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PMID: 19836329 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Review

Structure and signaling mechanism of Per-ARNT-Sim domains.

Structure (London, England : 1993) ·Vol. 17 ·No. 10 ·2009-10-14 ·Pages 1282-94

Möglich A, Ayers RA, Moffat K

Abstract

Per-ARNT-Sim (PAS) domains serve as versatile sensor and interaction modules in signal transduction proteins. PAS sensors detect chemical and physical stimuli and regulate the activity of functionally diverse effector domains. In contrast to this chemical, physical, and functional diversity, the structure of the core of PAS domains is broadly conserved and comprises a five-stranded antiparallel beta sheet and several alpha helices. Signals originate within the conserved core and generate structural and dynamic changes predominantly within the beta sheet, from which they propagate via amphipathic alpha-helical and coiled-coil linkers at the N or C termini of the core to the covalently attached effector domain. Effector domains are typically dimeric; their activity appears to be largely regulated by signal-dependent changes in quaternary structure and dynamics. The signaling mechanisms of PAS and other signaling domains share common features, and these commonalities can be exploited to enable structure-based design of artificial photosensors and chemosensors.

MeSH Terms
Amino Acid Sequence Animals Binding Sites Humans Models, Molecular Molecular Sequence Data Protein Serine-Threonine Kinases/chemistry,metabolism Protein Structure, Tertiary Signal Transduction
Chemicals
PAS domain kinases Protein Serine-Threonine Kinases
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Möglich Andreas
Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
Ayers Rebecca A
Moffat Keith
References (74)
74 references, click to expand
  1. Assembly of cell regulatory systems through protein interaction domains.
    Science. 2003 Apr 18;300(5618):445-52 PMID: 12702867
  2. Structure of the NCoA-1/SRC-1 PAS-B domain bound to the LXXLL motif of the STAT6 transactivation domain.
    J Mol Biol. 2004 Feb 13;336(2):319-29 PMID: 14757047
  3. Light-activated DNA binding in a designed allosteric protein.
    Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10709-14 PMID: 18667691
  4. Sensor complexes regulating two-component signal transduction.
    Curr Opin Struct Biol. 2007 Dec;17(6):706-15 PMID: 17913492
  5. An optomechanical transducer in the blue light receptor phototropin from Avena sativa.
    Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12357-61 PMID: 11606742
  6. 2.3 A X-ray structure of the heme-bound GAF domain of sensory histidine kinase DosT of Mycobacterium tuberculosis.
    Biochemistry. 2008 Nov 25;47(47):12523-31 PMID: 18980385
  7. Artificial ligand binding within the HIF2alpha PAS-B domain of the HIF2 transcription factor.
    Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):450-5 PMID: 19129502
  8. 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore.
    Biochemistry. 1995 May 16;34(19):6278-87 PMID: 7756254
  9. PAS domains: internal sensors of oxygen, redox potential, and light.
    Microbiol Mol Biol Rev. 1999 Jun;63(2):479-506 PMID: 10357859
  10. Tropomyosin coiled-coil interactions: evidence for an unstaggered structure.
    J Mol Biol. 1975 Oct 25;98(2):293-304 PMID: 1195389
  11. Structure of the entire cytoplasmic portion of a sensor histidine-kinase protein.
    EMBO J. 2005 Dec 21;24(24):4247-59 PMID: 16319927
  12. Conformational switching in the fungal light sensor Vivid.
    Science. 2007 May 18;316(5827):1054-7 PMID: 17510367
  13. Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing.
    Cell. 2006 Sep 22;126(6):1095-108 PMID: 16990134
  14. Design and signaling mechanism of light-regulated histidine kinases.
    J Mol Biol. 2009 Feb 6;385(5):1433-44 PMID: 19109976
  15. GGDEF domain is homologous to adenylyl cyclase.
    Proteins. 2001 Feb 1;42(2):210-6 PMID: 11119645
  16. The universal protein resource (UniProt).
    Nucleic Acids Res. 2008 Jan;36(Database issue):D190-5 PMID: 18045787
  17. The PAS fold. A redefinition of the PAS domain based upon structural prediction.
    Eur J Biochem. 2004 Mar;271(6):1198-208 PMID: 15009198
  18. Intermolecular complementation between two defective mutant signal-transducing receptors of Escherichia coli.
    Proc Natl Acad Sci U S A. 1991 Dec 15;88(24):11057-61 PMID: 1662380
