Coiled-coil helix rotation selects repressing or activating state of transcriptional regulator DhaR

Structure

Volumn 22, Issue 3, 2014, Pages 478-487

  Shi, Rong ^a,b   McDonald, Laura ^c   Cygler, Miroslaw ^d,e   Ekiel, Irena ^c,f  

^a PROTEO   (Canada)

^b UNIVERSITÉ LAVAL   (Canada)

^c Dept of Electrical and Computer Engineering   (Canada)

^d UNIVERSITY OF SASKATCHEWAN   (Canada)

^e MCGILL UNIVERSITY   (Canada)

^f NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; CIRCADIAN RHYTHM SIGNALING PROTEIN; DIHYDROXYACETONE; GAF PROTEIN; HELIX LOOP HELIX PROTEIN; HOMODIMER; PHOSPHODIESTERASE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR DHAR; UNCLASSIFIED DRUG; DHAK PROTEIN, E COLI; DHAL PROTEIN, E COLI; DHAR PROTEIN, E COLI; ESCHERICHIA COLI PROTEIN; PHOSPHOTRANSFERASE; TRANSACTIVATOR PROTEIN;

ARTICLE; DNA BINDING; DNA SUPERCOILING; ENZYME SUBUNIT; ESCHERICHIA COLI; GENE REPRESSION; MOLECULAR CLONING; NONHUMAN; OPERON; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STRUCTURE; TRANSCRIPTION REGULATION; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; PROTEIN TERTIARY STRUCTURE; SIGNAL TRANSDUCTION; X RAY CRYSTALLOGRAPHY;

BUTEA MONOSPERMA; ESCHERICHIA COLI;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY; SIGNAL TRANSDUCTION; TRANS-ACTIVATORS;

EID: 84896730967     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2013.11.012     Document Type: Article

References (44)

