X-ray structure of a Rex-family repressor/NADH complex insights into the mechanism of redox sensing

Structure

Volumn 13, Issue 1, 2005, Pages 43-54

  Sickmier, E Allen ^a   Brekasis, Dimitris ^b   Paranawithana, Shanthi ^a   Bonanno, Jeffrey B ^c   Paget, Mark S B ^b   Burley, Stephen K ^c   Kielkopf, Clara L ^a,c  

^a JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^b UNIVERSITY OF SUSSEX   (United Kingdom)

^c ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE; REX PROTEIN;

ALPHA CHAIN; ARTICLE; CARBOXY TERMINAL SEQUENCE; DIMERIZATION; DNA BINDING; GENE CONTROL; HYDROPHOBICITY; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; THERMUS AQUATICUS; TRANSCRIPTION REGULATION; X RAY ANALYSIS;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DNA; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ESCHERICHIA COLI; GENE PRODUCTS, REX; HYDROPHOBICITY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NAD; OPERON; OXIDATION-REDUCTION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SURFACE PLASMON RESONANCE; THERMUS;

EUKARYOTA; THERMUS AQUATICUS;

EID: 11844285686     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.10.012     Document Type: Article

References (65)

1. J.L. Avalos, I. Celic, S. Muhammad, M.S. Cosgrove, J.D. Boeke, and C. Wolberger Structure of a SIR2 enzyme bound to an acetylated p53 peptide Mol. Cell 10 2002 523 535
2. J.L. Avalos, J.D. Boeke, and C. Wolberger Structural basis for the mechanism and regulation of SIR2 enzymes Mol. Cell 13 2004 639 648
3. C.E. Bauer, S. Elsen, and T.H. Bird Mechanisms for redox control of gene expression Annu. Rev. Microbiol. 53 1999 495 523
4. M.J. Bennett, S. Choe, and D. Eisenberg Domain swapping: entangling alliances between proteins Proc. Natl. Acad. Sci. USA 91 1994 3127 3131
5. G. Blander, and L. Guarente The SIR2 family of protein deacetylases Annu. Rev. Biochem. 73 2004 417 435
6. M. Boll, G. Fuchs, and J. Heider Anaerobic oxidation of aromatic compounds and hydrocarbons Curr. Opin. Chem. Biol. 6 2002 604 611
7. D. Brekasis, and M.S.B. Paget A novel sensor of NADH/NAD+ redox poise in Streptomyces coelicolor A3(2) EMBO J. 22 2003 4856 4865
8. I. Brook Anaerobic infections in children Microbes Infect. 4 2002 1271 1280
9. A.T. Brunger, P.D. Adams, G.M. Clore, W.L. DeLano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, and N.S. Pannu Crystallography & NMR system: A new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54 1998 905 921
10. S.K. Burley, and G.A. Petsko Weakly polar interactions in proteins Adv. Protein Chem. 39 1988 125 189
11. CCP4 (Collaborative Computational Project, Number 4) (1994). The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol. Crystallogr. 50, 760-763.
12. J.H. Chang, H.C. Kim, K.Y. Hwang, J.W. Lee, S.P. Jackson, S.D. Bell, and Y. Cho Structural basis for the NAD-dependent deacetylase mechanism of SIR2 J. Biol. Chem. 277 2002 34489 34498
13. H. Choi, S. Kim, P. Mukhopadhyay, S. Cho, J. Woo, G. Storz, and S. Ryu Structural basis of the redox switch in the OxyR transcription factor Cell 105 2001 103 113
14. M.F. Christman, G. Storz, and B.N. Ames OxyR, a positive regulator of hydrogen peroxide-inducible genes in Escherichia coli and Salmonella typhimurium, is homologous to a family of bacterial regulatory proteins Proc. Natl. Acad. Sci. USA 86 1989 3484 3488
15. F. Colonna-Cesari, D. Perahia, M. Karplus, H. Eklund, C.I. Braden, and O. Tapia Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode J. Biol. Chem. 261 1986 15273 15280
16. R. Dixon, and D. Kahn Genetic regulation of biological nitrogen fixation Nat. Rev. Microbiol. 2 2004 621 631
17. X. Du, and J. Pene Identification, cloning and expression of p25, an AT-rich DNA-binding protein from the extreme thermophile, Thermus aquaticus YT-1 Nucleic Acids Res. 27 1999 1690 1697
