Structural Basis of the Signal Transduction in the Two-Component System

Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 631)


Two-component system (TCS) consists of two multi-domain proteins, a sensor histidine kinase (HK) and a response regulator (RR). In response to environmental change, the signal is transduced from HK to RR through phosphoryl transfer. At the first stage of structural biology of TCS, crystallographic and NMR analyses of domain blocks revealed the folds and the remarkable regions of sensor, dimerization and catalytic domains of HK and receiver and effecter domains of RR. As the second stage, the advanced researches of their multi-domain form and HK/RR complex showed the inter-domain and inter-molecular interactions and implied that the dynamic conformation changes are required in the signaling process. Thus, this chapter describes what these structural analyses of TCS proteins have contributed in understanding the cell signaling mechanism; signal input→phosphoryl transfer→signal output.


Catalytic Domain Response Regulator Histidine Kinase Heme Iron Receiver Domain 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 1.
    Ninfa EG, Atkinson MR, Kamberov, ES et al. Mechanism of autophosphorylation of Escherichia coli nitrogen regulator II (NRII or NtrB): transphosphorylation between subunits. J. Bacteriol 1993; 175:7024–7032.PubMedGoogle Scholar
  2. 2.
    Kato M, Mizuno T, Shimizu T et al. Insights into multistep phosphorelay from the crystal structure of the C-terminal HPt domain of ArcB. Cell 1997; 88:717–723.PubMedCrossRefGoogle Scholar
  3. 3.
    Kato M, Mizuno T, Shimizu T et al. Refined structure of the histidine-containing phosphotransfer (HPt) domain of the anaerobic sensor kinase ArcB from Escherichia coli at 1.57 A resolution. Acta Crystallogr 1999; D55:1842–1849.Google Scholar
  4. 4.
    Mizuno T, Matsubara M. Role of the histidine-containing phosphotransfer domain (HPt) in the multistep phosphorelay through the anaerobic hybrid sensor, ArcB. In: Inouye M, Dutta R, eds. Histidine Kinases in Signal Transduction. San Diego: Academic Press, 2003:165–190.CrossRefGoogle Scholar
  5. 5.
    Bilwes AM, Park SY, Quezada CM et al. Structure and function of CheA, the histidine kinase central to bacterial chemotaxis. In: Inouye M, Dutta R, eds. Histidine Kinase in Signal Transduction. San Diego: Academic Press, 2003:47–72.CrossRefGoogle Scholar
  6. 6.
    Wadhams GH, Armitage JP. Making sense of it all: bacterial chemotaxis. Nature Rev Mol Cell Biol 2004; 5:1024–1037.CrossRefGoogle Scholar
  7. 7.
    Mourey L, Da Re S, Pedelacq JD et al. Crystal structure of the CheA histidine phosphotransfer domain that mediates response regulator phosphorylation in bacterial chemotaxis. J Biol Chem 2001; 276:31074–31082.PubMedCrossRefGoogle Scholar
  8. 8.
    McEvoy MM, Hausrath AC, Randolph GB et al. Two binding modes reveal flexibility in kinase/response regulator interactions in the bacterial chemotaxis pathway. Proc Natl Acad Sci USA 1998; 95:7333–7338.PubMedCrossRefGoogle Scholar
  9. 9.
    Welch M, Chinardet N, Mourey L et al. Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY. Nature Struct Biol 1998; 5:25–29.PubMedCrossRefGoogle Scholar
  10. 10.
    Bilwes AM, Alex LA, Crane BR et al. Structure of CheA, a signal-transducing histidine kinase. Cell 1999; 96:131–141.PubMedCrossRefGoogle Scholar
  11. 11.
    Bilwes AM, Quezada CM, Croal LR et al. Nucleotide binding by the histidine kinase CheA. Nature Struct Biol 2001; 8:353–360.PubMedCrossRefGoogle Scholar
  12. 12.
    Park SY, Borbat PP, Gonzalez-Bonet G et al. Reconstruction of the chemotaxis receptor-kinase assembly. Nature Struct Mol Biol 2006; 13:400–407.CrossRefGoogle Scholar
  13. 13.
