Sensor domains of two-component regulatory systems

Current Opinion in Microbiology

Volumn 13, Issue 2, 2010, Pages 116-123

  Cheung, Jonah ^a   Hendrickson, Wayne A ^b  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOPLASM PROTEIN; DIMER; MEMBRANE RECEPTOR; PROTEIN HISTIDINE KINASE;

BACTERIAL GENETICS; ENZYME STRUCTURE; MOLECULAR INTERACTION; MOLECULAR SENSOR; NONHUMAN; PROTEIN DOMAIN; REGULATORY MECHANISM; REVIEW; SIGNAL TRANSDUCTION;

BACTERIA; BACTERIAL PROTEINS; CATALYTIC DOMAIN; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, MOLECULAR; PROTEIN KINASES; SIGNAL TRANSDUCTION;

EID: 77949918665     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2010.01.016     Document Type: Review

References (57)

1. Gao R., and Stock A.M. Biological insights from structures of two-component proteins. Annu Rev Microbiol 63 (2009) 133-154
2. Dutta R., Qin L., and Inouye M. Histidine kinases: diversity of domain organization. Mol Microbiol 34 (1999) 633-640
3. Kirby J.R. Chemotaxis-like regulatory systems: unique roles in diverse bacteria. Annu Rev Microbiol 63 (2009) 45-59
4. Cheung J., Bingman C.A., Reyngold M., Hendrickson W.A., and Waldburger C.D. Crystal structure of a functional dimer of the PhoQ sensor domain. J Biol Chem 283 (2008) 13762-13770. The structure of a biologically relevant PDC sensor domain dimer is characterized for the first time with supporting in vivo data.
5. Cho U.S., Bader M.W., Amaya M.F., Daley M.E., Klevit R.E., Miller S.I., and Xu W.Q. Metal bridges between the PhoQ sensor domain and the membrane regulate transmembrane signaling. J Mol Biol 356 (2006) 1193-1206
6. 4-dicarboxylate ligand binding are revealed by high resolution structures of PDC sensors DcuS and DctB.
7. Pappalardo L., Janausch I.G., Vijayan V., Zientz E., Junker J., Peti W., Zweckstetter M., Unden G., and Griesinger C. The NMR structure of the sensory domain of the membranous two-component fumarate sensor (histidine protein kinase) DcuS of Escherichia coli. J Biol Chem 278 (2003) 39185-39188
8. Reinelt S., Hofmann E., Gerharz T., Bott M., and Madden D.R. The structure of the periplasmic ligand-binding domain of the sensor kinase CitA reveals the first extracellular PAS domain. J Biol Chem 278 (2003) 39189-39196
9. Sevvana M., Vijayan V., Zweckstetter M., Reinelt S., Madden D.R., Herbst-Irmer R., Sheldrick G.M., Bott M., Griesinger C., and Becker S. A ligand-induced switch in the periplasmic domain of sensor histidine kinase CitA. J Mol Biol 377 (2008) 512-523. An important study detailing the mechanism of citrate binding in the CitA sensor, revealing conformational changes that occur between the ligand-bound and apo states.
10. Moglich A., Ayers R.A., and Moffat K. Structure and signaling mechanism of Per-ARNT-Sim domains. Structure 17 (2009) 1282-1294
11. Emami K., Topakas E., Nagy T., Henshaw J., Jackson K.A., Nelson K.E., Mongodin E.F., Murray J.W., Lewis R.J., and Gilbert H.J. Regulation of the xylan-degrading apparatus of Cellvibrio japonicus by a novel two-component system. J Biol Chem 284 (2009) 1086-1096
12. Neiditch M.B., Federle M.J., Miller S.T., Bassler B.L., and Hughson F.M. Regulation of LuxPQ receptor activity by the quorum-sensing signal autoinducer-2. Mol Cell 18 (2005) 507-518
13. Neiditch M.B., Federle M.J., Pompeani A.J., Kelly R.C., Swem D.L., Jeffrey P.D., Bassler B.L., and Hughson F.M. Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing. Cell 126 (2006) 1095-1108
14. 4-dicarboxylates sensing mechanism revealed by the crystal structures of DctB sensor domain. J Mol Biol 383 (2008) 49-61. Structures of the DctB sensor domain in the apo state and in various ligand-bound states reveals mechanisms of ligand binding, stereospecificity, and dimerization.
15. Yeh J.I., Biemann H.P., Prive G.G., Pandit J., Koshland D.E., and Kim S.H. High-resolution structures of the ligand binding domain of the wild-type bacterial aspartate receptor. J Mol Biol 262 (1996) 186-201
16. 2+ channel subunits and a class of prokaryotic chemotaxis receptors. Trends Biochem Sci 25 (2000) 535-537
17. Zhulin I.B., Nikolskaya A.N., and Galperin M.Y. Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in Bacteria and Archaea. J Bacteriol 185 (2003) 285-294