18. H. Eklund, J.P. Samma, L. Wallen, C.I. Branden, A. Akeson, and T.A. Jones Structure of a triclinic ternary complex of horse liver alcohol dehydrogenase at 2.9 A resolution J. Mol. Biol. 146 1981 561 587
19. H. Eklund, B.V. Plapp, J.P. Samama, and C.I. Branden Binding of substrate in a ternary complex of horse liver alcohol dehydrogenase J. Biol. Chem. 257 1982 14349 14358
20. R.M. Esnouf An extensively modified version of MolScript that includes greatly enhanced coloring capabilities J. Mol. Graph. Model. 15 1997 132 134
21. M.S. Finnin, J.R. Donigian, and N.P. Pavletich Structure of the histone deacetylase SIR2 Nat. Struct. Biol. 8 2001 621 625
22. E.R. Flores, F. Perez, and M. de la Torre Scale-up of Bacillus thuringiensis fermentation based on oxygen transfer J. Ferment. Bioeng. 83 1997 561 564
23. K.S. Gajiwala, and S.K. Burley Winged helix proteins Curr. Opin. Struct. Biol. 10 2000 110 116
24. D. Georgellis, O. Kwon, and E.C. Lin Quinones as the redox signal for the arc two-component system of bacteria Science 292 2001 2314 2316
25. T. Gomi, Y. Takata, T. Date, M. Fujioka, R.R. Aksamit, P.S. Backlund Jr., and G.L. Cantoni Site-directed mutagenesis of rat liver S- adenosylhomocysteinase. Effect of conversion of aspartic acid 244 to glutamic acid on coenzyme binding J. Biol. Chem. 265 1990 16102 16107
26. S. Hayward Identification of specific interactions that drive ligand-induced closure in five enzymes with classic domain movements J. Mol. Biol. 339 2004 1001 1021
27. S. Hayward, and R.A. Lee Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50 J. Mol. Graph. Model. 21 2002 181 183
28. W.A. Hendrickson Determination of macromolecular structures from anomalous diffraction of synchrotron radiation Science 254 1991 51 58
29. W.G. Hol Effects of the α-helix dipole upon the functioning and structure of proteins and peptides Adv. Biophys. 19 1985 133 165
30. L. Holm, and C. Sander Protein structure comparison by alignment of distance matrices J. Mol. Biol. 233 1993 123 138
31. J.L. Huffman, and R.G. Brennan Prokaryotic transcription regulators: more than just the helix-turn-helix motif Curr. Opin. Struct. Biol. 12 2002 98 106
32. S. Jones, and J.M. Thornton Protein-protein interactions: a review of protein dimer structures Prog. Biophys. Mol. Biol. 63 1995 31 65
33. T.A. Jones, J.Y. Zou, S.W. Cowan, and G. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallogr. A 47 1991 110 119
34. P.A. Jordan, A.J. Thomson, E.T. Ralph, J.R. Guest, and J. Green FNR is a direct oxygen sensor having a biphasic response curve FEBS Lett. 416 1997 349 352
35. 2: [4Fe-4S] to [2Fe-2S] conversion with loss of biological activity Proc. Natl. Acad. Sci. USA 94 1997 6087 6092
36. G.J. Kleywegt, and T.A. Jones Detection, delineation, measurement and display of cavities in macromolecular structures Acta Crystallogr. D50 1994 178 185
37. M. Klingenberg H.U. Bergmeyer Methods of Enzymatic Analysis 1963 Academic Press New York 531 537
38. P.J. Kraulis MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 24 1991 946 950
39. V. Kumar, J.E. Carlson, K.A. Ohgi, T.A. Edwards, D.W. Rose, C.R. Escalante, M.G. Rosenfeld, and A.K. Aggarwal Transcription corepressor CtBP is an NAD(+)-regulated dehydrogenase Mol. Cell 10 2002 857 869
40. L.A. LeBrun, D.H. Park, S. Ramaswamy, and B.V. Plapp Participation of histidine-51 in catalysis by horse liver alcohol dehydrogenase Biochemistry 43 2004 3014 3026
41. A.M. Lesk NAD-binding domains of dehydrogenases Curr. Opin. Struct. Biol. 5 1995 775 783
42. V. Leskovac, S. Trivic, B.M. Anderson, J.L. Urbauer, D.E. Bradshaw, and W.W. Cleland Comparison of the chemical mechanisms of action of yeast and equine liver alcohol dehydrogenase Eur. J. Biochem. 264 1999 840 847
