Crystal Structure of CO-sensing Transcription Activator CooA Bound to Exogenous Ligand Imidazole

Journal of Molecular Biology

Volumn 367, Issue 3, 2007, Pages 864-871

  Komori, Hirofumi ^a,b   Inagaki, Sayaka ^c,d   Yoshioka, Shiro ^c   Aono, Shigetoshi ^c   Higuchi, Yoshiki ^a,b  

^a UNIVERSITY OF HYOGO   (Japan)

^b RIKEN SPring 8 Center ^*  (Japan)

^c OKAZAKI INSTITUTE FOR INTEGRATIVE BIOSCIENCE   (Japan)

^d GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

CO sensor; CooA; DNA binding protein; heme protein; transcription regulation

Indexed keywords

CARBON MONOXIDE; DNA; IMIDAZOLE;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXYDOTHERMUS HYDROGENOFORMANS; CRYSTAL STRUCTURE; CRYSTALLIZATION; DNA BINDING; GENE ACTIVATION; GENETIC TRANSCRIPTION; LIGAND BINDING; NONHUMAN; PRIORITY JOURNAL; RECEPTOR BINDING; RHODOSPIRILLUM RUBRUM; SUBSTITUTION REACTION; THERMOPHILIC BACTERIUM;

CARBOXYDOTHERMUS HYDROGENOFORMANS; RHODOSPIRILLUM RUBRUM;

EID: 33847298449     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.01.043     Document Type: Article

References (31)

1. Chan M.K. Recent advances in heme-protein sensors. Curr. Opin. Chem. Biol. 336 (2001) 216-222
2. Aono S., Nakajima H., Saito K., and Okada M. A novel heme protein that acts as a carbon monoxide-dependent transcriptional activator in Rhodospirillum rubrum. Biochem. Biophys. Res. Commun. 228 (1996) 752-756
3. Shelver D., Kerby R.L., He Y., and Roberts G.P. CooA, a CO-sensing transcription factor from Rhodospirillum rubrum, is a CO-binding heme protein. Proc. Natl Acad. Sci. USA 94 (1997) 11216-11220
4. Aono S. Biochemical and biophysical properties of the CO-sensing transcriptional activator CooA. Accts Chem. Res. 36 (2003) 825-831
5. Roberts G.P., Kerby R.L., Youn H., and Conrad M. CooA, a paradigm for gas sensing regulatory proteins. J. Inorg. Biochem. 99 (2005) 280-292
6. Lanzilotta W.N., Schuller D.J., Thorsteinsson M.V., Kerby R.L., Roberts G.P., and Poulos T.L. Structure of the CO sensing transcription activator CooA. Nature Struct. Biol. 7 (2000) 876-880
7. McKay D.B., and Steitz T.A. Structure of catabolite gene activator protein at 2.9 Å resolution suggests binding to left-handed B-DNA. Nature 290 (1981) 744-749
8. Inagaki S., Masuda C., Akaishi T., Nakajima H., Yoshioka S., Ohta T., et al. Spectroscopic and redox properties of a CooA homologue from Carboxydothermus hydrogenoformans. J. Biol. Chem. 280 (2005) 3269-3274
9. Clark R.W., Lanz N.D., Lee A.J., Kerby R.L., Roberts G.P., and Burstyn J.N. Unexpected NO-dependent DNA binding by the CooA homolog from Carboxydothermus hydrogenoformans. Proc. Natl Acad. Sci. USA 103 (2006) 89186-89189
10. Youn H., Kerby R.L., Conrad M., and Roberts G.P. Functionally critical elements of CooA-related CO sensors. J. Bacteriol. 186 (2004) 1320-1329
11. Komori H., Satomoto K., Ueda Y., Shibata N., Inagaki S., Yoshioka S., et al. Crystallization and preliminary X-ray analysis of CooA from Carboxydothermus hydrogenoformans. Acta Crystallog. sect. F 62 (2006) 471-473
12. He Y., Gaal T., Karls R., Donohue T.J., Gourse R.L., and Roberts G.P. Transcription activation by CooA, the CO-sensing factor from Rhodospirillum rubrum. The interaction between CooA and the C-terminal domain of the alpha subunit of RNA polymerase. J. Biol. Chem. 274 (1999) 10840-10845
13. Aono S., Takasaki H., Unno H., Kamiya T., and Nakajima H. Recognition of target DNA and transcription activation by the CO-sensing transcriptional activator CooA. Biochem. Biophys. Res. Commun. 261 (1999) 270-275
14. Akiyama S., Fujisawa T., Ishimori K., Morishima I., and Aono S. Activation mechanisms of transcriptional regulator CooA revealed by small-angle X-ray scattering. J. Mol. Biol. 341 (2004) 651-668
15. Youn H., Kerby R.L., and Roberts G.P. Changing the ligand specificity of CooA, a highly specific heme-based CO sensor. J. Biol. Chem. 279 (2004) 45744-45752
16. Aono S., Ohkubo K., Matsuo T., and Nakajima H. Redox-controlled ligand exchange of the heme in the CO-sensing transcriptional activator CooA. J. Biol. Chem. 273 (1998) 25757-25764
17. Yamashita T., Hoashi Y., Tomisugi Y., Ishikawa Y., and Uno T. The C-helix in CooA rolls upon CO binding to ferrous heme. J. Biol. Chem. 279 (2004) 47320-47325
18. Sakai K., Matsui Y., Kouyama T., Shiro Y., and Adachi S. Optical monitoring of freeze-trapped reaction intermediates in protein crystals: a microspectrophotometer for cryogenic protein crystallography. J. Appl. Crystallog. 35 (2002) 270-273
19. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
20. Pflugrath J.W. The finer things in X-ray diffraction data collection. Acta Crystallog. sect. D 55 (1999) 1718-1725
21. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
22. Bricogne G., Vonrhein C., Flensburg C., Schiltz M., and Paciorek W. Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallog. sect. D 59 (2003) 2023-2030
23. Jones T.A., and Kjeldgaard M. O-The Manual (1994), Uppsala University, Sweden
24. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D 54 (1998) 905-921
25. Winn M.D., Isupov M.N., and Murshudov G.N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallog. sect. D 57 (2001) 122-133
26. Brunger A.T. The free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355 (1992) 472-474
27. Laskowski R.J., Macarthur M.W., Moss D.S., and Thornton J.M. PROCHECH: A program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26 (1993) 283-290
28. Davis I.W., Murray L.W., Richardson J.S., and Richardson D.C. MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucl. Acids Res. 32 (2004) 615-619
29. Kraulis P.J. MOLSCRIPT: a program package to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24 (1991) 946-950
30. Lawrence M.C., and Bourke P. CONSCRIPT: a program for generating electron density isosurfaces for presentation in protein crystallography. J. Appl. Crystallog. 33 (2000) 990-991
31. Merrit E.A., and Murphy M.E. Raster3D Version 2.0: a program for photorealistic molecular graphics. Acta Crystallog. sect. D 50 (1994) 869-873