  19. The Drosophila single-minded gene encodes a helix-loop-helix protein that acts as a master regulator of CNS midline development.
    Cell. 1991 Dec 20;67(6):1157-67 PMID: 1760843
  20. PAS is a dimerization domain common to Drosophila period and several transcription factors.
    Nature. 1993 Jul 15;364(6434):259-62 PMID: 8391649
  21. Cascade regulation of nif gene expression in Rhizobium meliloti.
    Cell. 1988 Aug 26;54(5):671-83 PMID: 2842062
  22. Bacterial signal transduction network in a genomic perspective.
    Environ Microbiol. 2004 Jun;6(6):552-67 PMID: 15142243
  23. Photoexcited structure of a plant photoreceptor domain reveals a light-driven molecular switch.
    Plant Cell. 2002 May;14(5):1067-75 PMID: 12034897
  24. PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox.
    Trends Biochem Sci. 1997 Sep;22(9):331-3 PMID: 9301332
  25. Surface sites for engineering allosteric control in proteins.
    Science. 2008 Oct 17;322(5900):438-42 PMID: 18927392
  26. Cache - a signaling domain common to animal Ca(2+)-channel subunits and a class of prokaryotic chemotaxis receptors.
    Trends Biochem Sci. 2000 Nov;25(11):535-7 PMID: 11084361
  27. Changes in quaternary structure in the signaling mechanisms of PAS domains.
    Biochemistry. 2008 Nov 18;47(46):12078-86 PMID: 18942854
  28. Structural basis for light-dependent signaling in the dimeric LOV domain of the photosensor YtvA.
    J Mol Biol. 2007 Oct 12;373(1):112-26 PMID: 17764689
  29. Arabidopsis NPH1: a protein kinase with a putative redox-sensing domain.
    Science. 1997 Dec 19;278(5346):2120-3 PMID: 9405347
  30. C4-dicarboxylates sensing mechanism revealed by the crystal structures of DctB sensor domain.
    J Mol Biol. 2008 Oct 31;383(1):49-61 PMID: 18725229
  31. Structure of a protein photocycle intermediate by millisecond time-resolved crystallography.
    Science. 1997 Mar 7;275(5305):1471-5 PMID: 9045611
  32. Crystal structure and functional analysis of the HERG potassium channel N terminus: a eukaryotic PAS domain.
    Cell. 1998 Nov 25;95(5):649-55 PMID: 9845367
  33. Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors.
    Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2885-90 PMID: 17299051
  34. Crystal structures of deoxy and CO-bound bjFixLH reveal details of ligand recognition and signaling.
    Biochemistry. 2005 Mar 29;44(12):4627-35 PMID: 15779889
  35. Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction.
    Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14715-20 PMID: 18799746
  36. Structural basis of a phototropin light switch.
    Science. 2003 Sep 12;301(5639):1541-4 PMID: 12970567
  37. Structural basis of activity and allosteric control of diguanylate cyclase.
    Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17084-9 PMID: 15569936
  38. Elasticity of alpha-helical coiled coils.
    Phys Rev Lett. 2006 Dec 15;97(24):248101 PMID: 17280328
  39. Estimation of the available free energy in a LOV2-J alpha photoswitch.
    Nat Chem Biol. 2008 Aug;4(8):491-7 PMID: 18604202
  40. Pfam: clans, web tools and services.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51 PMID: 16381856
  41. Comparison of experimental binding data and theoretical models in proteins containing subunits.
    Biochemistry. 1966 Jan;5(1):365-85 PMID: 5938952
  42. A redox-controlled molecular switch revealed by the crystal structure of a bacterial heme PAS sensor.
    J Biol Chem. 2004 May 7;279(19):20186-93 PMID: 14982921
  43. Stimulus perception in bacterial signal-transducing histidine kinases.
    Microbiol Mol Biol Rev. 2006 Dec;70(4):910-38 PMID: 17158704
  44. Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2.
    J Mol Biol. 2008 Sep 5;381(3):718-33 PMID: 18585389
  45. PAS: a multifunctional domain family comes to light.
    Curr Biol. 1997 Nov 1;7(11):R674-7 PMID: 9382818
  46. Crystal structure of a functional dimer of the PhoQ sensor domain.
    J Biol Chem. 2008 May 16;283(20):13762-70 PMID: 18348979
  47. Structure of the redox sensor domain of Azotobacter vinelandii NifL at atomic resolution: signaling, dimerization, and mechanism.
    Biochemistry. 2007 Mar 27;46(12):3614-23 PMID: 17319691
  48. The GAF domain: an evolutionary link between diverse phototransducing proteins.
    Trends Biochem Sci. 1997 Dec;22(12):458-9 PMID: 9433123