43. E.A. Merritt, and D.J. Bacon Raster3D: photorealistic molecular graphics Methods Enzymol. 277 1997 505 524
44. J. Min, J. Landry, R. Sternglanz, and R.M. Xu Crystal structure of a SIR2 homolog-NAD complex Cell 105 2001 269 279
45. D.A. Murdoch Gram-positive anaerobic cocci Clin. Microbiol. Rev. 11 1998 81 120
46. M. Nardini, S. Spano, C. Cericola, A. Pesce, A. Massaro, E. Millo, A. Luini, D. Corda, and M. Bolognesi CtBP/BARS: a dual-function protein involved in transcription co-repression and Golgi membrane fission EMBO J. 22 2003 3122 3130
47. P. Orth, D. Schnappinger, W. Hillen, W. Saenger, and W. Hinrichs Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system Nat. Struct. Biol. 7 2000 215 219
48. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data in oscillation mode Methods Enzymol. 276 1997 307 326
49. H.D. Park, K.M. Guinn, M.I. Harrell, R. Liao, M.I. Voskuil, M. Tompa, G.K. Schoolnik, and D.R. Sherman Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis Mol. Microbiol. 48 2003 833 843
50. T. Patschkowski, D.M. Bates, and P.J. Kiley Mechanisms for sensing and responding to oxygen deprivation G. Storz R. Hengge-Aronis Bacterial Stress Responses 2000 ASM Press Washington, DC 61 78
51. U. Pieper, N. Eswar, H. Braberg, M.S. Madhusudhan, F.P. Davis, A.C. Stuart, N. Mirkovic, A. Rossi, M.A. Marti-Renom, and A. Fiser MODBASE, a database of annotated comparative protein structure models, and associated resources Nucleic Acids Res. 32 2004 D217 D222
52. S.T. Rao, and M.G. Rossmann Comparison of super- secondary structures in proteins J. Mol. Biol. 76 1973 241 256
53. W. Saenger, P. Orth, C. Kisker, W. Hillen, and W. Hinrichs The tetracycline repressor: a paradigm for a biological switch Angew. Chem. Int. Ed. Engl. 39 2000 2042 2052
54. M. Saraste, P.R. Sibbald, and A. Wittinghofer The P-loop: a common motif in ATP- and GTP-binding proteins Trends Bio chem. Sci. 15 1990 430 434
55. H. Sassi, A.M. Deschamps, and J.M. Lebeault Process analysis of L-lysine fermentation with Corynebacterium glutamicum under different oxygen and carbon dioxide supplies and redox potentials Process Biochem. 31 1996 493 497
56. B.L. Taylor, I.B. Zhulin, and M.S. Johnson Aerotaxis and other energy-sensing behavior in bacteria Annu. Rev. Microbiol. 53 1999 103 128
57. D.M. van Aalten, C.C. DiRusso, J. Knudsen, and R.K. Wierenga Crystal structure of FadR, a fatty acid-responsive transcription factor with a novel acyl coenzyme A-binding fold EMBO J. 19 2000 5167 5177
58. D.M. van Aalten, C.C. DiRusso, and J. Knudsen The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR EMBO J. 20 2001 2041 2050
59. J.D. Van Hamme, A. Singh, and O.P. Ward Recent advances in petroleum microbiology Microbiol. Mol. Biol. Rev. 67 2003 503 549
60. C.M. Weeks, and R. Miller Optimizing Shake-and-Bake for proteins Acta Crystallogr. D Biol. Crystallogr. 55 1999 492 500
61. D.H. Williamson, P. Lund, and H.A. Krebs The redox state of free nicotinamide-adenine dinucleotide in the cytoplasm and mitochondria of rat liver Biochem. J. 103 1967 514 527
62. Y. Xu, R.J. Heath, Z. Li, C.O. Rock, and S.W. White The FadR.DNA complex. Transcriptional control of fatty acid metabolism in Escherichia coli J. Biol. Chem. 276 2001 17373 17379
63. W. Zhang, and G.N. Phillips Jr. Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry Structure 11 2003 1097 1110
64. K. Zhao, X. Chai, A. Clements, and R. Marmorstein Structure and autoregulation of the yeast Hst2 homolog of SIR2 Nat. Struct. Biol. 10 2003 864 871
65. K. Zhao, X. Chai, and R. Marmorstein Structure of the yeast Hst2 protein deacetylase in ternary complex with 2′-O-acetyl ADP ribose and histone peptide Structure 11 2003 1403 1411