18. Anantharaman V., and Aravind L. The CHASE domain: a predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors. Trends Biochem Sci 26 (2001) 579-582
19. Mougel C., and Zhulin I.B. CHASE: an extracellular sensing domain common to transmembrane receptors from prokaryotes, lower eukaryotes and plants. Trends Biochem Sci 26 (2001) 582-584
20. Cheung J., and Hendrickson W.A. Structural analysis of ligand stimulation of the histidine kinase NarX. Structure 17 (2009) 190-201. A difference distance matrix analysis of structures of the all-helical NarX sensor domain in both nitrate-bound and apo states reveals a piston-sliding conformational change between the N- and C-terminal helices. This study brings new light to a well-studied two-component system and reveals similar mechanisms of function to chemotaxis receptors.
21. Moore J.O., and Hendrickson W.A. Structural analysis of sensor domains from the TMAO-responsive histidine kinase receptor TorS. Structure 17 (2009) 1195-1204
22. Baraquet C., Theraulaz L., Guiral M., Lafitte D., Mejean V., and Jourlin-Castelli C. TorT: a member of a new periplasmic binding protein family, triggers induction of the tor respiratory system upon trimethylamine N-oxide electron-acceptor binding in Escherichia coli. J Biol Chem 281 (2006) 38189-38199
23. Cheung J., Le-Khac M., and Hendrickson W.A. Crystal structure of a histidine kinase sensor domain with similarity to periplasmic binding proteins. Proteins 77 (2009) 235-241
24. Albanesi D., Martin M., Trajtenberg F., Mansilla M.C., Haouz A., Alzari P.M., de Mendoza D., and Buschiazzo A. Structural plasticity and catalysis regulation of a thermosensor histidine kinase. Proc Natl Acad Sci USA 106 (2009) 16185-16190
25. Martin M., Albanesi D., Alzari P.M., and de Mendoza D. Functional in vitro assembly of the integral membrane bacterial thermosensor DesK. Prot Expr Purif 66 (2009) 39-45
26. Bogel G., Schrempf H., and Lucana D.O. The heme-binding protein HbpS regulates the activity of the Streptomyces reticuli iron-sensing histidine kinase SenS in a redox-dependent manner. Amino Acids 37 (2009) 681-691
27. Voet-van-Vormizeele J., and Groth G. Ethylene controls autophosphorylation of the histidine kinase domain in ethylene receptor ETR1. Mol Plant 1 (2008) 380-387
28. Geisinger E., George E.A., Muir T.W., and Novick R.P. Identification of ligand specificity determinants in AgrC, the Staphylococcus aureus quorum-sensing receptor. J Biol Chem 283 (2008) 8930-8938
29. Jensen R.O., Winzer K., Clarke S.R., Chan W.C., and Williams P. Differential recognition of Staphylococcus aureus quorum-sensing signals depends on both extracellular loops 1 and 2 of the transmembrane sensor AgrC. J Mol Biol 381 (2008) 300-309
30. Gordeliy V.I., Labahn J., Moukhametzianov R., Efremov R., Granzin J., Schlesinger R., Buldt G., Savopol T., Scheidig A.J., Klare J.P., et al. Molecular basis of transmembrane signalling by sensory rhodopsin II-transducer complex. Nature 419 (2002) 484-487
31. Ayers R.A., and Moffat K. Changes in quaternary structure in the signaling mechanisms of PAS domains. Biochemistry 47 (2008) 12078-12086. Analysis of high resolution structures of the FixL sensor crystallized in different space groups and in various ligand-bound states reveal a relatively plastic conserved dimer interface with implications for mechanisms of signaling.
32. Dunham C.M., Dioum E.M., Tuckerman J.R., Gonzalez G., Scott W.G., and Gilles-Gonzalez M.A. A distal arginine in oxygen-sensing Heme-PAS domains is essential to ligand binding, signal transduction, and structure. Biochemistry 42 (2003) 7701-7708
33. Gilles-Gonzalez M.A., Caceres A.I., Sousa E.H.S., Tomchick D.R., Brautigam C.A., Gonzalez C., and Machius M. A proximal arginine R206 participates in switching of the Bradyrhizobium japonicum FixL oxygen sensor. J Mol Biol 360 (2006) 80-89
34. Gong W., Hao B., Mansy S.S., Gonzalez G., Gilles-Gonzalez M.A., and Chan M.K. Structure of a biological oxygen sensor: a new mechanism for heme-driven signal transduction. Proc Natl Acad Sci USA 95 (1998) 15177-15182
35. Gong W.M., Hao B., and Chan M.K. New mechanistic insights from structural studies of the oxygen-sensing domain of Bradyrhizobium japonicum FixL. Biochemistry 39 (2000) 3955-3962