1. V. Anantharaman, S. Balaji, and L. Aravind The signaling helix: a common functional theme in diverse signaling proteins Biol. Direct 1 2006 25
2. A. Andreeva, D. Howorth, J.M. Chandonia, S.E. Brenner, T.J. Hubbard, C. Chothia, and A.G. Murzin Data growth and its impact on the SCOP database: new developments Nucleic Acids Res. 36 Database issue 2008 D419 D425
3. C. Bächler, K. Flükiger-Brühwiler, P. Schneider, P. Bähler, and B. Erni From ATP as substrate to ADP as coenzyme: functional evolution of the nucleotide binding subunit of dihydroxyacetone kinases J. Biol. Chem. 280 2005 18321 18325
4. C. Bächler, P. Schneider, P. Bähler, A. Lustig, and B. Erni Escherichia coli dihydroxyacetone kinase controls gene expression by binding to transcription factor DhaR EMBO J. 24 2005 283 293
5. M. Buck, M.T. Gallegos, D.J. Studholme, Y. Guo, and J.D. Gralla The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor J. Bacteriol. 182 2000 4129 4136
6. M. Bush, and R. Dixon The role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription Microbiol. Mol. Biol. Rev. 76 2012 497 529
7. F.M. Commichau, and J. Stülke Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression Mol. Microbiol. 67 2008 692 702
8. R. Croasdale, F.J. Ivins, F. Muskett, T. Daviter, D.J. Scott, T. Hardy, S.J. Smerdon, A.M. Fry, and M. Pfuhl An undecided coiled coil: the leucine zipper of Nek2 kinase exhibits atypical conformational exchange dynamics J. Biol. Chem. 286 2011 27537 27547
9. M. Doucleff, B. Chen, A.E. Maris, D.E. Wemmer, E. Kondrashkina, and B.T. Nixon Negative regulation of AAA + ATPase assembly by two component receiver domains: a transcription activation mechanism that is conserved in mesophilic and extremely hyperthermophilic bacteria J. Mol. Biol. 353 2005 242 255
10. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132
11. B. Erni, C. Siebold, S. Christen, A. Srinivas, A. Oberholzer, and U. Baumann Small substrate, big surprise: fold, function and phylogeny of dihydroxyacetone kinases Cell. Mol. Life Sci. 63 2006 890 900
12. R. Gutknecht, R. Beutler, L.F. Garcia-Alles, U. Baumann, and B. Erni The dihydroxyacetone kinase of Escherichia coli utilizes a phosphoprotein instead of ATP as phosphoryl donor EMBO J. 20 2001 2480 2486
13. J.T. Henry, and S. Crosson Ligand-binding PAS domains in a genomic, cellular, and structural context Annu. Rev. Microbiol. 65 2011 261 286
14. Y.-S.J. Ho, L.M. Burden, and J.H. Hurley Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor EMBO J. 19 2000 5288 5299
15. L. Holm, and C. Sander Dali: a network tool for protein structure comparison Trends Biochem. Sci. 20 1995 478 480
16. M. Hulko, F. Berndt, M. Gruber, J.U. Linder, V. Truffault, A. Schultz, J. Martin, J.E. Schultz, A.N. Lupas, and M. Coles The HAMP domain structure implies helix rotation in transmembrane signaling Cell 126 2006 929 940
17. N. Joly, N. Zhang, M. Buck, and X. Zhang Coupling AAA protein function to regulated gene expression Biochim. Biophys. Acta 1823 2012 108 116
18. T. Kon, K. Imamula, A.J. Roberts, R. Ohkura, P.J. Knight, I.R. Gibbons, S.A. Burgess, and K. Sutoh Helix sliding in the stalk coiled coil of dynein couples ATPase and microtubule binding Nat. Struct. Mol. Biol. 16 2009 325 333
19. E. Krissinel, and K. Henrick Inference of macromolecular assemblies from crystalline state J. Mol. Biol. 372 2007 774 797
20. M. Landau, I. Mayrose, Y. Rosenberg, F. Glaser, E. Martz, T. Pupko, and N. Ben-Tal ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures Nucleic Acids Res. 33 Web Server issue 2005 W299 W302
21. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Cryst. 26 1993 283 291
22. T.E. Lewis, I. Sillitoe, A. Andreeva, T.L. Blundell, D.W. Buchan, C. Chothia, A. Cuff, J.M. Dana, I. Filippis, and J. Gough et al. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains Nucleic Acids Res. 41 Database issue 2013 D499 D507
23. S.E. Martinez, J.A. Beavo, and W.G. Hol GAF domains: two-billion-year-old molecular switches that bind cyclic nucleotides Mol. Interv. 2 2002 317 323
24. S.E. Martinez, S. Bruder, A. Schultz, N. Zheng, J.E. Schultz, J.A. Beavo, and J.U. Linder Crystal structure of the tandem GAF domains from a cyanobacterial adenylyl cyclase: modes of ligand binding and dimerization Proc. Natl. Acad. Sci. USA 102 2005 3082 3087
25. B.W. Matthews Solvent content of protein crystals J. Mol. Biol. 33 1968 491 497
26. E.E. Matthews, M. Zoonens, and D.M. Engelman Dynamic helix interactions in transmembrane signaling Cell 127 2006 447 450
27. A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni, and R.J. Read Phaser crystallographic software J. Appl. Cryst. 40 2007 658 674
28. A. Möglich, R.A. Ayers, and K. Moffat Structure and signaling mechanism of Per-ARNT-Sim domains Structure 17 2009 1282 1294
29. G.N. Murshudov, A.A. Vagin, and E.J. Dodson Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr. D Biol. Crystallogr. 53 1997 240 255
30. A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
31. E.K. O'Shea, R. Rutkowski, and P.S. Kim Evidence that the leucine zipper is a coiled coil Science 243 1989 538 542
32. A.E. Oberholzer, M. Bumann, P. Schneider, C. Bächler, C. Siebold, U. Baumann, and B. Erni Crystal structure of the phosphoenolpyruvate-binding enzyme I-domain from the Thermoanaerobacter tengcongensis PEP: sugar phosphotransferase system (PTS) J. Mol. Biol. 346 2005 521 532
33. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1997 307 326
34. J. Pittard, H. Camakaris, and J. Yang The TyrR regulon Mol. Microbiol. 55 2005 16 26
35. L.M. Podust, A. Ioanoviciu, and P.R. Ortiz de Montellano 2.3 A X-ray structure of the heme-bound GAF domain of sensory histidine kinase DosT of Mycobacterium tuberculosis Biochemistry 47 2008 12523 12531
36. J.E. Schultz Structural and biochemical aspects of tandem GAF domains Handbook Exp. Pharmacol. 2009 93 109
37. J. Schumacher, N. Joly, M. Rappas, X. Zhang, and M. Buck Structures and organisation of AAA+ enhancer binding proteins in transcriptional activation J. Struct. Biol. 156 2006 190 199
38. R. Shi, L. McDonald, Q. Cui, A. Matte, M. Cygler, and I. Ekiel Structural and mechanistic insight into covalent substrate binding by Escherichia coli dihydroxyacetone kinase Proc. Natl. Acad. Sci. USA 108 2011 1302 1307
39. C. Siebold, L.F. García-Alles, B. Erni, and U. Baumann A mechanism of covalent substrate binding in the x-ray structure of subunit K of the Escherichia coli dihydroxyacetone kinase Proc. Natl. Acad. Sci. USA 100 2003 8188 8192
40. D.J. Studholme, and R. Dixon Domain architectures of sigma54-dependent transcriptional activators J. Bacteriol. 185 2003 1757 1767
41. T.C. Terwilliger Automated main-chain model building by template matching and iterative fragment extension Acta Crystallogr. D Biol. Crystallogr. 59 2003 38 44
42. P.A. Tucker, and L. Sallai The AAA+ superfamily - a myriad of motions Curr. Opin. Struct. Biol. 17 2007 641 652
43. A. Winkler, U. Heintz, R. Lindner, J. Reinstein, R.L. Shoeman, and I. Schlichting A ternary AppA-PpsR-DNA complex mediates light regulation of photosynthesis-related gene expression Nat. Struct. Mol. Biol. 20 2013 859 867
44. Z. Xi, Y. Gao, G. Sirinakis, H. Guo, and Y. Zhang Single-molecule observation of helix staggering, sliding, and coiled coil misfolding Proc. Natl. Acad. Sci. USA 109 2012 5711 5716