Role of a PAS sensor domain in the Mycobacterium tuberculosis transcription regulator Rv1364c

Biochemical and Biophysical Research Communications

Volumn 398, Issue 3, 2010, Pages 342-349

  Jaiswal, Ravi Kumar ^a   Manjeera, G ^a   Gopal, B ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Dimerization; Environmental sensor; PAS; Rv1364c; Transcriptional regulator

Indexed keywords

AROMATIC HYDROCARBON RECEPTOR; BACTERIAL PROTEIN; CARRIER PROTEIN; HOMODIMER; PERIOD CLOCK PROTEIN; PHOSPHATASE; PROTEIN PAS; SIGMA FACTOR; SINGLE MINDED PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENOME; BIOSENSOR; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DIMERIZATION; GENE CONTROL; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; RAT; REGULATORY MECHANISM; SIGNAL TRANSDUCTION; STRESS; THERMOSTABILITY; TRANSCRIPTION REGULATION; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY; PROTEIN-SERINE-THREONINE KINASES; SCATTERING, SMALL ANGLE; SIGMA FACTOR; TRANSCRIPTION FACTORS;

MYCOBACTERIUM TUBERCULOSIS;

EID: 77955275743     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2010.06.027     Document Type: Article

References (35)

1. Gebhard S., Humpel A., McLellan A.D., Cook G.M. The alternative sigma factor SigF of Mycobacterium smegmatis is required for survival of heat shock, acidic pH and oxidative stress. Microbiology 2008, 154:2786-2795.
2. Sachdeva P., Narayan A., Misra R., Brahmachari V., Singh Y. Loss of kinase activity in Mycobacterium tuberculosis multidomain protein Rv1364c. FEBS J. 2008, 275:6295-6308.
3. Parida B.K., Douglas T., Nino C., Dhandayuthapani S. Interactions of anti-sigma factor antagonists of Mycobacterium tuberculosis in the yeast two-hybrid system. Tuberculosis 2005, 85:347-355.
4. Greenstein A.E., Hammel M., Cavazos A., Alber T. Interdomain communication in the Mycobacterium tuberculosis environmental phosphatase Rv1364c. J. Biol. Chem. 2009, 284:29828-29835.
5. Moglich A., Ayers R.A., Moffat K. Structure and signaling mechanism of Per-ARNT-Sim domains. Structure 2009, 17:1282-1294.
6. Zhulin I.B., Taylor B.L., Dixon R. PAS domain S-boxes in archaea, bacteria and sensors for oxygen and redox. Trends Biochem. Sci. 1997, 22:331-333.
7. Taylor B.L., Zhulin I.B. PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev. 1999, 63:479-506.
8. A.G.W. Leslie, Recent changes to the MOSFLM package for processing film and image plate data, Joint CCP4+ESF-EAMCB Newsletter on Protein Crystallography, vol. 26, 1992.
9. The CCP4 suite: programs for protein crystallography, Acta Crystallogr., Sect D 50 (1994) 760-763.
10. Adams P.D., Grosse-Kunstleve R.W., Hung L.W., Ioerger T.R., McCoy A.J., Moriarty N.W., Read R.J., Sacchettini J.C., Sauter N.K., Terwilliger T.C. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr., Sect. D 2002, 58:1948-1954.
11. Painter J., Merritt E.A. TLSMD web server for the generation of multi-group TLS models. J. Appl. Crystallogr. 2006, 39:109-111.
12. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr., Sect. D 2004, 60:2126-2132.
13. de Groot B.L., van Aalten D.M.F., Scheek R.M., Amadei A., Vriend G., Berendsen H.J.C. Prediction of protein conformational freedom from distance constraints. Proteins: Structure, Function, and Genetics 1997, 29:240-251.
14. Vreede J., van der Horst M.A., Hellingwerf K.J., Crielaard W., van Aalten D.M.F. PAS domains: common structure and common flexibility. J. Biol. Chem. 2003, 278:18434-18439.
15. Lindahl E., Hess B., van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model 2001, 7:306-317.
16. J. Felsenstein, PHYLIP (Phylogeny Inference Package) Version 3.6, Department of Genome Sciences, University of Washington, Seattle, 2005.