    Stock AM, West AH. Response regulator proteins and their interaction with histidine kinase. In: Inouye M, Dutta R, eds. Histidine Kinase in Signal Transduction. San Diego: Academic Press, 2003:237–271.CrossRefGoogle Scholar
  14. 14.
    West AH, Martinez-Hackert E, Stock AM. Crystal structure of the catalytic domain of the chemotaxis receptor methylesterase, CheB. J Mol Biol 1995; 250:276–290.PubMedCrossRefGoogle Scholar
  15. 15.
    Djordjevic S, Goudreau PN, Xu Q et al. Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain. Proc Natl Acad Sci USA 1998; 95:1381–1386.PubMedCrossRefGoogle Scholar
  16. 16.
    Tomomori C, Tanaka T, Dutta R et al. Solution structure of the homodimeric core domain of Escherichia coli histidine kinase EnvZ. Nature Struct Biol 1999; 6:729–734.PubMedCrossRefGoogle Scholar
  17. 17.
    Marina A, Mott C, Auyzenberg A et al. Structural and mutational analysis of the PhoQ histidine kinase catalytic domain. Insight into the reaction mechanism. J Biol Chem 2001; 276:41182–41190.PubMedCrossRefGoogle Scholar
  18. 18.
    Tanaka T, Saha SK, Tomomori C et al. NMR structure of the histidine kinase domain of the E. coli osmosensor EnvZ. Nature, 1998; 396:88–92.PubMedCrossRefGoogle Scholar
  19. 19.
    Song Y, Peisach D, Pioszak AA et al. Crystal structure of the C-terminal domain of the two-component system transmitter protein nitrogen regulator II (NRII; NtrB), regulator of nitrogen assimilation in Escherichia coli. Biochemistry 2004; 43:6670–6678.PubMedCrossRefGoogle Scholar
  20. 20.
    Nowak E, Panjikar S, Morth JP et al. Structural and functional aspects of the sensor histidine kinase PrrB from Mycobacterium tuberculosis. Structure 2006; 14:275–285.PubMedCrossRefGoogle Scholar
  21. 21.
    Wigley DB, Davies GJ, Dodson EJ et al. Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 1991; 351:624–629.PubMedCrossRefGoogle Scholar
  22. 22.
    Ban C, Junop M, Yang W. Transformation of MutL by ATP binding and hydrolysis: a switch in DNA mismatch repair. Cell 1999; 97:85–97.PubMedCrossRefGoogle Scholar
  23. 23.
    Prodromou C, Roe SM, O’Brien R et al. Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone. Cell 1997; 90:65–75.PubMedCrossRefGoogle Scholar
  24. 24.
    Jeffery CJ, Koshland DE, Jr. Three-dimensional structural model of the serine receptor ligand-binding domain. Protein Sci 1993; 2:559–566.PubMedCrossRefGoogle Scholar
  25. 25.
    Yeh JI, Biemann HP, Pandit J et al. The three-dimensional structure of the ligand-binding domain of a wild-type bacterial chemotaxis receptor. Structural comparison to the cross-linked mutant forms and conformational changes upon ligand binding. J Biol Chem 1993; 268:9787–9792.PubMedGoogle Scholar
  26. 26.
    Yeh JI, Biemann HP, Prive GG et al. High-resolution structures of the lignad binding domain of the wild-type bacterial aspartate receptor. J Mol Biol 1996; 262:186–201.PubMedCrossRefGoogle Scholar
  27. 27.
    Falke JJ, Koshland DE, Jr. Global flexibility in a sensory receptor: a site-directed cross-linking approach. Science 1987; 237:1596–1600.PubMedCrossRefGoogle Scholar
  28. 28.
    Chen X, Schauder S, Potier N et al. Structural identification of a bacterial quorum-sensing signal containing boron. Nature 2002; 415:545–549.PubMedCrossRefGoogle Scholar
  29. 29.
