbohydrate esterase displays divergent catalytic and noncatalytic binding functions PLoS Biol. 7 2009 e71
22. Basak A.K., Gouet P., Grimes J., Roy P., and Stuart D. Crystal structure of the top domain of African horse sickness virus VP7: comparisons with bluetongue virus VP7 J. Virol. 70 1996 3797 3806
23. Rajavel M., Mitra A., and Gopal B. Role of Bacillus subtilis BacB in the synthesis of bacilysin J. Biol. Chem. 284 2009 31882 31892
24. Ikura T., and Ito N. Requirements for peptidyl-prolyl isomerization activity: a comprehensive mutational analysis of the substrate-binding cavity of FK506-binding protein 12 Protein Sci. 16 2007 2618 2625
25. Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., and Baba M. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection Mol. Syst. Biol. 2 2006 2006 2008
26. Hynson, R. M., Kwan, A. H., Jacques, D. A., Mackay, J. P. & Trewhella, J. (1)H, (13)C and (15)N backbone and side chain resonance assignments of the N-terminal domain of the histidine kinase inhibitor KipI from Bacillus subtilis. Biomol NMR Assign.
27. Yokoyama S., Hirota H., Kigawa T., Yabuki T., Shirouzu M., and Terada T. Structural genomics projects in Japan Nat. Struct. Biol. 7 Suppl 2000 943 945
28. Glinka C.J., Barker J.G., Hammouda B., Krueger S., Moyer J.J., and Orts W.J. The 30 m small-angle neutron scattering instruments at the National Institute of Standards and Technology J. Appl. Crystallogr. 31 1998 430 445
29. Konarev P., Volkov V.V., Sokolova A.V., Koch M.H.J., and Svergun D.I. Primus: a Windows PC-based system for small-angle scattering data analysis J. Appl. Crystallogr. 36 2003 1277 1282
30. Svergun D. Determination of the regularization parameter in indirect-transform methods using perceptual criteria J. Appl. Crystallogr. 25 1992 495 503
31. Whitten A.E., Cai S.Z., and Trewhella J. MULCh: modules for the analysis of small-angle neutron contrast variation data from biomolecular assemblies J. Appl. Crystallogr. 41 2008 222 226
32. Svergun D.I., Barberato C., and Koch M.H. CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates J. Appl. Crystallogr. 28 1995 768 773
33. Svergun D.I., Richard S., Koch M.H.J., Sayers Z., Kuprin S., and Zaccai G. Protein hydration in solution: Experimental observation by x-ray and neutron scattering Proc. Natl Acad. Sci. USA 95 1998 2267 2272
34. Goddard T.D., and Kneller D.G. SPARKY 3 2005 University of California San Francisco
35. Cornilescu G., Delaglio F., and Bax A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology J. Biomol. NMR 13 1999 289 302
36. Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin T.E., and Nilges M. ARIA2: automated NOE assignment and data integration in NMR structure calculation Bioinformatics 23 2007 381 382
37. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
38. Laskowski R.A., Rullmannn J.A., MacArthur M.W., Kaptein R., and Thornton J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR J. Biomol. NMR 8 1996 477 486
39. Koradi, R., Billeter, M. & Wuthrich, K. (1996). MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-5, 29-32.
40. McPhillips T.M., McPhillips S.E., Chiu H.J., Cohen A.E., Deacon A.M., and Ellis P.J. Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines J. Synchrotron. Radiat. 9 2002 401 406
41. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode Macromol. Crystallogr., Part A 276 1997 307 326
42. McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., and Read R.J. Phaser crystallographic software J. Appl. Crystallogr. 40 2007 658 674
43. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr., Sect D: Biol. Crystallogr. 53 1997 240 255
44. Davis I.W., Leaver-Fay A., Chen V.B., Block J.N., Kapral G.J., and Wang X. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Nucleic Acids Res. 35 2007 W375 W383