17. Park H., Suquet C., Satterlee J.D., Kang C. Insights into signal transduction involving PAS domain oxygen-sensing heme proteins from the X-ray crystal structure of Escherichia coli Dos heme domain (Ec DosH). Biochemistry 2004, 43:2738-2746.
18. Miyatake H., Mukai M., Park S.Y., Adachi S., Tamura K., Nakamura H., Nakamura K., Tsuchiya T., Iizuka T., Shiro Y. Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies. J. Mol. Biol. 2000, 301:415-431.
19. Key J., Hefti M., Purcell E.B., Moffat K. Structure of the redox sensor domain of Azotobacter vinelandii NifL at atomic resolution: signaling, dimerization, and mechanism. Biochemistry 2007, 46:3614-3623.
20. Gong W., Hao B., Mansy S.S., Gonzalez G., Gilles-Gonzalez M.A., Chan M.K. Structure of a biological oxygen sensor: a new mechanism for heme-driven signal transduction. Proc. Natl. Acad Sci. USA 1998, 95:15177-15182.
21. Scheuermann T.H., Tomchick D.R., Machius M., Guo Y., Bruick R.K., Gardner K.H. Artificial ligand binding within the HIF2alpha PAS-B domain of the HIF2 transcription factor. Proc. Natl. Acad. Sci. USA 2009, 106:450-455.
22. O'Brien P.J., Herschlag D. Functional interrelationships in the alkaline phosphatase superfamily: phosphodiesterase activity of Escherichia coli alkaline phosphatase. Biochemistry 2001, 40:5691-5699.
23. R.B. McComb, G.N. Bowser Jr., S. Posen, Alkaline Phosphatase, Plenum Press, New York, 1979.
24. Fedorov R., Schlichting I., Hartmann E., Domratcheva T., Fuhrmann M., Hegemann P. Crystal structures and molecular mechanism of a light-induced signaling switch: the Phot-LOV1 domain from Chlamydomonas reinhardtii. Biophys. J. 2003, 84:2474-2482.
25. Rajagopal S., Moffat K. Crystal structure of a photoactive yellow protein from a sensor histidine kinase: conformational variability and signal transduction. Proc. Natl. Acad. Sci. USA 2003, 100:1649-1654.
26. Getzoff E.D., Gutwin K.N., Genick U.K. Anticipatory active-site motions and chromophore distortion prime photoreceptor PYP for light activation. Nat. Struct. Biol. 2003, 10:663-668.
27. C.E. Timothy L. Bailey, Fitting a mixture model by expectation maximization to discover motifs in biopolymers, in: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, California, 1994, pp. 28-36.
28. Dundas J., Ouyang Z., Tseng J., Binkowski A., Turpaz Y., Liang J. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucl. Acids Res. 2006, 34:116-118.
29. Li M.S., Waddell S.J., Monahan I.M., Mangan J.A., Martin S.L., Everett M.J., Butcher P.D. Increased transcription of a potential sigma factor regulatory gene Rv1364c in Mycobacterium bovis BCG while residing in macrophages indicates use of alternative promoters. FEMS Microbiol. Lett. 2004, 233:333-339.
30. Chen P., Ruiz R.E., Li Q., Silver R.F., Bishai W.R. Construction and characterization of a Mycobacterium tuberculosis mutant lacking the alternate sigma factor gene, sigF. Infect. Immun. 2000, 68:5575-5580.
31. Beaucher J., Rodrigue S., Jacques P.E., Smith I., Brzezinski R., Gaudreau L. Novel Mycobacterium tuberculosis anti-sigma factor antagonists control sigmaF activity by distinct mechanisms. Mol. Microbiol. 2002, 45:1527-1540.
32. Malik S.S., Luthra A., Srivastava S.K., Ramachandran R. Mycobacterium tuberculosis UsfX (Rv3287c) exhibits novel nucleotide binding and hydrolysis properties. Biochem. Biophys. Res. Commun. 2008, 375:465-470.
33. Gutu A.D., Wayne K.J., Sham L.T., Winkler M.E. Kinetic characterization of the WalRKSpn (VicRK) two-component system of Streptococcus pneumoniae: dependence of WalKSpn (VicK) phosphatase activity on its PAS domain. J. Bacteriol. 2010, 192:2346-2358.
34. Moglich A., Moffat K. Structural basis for light-dependent signaling in the dimeric LOV domain of the photosensor YtvA. J. Mol. Biol. 2007, 373:112-126.
35. Maeda Y., Koga H., Yamada H., Ueda T., Imoto T. Effective renaturation of reduced lysozyme by gentle removal of urea. Protein Eng. 1995, 8:201-205.