    Neiditch MB, Federle MJ, Miller ST et al. Regulation of LuxPQ receptor activity by the quorum-sensing signal autoinducer-2. Mol Cell 2005; 18:507–518.PubMedCrossRefGoogle Scholar
  30. 30.
    Neiditch MB, Federle MJ, Pompeani AJ et al. Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing. Cell 2006; 126:1095–1108.PubMedCrossRefGoogle Scholar
  31. 31.
    Schaller GE, Bleecker AB. Ethylene-binding sites generated in yeast expressing the Arabidopsis ETR1 gene. Science 1995; 270:1809–1811.PubMedCrossRefGoogle Scholar
  32. 32.
    Rodriguez FI, Esch JJ, Hall AE et al. A copper cofactor for the ethylene receptor ETR1 from Arabidopsis. Science, 1999; 283:996–998.PubMedCrossRefGoogle Scholar
  33. 33.
    Rockwell NC, Su YS, Lagarias JC. Phytochrome structure and signaling mechanisms. Annu Rev Plant Biol 2006; 57:837–858.PubMedCrossRefGoogle Scholar
  34. 34.
    Wagner JR, Brunzelle JS, Forest KT et al. A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature 2005; 438:325–331.PubMedCrossRefGoogle Scholar
  35. 35.
    Volz K, Matsumura P. Crystal structure of Escherichia coli CheY refined at 1.7-A resolution. J Biol Chem 1991; 266:15511–15519.PubMedGoogle Scholar
  36. 36.
    Madhusudan, Zapf J, Whiteley JM et al. Crystal structure of a phosphatase-resistant mutant of sporulation response regulator Spo0F from Bacillus subtilis. Structure 1996; 4:679–690.PubMedCrossRefGoogle Scholar
  37. 37.
    Volkman BF, Nohaile MJ, Amy NK et al. Three-dimensional solution structure of the N-terminal receiver domain of NTRC. Biochemistry 1995; 34:1413–1424.PubMedCrossRefGoogle Scholar
  38. 38.
    Baikalov I, Schroder I, Kaczor-Grzeskowiak M et al. Structure of the Escherichia coli response regulator NarL. Biochemistry 1996; 35:11053–11061.PubMedCrossRefGoogle Scholar
  39. 39.
    Sola M, Gomis-Ruth FX, Serrano L et al. Three-dimensional crystal structure of the transcription factor PhoB receiver domain. J Mol Biol 1999; 285:675–687.PubMedCrossRefGoogle Scholar
  40. 40.
    Birck C, Mourey L, Gouet P et al. Conformational changes induced by phosphorylation of the FixJ receiver domain. Structure 1999; 7:1505–1515.PubMedCrossRefGoogle Scholar
  41. 41.
    Lewis RJ, Muchova K, Brannigan JA et al. Domain swapping in the sporulation response regulator Spo0A. J Mol Biol 2000; 297:757–770.PubMedCrossRefGoogle Scholar
  42. 42.
    Muller-Dieckmann HJ, Grantz AA, Kim SH. The structure of the signal receiver domain of the Arabidopsis thaliana ethylene receptor ETR1. Structure 1999; 7:1547–1556.PubMedCrossRefGoogle Scholar
  43. 43.
    Buckler DR, Zhou Y, Stock AM. Evidence of intradomain and interdomain flexibility in an OmpR/PhoB homolog from Thermotoga maritima. Structure 2002; 10:153–164.PubMedCrossRefGoogle Scholar
  44. 44.
    Guillet V, Ohta N, Cabantous S et al Crystallographic and biochemical studies of DivK reveal novel, features of an essential response regulator in Caulobacter crescentus. J Biol Chem 2002; 277:42003–42010.PubMedCrossRefGoogle Scholar
  45. 45.
    Birck C, Chen Y, Hullett FM et al. The crystal structure of the phosphorylation domain in PhoP reveals a functional tandem association mediated by an asymmetric interface. J Bacteriol 2003; 185:254–261.PubMedCrossRefGoogle Scholar
  46. 46.