36. Hao B., Isaza C., Arndt J., Soltis M., and Chan M.K. Structure-based mechanism of O-2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum. Biochemistry 41 (2002) 12952-12958
37. Key J., and Moffat K. Crystal structures of deoxy and CO-bound bjFixLH reveal details of ligand recognition and signaling. Biochemistry 44 (2005) 4627-4635
38. Key J., Srajer V., Pahl R., and Moffat K. Time-resolved crystallographic studies of the heme domain of the oxygen sensor FixL: structural dynamics of ligand rebinding and their relation to signal transduction. Biochemistry 46 (2007) 4706-4715. Time-resolved structural studies reveals dynamics and conformational changes between ligand-bound and ligand-free states in the well-studied FixL sensor domain, with implications for mechanisms of function.
39. Miyatake H., Mukai M., Park S.Y., Adachi S., Tamura K., Nakamura H., Nakamura K., Tsuchiya T., Iizuka T., and Shiro Y. Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies. J Mol Biol 301 (2000) 415-431
40. Mullner M., Hammel O., Mienert B., Schlag S., Bill E., and Unden G. A PAS domain with an oxygen labile [4Fe-4S](2+) cluster in the oxygen sensor kinase NreB of Staphylococcus carnosus. Biochemistry 47 (2008) 13921-13932
41. Purcell E.B., Siegal-Gaskins D., Rawling D.C., Fiebig A., and Crosson S. A photosensory two-component system regulates bacterial cell attachment. Proc Natl Acad Sci USA 104 (2007) 18241-18246
42. Ukaegbu U.E., and Rosenzweig A.C. Structure of the Redox Sensor Domain of Methylococcus capsulatus (Bath) MmoS. Biochemistry 48 (2009) 2207-2215
43. Bekker M., Alexeeva S., Laan W., Sawers G., Teixeira de Mattos J., and Hellingwerf K. The ArcBA two-component system of Escherichia coli is regulated by the redox state of both the ubiquinone and the menaquinone pool. J Bacteriol 192 (2010) 746-754
44. Malpica R., Franco B., Rodriguez C., Kwon O., and Georgellis D. Identification of a quinone-sensitive redox switch in the ArcB sensor kinase. Proc Natl Acad Sci USA 101 (2004) 13318-13323
45. Holm L., and Sander C. Protein-structure comparison by alignment of distance matrices. J Mol Biol 233 (1993) 123-138
46. Ho Y.S.J., Burden L.M., and Hurley J.H. Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor (vol 19, p. 5288, 2000). EMBO J 20 (2001) 1483-11483
47. Cho H.Y., Cho H.J., Kim Y.M., Oh J.I., and Kang B.S. Structural Insight into the Heme-based Redox Sensing by DosS from Mycobacterium tuberculosis. J Biol Chem 284 (2009) 13057-13067
48. Podust L.M., Ioanoviciu A., and Ortiz de Montellano P.R. 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
49. Lee J.M., Cho H.Y., Cho H.J., Ko I.J., Park S.W., Baik H.S., Oh J.H., Eom C.Y., Kim Y.M., Kang B.S., et al. O-2- and NO-sensing mechanism through the DevSR two-component system in Mycobacterium smegmatis. J Bacteriol 190 (2008) 6795-6804
50. Yang X., Kuk J., and Moffat K. Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction. Proc Natl Acad Sci USA 105 (2008) 14715-14720
51. Yang X.J., Kuk J., and Moffat K. Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome. Proc Natl Acad Sci USA 106 (2009) 15639-15644. Structural studies of the entire dimeric photosensory core of a bacteriophytochrome in different signaling states reveal global conformational changes as well as conformational changes near the chromophore binding site and of the chromophore itself.
52. Essen L.O., Mailliet J., and Hughes J. The structure of a complete phytochrome sensory module in the Pr ground state. Proc Natl Acad Sci USA 105 (2008) 14709-14714
53. Wagner J.R., Zhang J.R., Brunzelle J.S., Vierstra R.D., and Forest K.T. High resolution structure of Deinococcus bacteriophytochrome yields new insights into phytochrome architecture and evolution. J Biol Chem 282 (2007) 12298-12309
54. Yang X., Stojkovic E.A., Kuk J., and Moffatt K. Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion. Proc Natl Acad Sci USA 104 (2007) 12571-12576
55. Grasberger B., Minton A.P., Delisi C., and Metzger H. Interaction between proteins localized in membranes. Proc Natl Acad Sci USA 83 (1986) 6258-6262
56. Marina A., Waldburger C.D., and Hendrickson W.A. Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein. EMBO J 24 (2005) 4247-4259
57. Chervitz S.A., and Falke J.J. Molecular mechanism of transmembrane signaling by the aspartate receptor: a model. Proc Natl Acad Sci USA 93 (1996) 2545-2550