Crystal structure of the intermediate complex of the arginine repressor from mycobacterium tuberculosis bound with its DNA Operator reveals detailed mechanism of arginine repression

Journal of Molecular Biology

Volumn 399, Issue 2, 2010, Pages 240-254

  Cherney, Leonid T ^a   Cherney, Maia M ^a   Garen, Craig R ^a   James, Michael N G ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Arginine repressor protein; ArgR DNA operator complex; DNA binding; Mycobacterium tuberculosis; X ray crystallography

Indexed keywords

ARGININE; DNA;

AMINO ACID ANALYSIS; AMINO ACID SYNTHESIS; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; GENE CONTROL; GENE DOSAGE; GENE IDENTIFICATION; GENE REPRESSION; GENETIC ANALYSIS; ISOMERIZATION; LIGAND BINDING; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; OPERATOR GENE; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

MYCOBACTERIUM TUBERCULOSIS;

EID: 77953082228     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.03.065     Document Type: Article

References (39)

1. Murillo A.C., Li H.Y., Alber T., Baker E.N., Berger J.M., Cherney L.T., et al. High throughput crystallography of TB drug targets. Infect. Disord. Drug Targets 2007, 7:127-139.
2. Sassetti C.M., Boyd D.H., Rubin E.J. Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 2003, 48:77-84.
3. 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 (London) 1998, 393:537-544.
4. Makarova K.S., Mironov A.A., Gelfand M.S. Conservation of the binding site for the arginine repressor in all bacterial lineages. Genome Biol. 2001, 2. research0013.1-0013.8.
5. Lim D., Oppenheim J.D., Eckhardt T., Maas W.K. Nucleotide sequence of the argR gene of Escherichia coli K-12 and isolation of its product, the arginine repressor. Proc. Natl Acad. Sci. USA 1987, 84:6697-6701.
6. Maas W.K. The arginine repressor of Escherichia coli. Microbiol. Rev. 1994, 58:631-640.
7. Dion M., Charlier D., Wang H., Gigot D., Savchenko A., Hallet J.-N., et al. The highly thermostable arginine repressor of Bacillus stearothermophilus: gene cloning and repressor-operator interactions. Mol. Microbiol. 1997, 25:385-398.
8. Van Duyne G.D., Ghosh G., Maas W.K., Sigler P.B. Structure of the oligomerization and l-arginine binding domain of the arginine repressor of Escherichia coli. J. Mol. Biol. 1996, 256:377-391.
9. Sunnerhagen M., Nilges M., Otting G., Carey J. Solution structure of the DNA-binding domain and model for the complex of multifunctional hexameric arginine repressor with DNA. Nat. Struct. Biol. 1997, 4:819-826.
10. Ni J., Sakanyan V., Charlier D., Glansdorff N., Van Duyne G.D. Structure of the arginine repressor from Bacillus stearothermophilus. Nat. Struct. Biol. 1999, 6:427-432.
11. Dennis C.A., Glykos N.M., Parsons M.R., Phillips S.E.V. The structure of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2002, 58:421-430.
12. Garnett J.A., Baumberg S., Stockley P.G., Phillips S.E.V. A high-resolution structure of the DNA-binding domain of AhrC, the arginine repressor/activator protein from Bacillus subtilis. Acta Crystallogr. F 2007, 63:914-917.
13. Garnett J.A., Baumberg S., Stockley P.G., Phillips S.E.V. Structure of the C-terminal effector-binding domain of AhrC bound to its corepressor l-arginine. Acta Crystallogr. F 2007, 63:918-921.
14. Cherney L.T., Cherney M.M., Garen C.R., Lu G.J., James M.N.G. Structure of the C-terminal domain of the arginine repressor protein from Mycobacterium tuberculosis. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2008, 64:950-956.
15. Garnett J.A., Marincs F., Baumberg S., Stockley P.G., Phillips S.E.V. Structure and function of the arginine repressor-operator complex from Bacillus subtilis. J. Mol. Biol. 2008, 379:284-298.