  49. N- and C-terminal flanking regions modulate light-induced signal transduction in the LOV2 domain of the blue light sensor phototropin 1 from Avena sativa.
    Biochemistry. 2007 Dec 11;46(49):14001-9 PMID: 18001137
  50. The structure of a complete phytochrome sensory module in the Pr ground state.
    Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14709-14 PMID: 18799745
  51. A ligand-induced switch in the periplasmic domain of sensor histidine kinase CitA.
    J Mol Biol. 2008 Mar 21;377(2):512-23 PMID: 18258261
  52. Role of the PAS domain in regulation of dimerization and DNA binding specificity of the dioxin receptor.
    Mol Cell Biol. 1998 Jul;18(7):4079-88 PMID: 9632792
  53. Crystal structures and molecular mechanism of a light-induced signaling switch: The Phot-LOV1 domain from Chlamydomonas reinhardtii.
    Biophys J. 2003 Apr;84(4):2474-82 PMID: 12668455
  54. Profile hidden Markov models.
    Bioinformatics. 1998;14(9):755-63 PMID: 9918945
  55. A structural pathway for signaling in the E46Q mutant of photoactive yellow protein.
    Structure. 2005 Jan;13(1):55-63 PMID: 15642261
  56. Crystal structure and interactions of the PAS repeat region of the Drosophila clock protein PERIOD.
    Mol Cell. 2005 Jan 7;17(1):69-82 PMID: 15629718
  57. White Collar-1, a circadian blue light photoreceptor, binding to the frequency promoter.
    Science. 2002 Aug 2;297(5582):815-9 PMID: 12098706
  58. Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor.
    EMBO J. 2000 Oct 16;19(20):5288-99 PMID: 11032796
  59. BLUF: a novel FAD-binding domain involved in sensory transduction in microorganisms.
    Trends Biochem Sci. 2002 Oct;27(10):497-500 PMID: 12368079
  60. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  61. The signaling helix: a common functional theme in diverse signaling proteins.
    Biol Direct. 2006 Sep 05;1:25 PMID: 16953892
  62. A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome.
    Nature. 2005 Nov 17;438(7066):325-31 PMID: 16292304
  63. Changes at the KinA PAS-A dimerization interface influence histidine kinase function.
    Biochemistry. 2008 Apr 1;47(13):4051-64 PMID: 18324779
  64. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D198-201 PMID: 17145705
  65. Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: crystallographic, mutagenesis and resonance Raman spectroscopic studies.
    J Mol Biol. 2000 Aug 11;301(2):415-31 PMID: 10926518
  66. Arabidopsis NPH1: a flavoprotein with the properties of a photoreceptor for phototropism.
    Science. 1998 Nov 27;282(5394):1698-701 PMID: 9831559
  67. ARNT PAS-B has a fragile native state structure with an alternative beta-sheet register nearby in sequence space.
    Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2617-22 PMID: 19196990
  68. Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains.
    J Mol Biol. 2001 Apr 13;307(5):1271-92 PMID: 11292341
  69. ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.
    J Mol Biol. 1965 May;12:88-118 PMID: 14343300
  70. Dynamic helix interactions in transmembrane signaling.
    Cell. 2006 Nov 3;127(3):447-50 PMID: 17081964
  71. Cloning of a factor required for activity of the Ah (dioxin) receptor.
    Science. 1991 May 17;252(5008):954-8 PMID: 1852076
  72. The LOV domain family: photoresponsive signaling modules coupled to diverse output domains.
    Biochemistry. 2003 Jan 14;42(1):2-10 PMID: 12515534
  73. Structural basis of ARNT PAS-B dimerization: use of a common beta-sheet interface for hetero- and homodimerization.
    J Mol Biol. 2005 Oct 28;353(3):664-77 PMID: 16181639
  74. PAS-mediated dimerization of soluble guanylyl cyclase revealed by signal transduction histidine kinase domain crystal structure.
    J Biol Chem. 2008 Jan 11;283(2):1167-78 PMID: 18006497
Article Info
Journal
Structure (London, England : 1993)
Abbr.
Structure
ISSN
1878-4186
DOI
10.1016/j.str.2009.08.011
Published
2009-10-14
Pages
1282-94
Language
English
Region
United States
NLM ID
101087697
PMCID
PMC3092527
Subset
IM
Grants
NCRR NIH HHS · P41 RR007707 · United States
NCRR NIH HHS · P41 RR007707-130233 · United States
NIGMS NIH HHS · GM 036452 · United States
NIGMS NIH HHS · R37 GM036452 · United States
NIGMS NIH HHS · R01 GM036452-24 · United States
NIGMS NIH HHS · R01 GM036452 · United States
NCRR NIH HHS · P41 RR007707-17 · United States
External Links
PubMed source DOI: 10.1016/j.str.2009.08.011 PMC Full Text View journal details
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