    Riepl H, Scharf B, Schmitt R et al. Solution structures of the inactive and BeF3-activated response regulator CheY2. J Mol Biol 2004; 338:287–297.PubMedCrossRefGoogle Scholar
  47. 47.
    Toro-Roman A, Mack TR, Stock AM. Structural analysis and solution studies of the activated regulatory domain of the response regulator ArcA: a symmetric dimer mediated by the alpha4-beta5-alpha5 face. J Mol Biol 2005; 349:11–26.PubMedCrossRefGoogle Scholar
  48. 48.
    Toro-Roman A, Wu T, Stock AM. A common dimerization interface in bacterial response regulators KdpE and TorR. Protein Sci 2005; 14:3077–3088.PubMedCrossRefGoogle Scholar
  49. 49.
    Nowak E, Panjikar S, Konarev P et al. The structural basis of signal transduction for the response regulator PrrA from Mycobacterium tuberculosis. J Biol Chem 2006; 281:9659–9666.PubMedCrossRefGoogle Scholar
  50. 50.
    Cho HS, Lee SY, Yan D et al. NMR structure of activated CheY. J Mol Biol 2000; 297:543–551.PubMedCrossRefGoogle Scholar
  51. 51.
    Lee SY, Cho HS, Pelton JG et al. Crystal structure of activated CheY. Comparison with other activated receiver domains. J Biol Chem 2001; 276:16425–16431.PubMedCrossRefGoogle Scholar
  52. 52.
    Halkides CJ, Zhu X, Phillion DP et al. Synthesis and biochemical characterization of an analogue of CheY-phosphate, a signal transduction protein in bacterial chemotaxis. Biochemistry 1998; 37:13674–13680.PubMedCrossRefGoogle Scholar
  53. 53.
    Halkides CJ, McEvoy MM, Casper E et al. The 1.9 A resolution crystal structure of phosphono-CheY, an analogue of the active form of the response regulator, CheY. Biochemistry 2000; 39:5280–5286.PubMedCrossRefGoogle Scholar
  54. 54.
    Lee SY, Cho HS, Pelton JG et al. Crystal structure of an activated response regulator bound to its target. Nature Struc Biol 2001; 8:52–56.CrossRefGoogle Scholar
  55. 55.
    Gouet P, Fabry B, Guillet V et al. Structural transitions in the FixJ receiver domain. Structure 1999; 7:1517–1526.PubMedCrossRefGoogle Scholar
  56. 56.
    Baikalov I, Schroder I, Kaczor-Grzeskowiak M et al. NarL dimerization? Suggestive evidence from a new crystal form. Biochemistry 1998; 37:3665–3676.PubMedCrossRefGoogle Scholar
  57. 57.
    Lee SY, De La Torre A, Yan D et al. Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ATPase domains. Genes Dev 2003; 17:2552–2563.PubMedCrossRefGoogle Scholar
  58. 58.
    Maris AE, Sawaya MR, Kaczor-Grzeskowiak M et al. Dimerization allows DNA target site recognition by the NarL response regulator. Nature Struct Biol 2002; 9:771–778.PubMedCrossRefGoogle Scholar
  59. 59.
    Bassler BL, Wright M, Showalter RE et al. Intercellular signalling in Vibrio harveyi: sequence and function of genes regulating expression of luminescence. Mol Microbiol 1993; 9:773–786.PubMedCrossRefGoogle Scholar
  60. 60.
    Bassler BL, Wright M, Silverman MR. Multiple signalling systems controlling expression of luminescence in Vibrio harveyi: sequence and function of genes encoding a second sensory pathway. Mol Microbiol 1994; 13:273–286.PubMedCrossRefGoogle Scholar
  61. 61.
    Marina A, Waldburger CD Hendrickson WA. Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein. EMBO J 2005; 24:4247–4259.PubMedCrossRefGoogle Scholar
  62. 62.
    Zapf J, Sen U, Madhusudan et al. A transient interaction between two phosphorelay proteins trapped in a crystal, lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction. Structure 2000; 8:851–862.PubMedCrossRefGoogle Scholar
  63. 63.