16. Cherney L.T., Cherney M.M., Garen C.R., Lu G.J., James M.N.G. Crystal structure of the arginine repressor protein in complex with the DNA operator from Mycobacterium tuberculosis. J. Mol. Biol. 2008, 384:1330-1340.
17. Cherney L.T., Cherney M.M., Garen C.R., Lu G.J., James M.N.G. The structure of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator and co-repressor, l-arginine. J. Mol. Biol. 2009, 388:85-97.
18. Tian G., Maas W.K. Mutational analysis of the arginine repressor of Escherichia coli. Mol. Microbiol. 1994, 13:599-608.
19. Tian G., Lim D., Oppenheim J.D., Maas W.K. Explanation for different types of regulation of arginine biosynthesis in Escherichia coli B and Escherichia coli K12 caused by a difference between their arginine repressors. J. Mol. Biol. 1994, 235:221-230.
20. Chen S.H., Merican A.F., Sherratt D.J. DNA binding of Escherichia coli arginine repressor mutants altered in oligomeric state. Mol. Microbiol. 1997, 24:1143-1156.
21. Miller C.M., Baumberg S., Stockley P.G. Operator interactions by the Bacillus subtilis arginine repressor/activator, AhrC: novel positioning and DNA-mediated assembly of a transcriptional activator at catabolic sites. Mol. Microbiol. 1997, 26:37-48.
22. Cantor C.R., Schimmel P.R. Biophysical Chemistry. Part III: The Behavior of Biological Macromolecules 1980, W. H. Freeman, San Francisco, CA.
23. McNae I.W., Kan D., Kontopidis G., Patterson A., Taylor P., Worrall L., Walkinshaw M. Studying protein-ligand interactions using protein crystallography. Crystallogr. Rev. 2005, 11:61-71.
24. Krissinel E., Henrick K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 2007, 372:774-797. (http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html).
25. Lu G.J., Garen C.R., Cherney M.M., Cherney L.T., Lee C., James M.N.G. Expression, purification and preliminary X-ray analysis of the C-terminal domain of an arginine repressor protein from Mycobacterium tuberculosis. Acta Crystallogr. F 2007, 63:936-939.
26. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1997, 276:307-326.
27. Vagin A., Teplyakov A.J. MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 1997, 30:1022-1025.
28. Adams P.D., Grosse-Kunstleve R.W., Hung L.-W., Ioerger T.R., McCoy A.J., Moriarty N.W., et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2002, 58:1948-1954.
29. Afonine P.V., Grosse-Kunstleve R.W., Adams P.D. A robust bulk-solvent correction and anisotropic scaling procedure. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2005, 61:850-855.
30. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallog., Sect. D: Biol. Crystallogr. 2004, 60:2126-2132.
31. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK-a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993, 26:283-291.
32. Lu X.-J., Olson Wilma K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids. Res. 2003, 31:5108-5121.
33. Lavery R., Sklenar H.J. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 1988, 6:63-91.
34. Gabb H.A., Jackson R.M., Sternberg M.J.E. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol. 1997, 272:106-120. (http://www.bmm.icnet.uk/docking/).
35. Moont G., Gabb H.A., Sternberg M.J.E. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999, 35:364-373.
36. Cohen G.E. ALIGN: a program to superimpose protein coordinates, accounting for insertions and deletions. J. Appl. Crystallogr. 1997, 30:1160-1161.
37. DeLano, W. L. (2002). The PyMOL Molecular Graphics System. (). http://pymol.sourceforge.net/.
38. Shishkin O.V., Elstner M., Frauenheim T., Suhai S. Structure of stacked dimers of N-methylated Watson-Crick adenine-thymine base pairs. Int. J. Mol. Sci. 2003, 4:537-547.
39. JureČka P., Nachtigall P., Hobza P. RI-MP2 calculations with extended basis set-a promising tool for study of H-bonded and stacked DNA base pairs. Phys. Chem. Chem. Phys. 2001, 3:4578-4582.