    Varughese KI, Tsigelny I, Zhao H. The crystal structure of beryllofluoride Spo0F in complex with the phosphotransferase Spo0B represents a phosphotransfer pretransition state. J Bacteriol 2006; 188:4970–4977.PubMedCrossRefGoogle Scholar
  64. 64.
    Tanaka A, Nakamura H, Shiro Y et al. Roles of the heme distal residues of FixL in O2 sensing: a single convergent structure of the heme moiety is relevant to the downregulation of kinase activity. Biochemistry 2006; 45:2515–2523.PubMedCrossRefGoogle Scholar
  65. 65.
    Gilles-Gonzalez MA, Ditta GS, Helinski DR. A haemoprotein with kinase activity encoded by the oxygen sensor of Rhizobium meliloti. Nature 1991; 250:170–172.CrossRefGoogle Scholar
  66. 66.
    Saito K, Ito E, Hosono K et al. The uncoupling of oxygen sensing, phosphorylation signalling and transcriptional activation in oxygen sensor FixL and FixJ mutants. Mol Microbiol 2003; 48:373–383.PubMedCrossRefGoogle Scholar
  67. 67.
    Gong W, Hao B, Mansy SS et al. Structure of a biological oxygen sensor: a new mechanism for heme-driven signal transduction. Proc Natl Acad Sci USA, 1998; 95:15177–15182.PubMedCrossRefGoogle Scholar
  68. 68.
    Miyatake H, Mukai M, Park SY et al. Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies. J Mol Biol 2000; 301:415–431.PubMedCrossRefGoogle Scholar
  69. 69.
    Akimoto, S, Tanaka A, Nakamura K et al. O2-specific regulation of the ferrous heme-based sensor kinase FixL from Sinorhizobium meliloti and its aberrant inactivation in the ferric form. Biochem Biophys Res Commun 2003; 304:136–142.PubMedCrossRefGoogle Scholar
  70. 70.
    Hao B, Isaza C, Arndt J et al. Structure-based mechanism of O2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum. Biochemistry 2002; 41:12952–12958.PubMedCrossRefGoogle Scholar
  71. 71.
    Gong W, Hao B, Chan MK. New mechanistic insights from structural studies of the oxygen-sensing domain of Bradyrhizobium japonicum FixL. Biochemistry, 2000; 39:3955–3962.PubMedCrossRefGoogle Scholar
  72. 72.
    Yamada S, Akiyama S, Sugimoto H et al. The signaling pathway in histidine kinase and the response regulator complex revealed by X-ray crystallography and solution scattering. J Mol Biol 2006; 362:123–139.PubMedCrossRefGoogle Scholar
  73. 73.
    Kumita H, Yamada S, Nakamura H et al. Chimeric sensory kinases containing O2 sensor domain of FixL and histidine kinase domain from thermophile. Biochim Biophys Acta 2003; 1646:136–144.PubMedGoogle Scholar
  74. 74.
    Nelson KE, Clayton RA, Gill SR et al. Evidence for lateral gene transfer between Archaca and bacteria from genome sequence of Thermotoga maritima. Nature 1999; 399:323–329.PubMedCrossRefGoogle Scholar
  75. 75.
    Yamada S, Nakamura H, Kinoshita E et al. Separation of a phosphorylated histidine protein using phosphate affinity polyacrylamide gel electrophoresis. Anal Biochem 2007; 360:160–162.PubMedCrossRefGoogle Scholar
  76. 76.
    Nakamura H, Kumita H, Imai K et al. ADP reduces the oxygen-binding affinity of a sensory histidine kinase, FixL: the possibility of an enhanced reciprocating kinase reaction. Proc Natl Acad Sci USA, 2004; 101:2742–2746.PubMedCrossRefGoogle Scholar

Copyright information

© Landes Bioscience and Springer Science+Business Media 2008

Authors and Affiliations

  1. 1.Biometal Science Laboratory, RIKEN SPring-8 CenterHarima InstituteHyogoJapan

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