Home LiteratureArticle Details
PMID: 21505417 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Crystal structure of the intraflagellar transport complex 25/27.

The EMBO journal ·Vol. 30 ·No. 10 ·2011-05-18 ·Pages 1907-18

Bhogaraju S, Taschner M, Morawetz M, Basquin C, Lorentzen E

Abstract

The cilium is an important organelle that is found on many eukaryotic cells, where it serves essential functions in motility, sensory reception and signalling. Intraflagellar transport (IFT) is a vital process for the formation and maintenance of cilia. We have determined the crystal structure of Chlamydomonas reinhardtii IFT25/27, an IFT sub-complex, at 2.6 Å resolution. IFT25 and IFT27 interact via a conserved interface that we verify biochemically using structure-guided mutagenesis. IFT27 displays the fold of Rab-like small guanosine triphosphate hydrolases (GTPases), binds GTP and GDP with micromolar affinity and has very low intrinsic GTPase activity, suggesting that it likely requires a GTPase-activating protein (GAP) for robust GTP turnover. A patch of conserved surface residues contributed by both IFT25 and IFT27 is found adjacent to the GTP-binding site and could mediate the binding to other IFT proteins as well as to a potential GAP. These results provide the first step towards a high-resolution structural understanding of the IFT complex.

MeSH Terms
Amino Acid Sequence Carrier Proteins/chemistry,genetics,metabolism Chlamydomonas reinhardtii/chemistry,genetics Crystallography, X-Ray DNA Mutational Analysis Guanosine Diphosphate/metabolism Guanosine Triphosphate/metabolism Models, Molecular Molecular Sequence Data Mutagenesis, Site-Directed Protein Binding Protein Interaction Domains and Motifs Protein Interaction Mapping Protein Structure, Quaternary Sequence Homology, Amino Acid
Chemicals
Carrier Proteins Guanosine Diphosphate Guanosine Triphosphate
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Bhogaraju Sagar
Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany.
Taschner Michael
Morawetz Michaela
Basquin Claire
Lorentzen Esben
References (74)
74 references, click to expand
  1. Intraflagellar transport protein 27 is a small G protein involved in cell-cycle control.
    Curr Biol. 2007 Feb 6;17(3):193-202 PMID: 17276912
  2. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W299-302 PMID: 15980475
  3. Gli2 and Gli3 localize to cilia and require the intraflagellar transport protein polaris for processing and function.
    PLoS Genet. 2005 Oct;1(4):e53 PMID: 16254602
  4. Likelihood-enhanced fast rotation functions.
    Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):432-8 PMID: 14993666
  5. Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.
    Proteins. 2009 Apr;75(1):147-67 PMID: 18816799
  6. Functional coordination of intraflagellar transport motors.
    Nature. 2005 Jul 28;436(7050):583-7 PMID: 16049494
  7. The major alpha-tubulin K40 acetyltransferase alphaTAT1 promotes rapid ciliogenesis and efficient mechanosensation.
    Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21517-22 PMID: 21068373
  8. TBC-domain GAPs for Rab GTPases accelerate GTP hydrolysis by a dual-finger mechanism.
    Nature. 2006 Jul 20;442(7100):303-6 PMID: 16855591
  9. The guanine nucleotide-binding switch in three dimensions.
    Science. 2001 Nov 9;294(5545):1299-304 PMID: 11701921
  10. Chlamydomonas IFT172 is encoded by FLA11, interacts with CrEB1, and regulates IFT at the flagellar tip.
    Curr Biol. 2005 Feb 8;15(3):262-6 PMID: 15694311
  11. Identification of signaling pathways regulating primary cilium length and flow-mediated adaptation.
    Curr Biol. 2010 Jan 26;20(2):182-7 PMID: 20096584
  12. A genetic screen in zebrafish identifies cilia genes as a principal cause of cystic kidney.
    Development. 2004 Aug;131(16):4085-93 PMID: 15269167
  13. The conserved Bardet-Biedl syndrome proteins assemble a coat that traffics membrane proteins to cilia.
    Cell. 2010 Jun 25;141(7):1208-19 PMID: 20603001
  14. Cilia and flagella revealed: from flagellar assembly in Chlamydomonas to human obesity disorders.
    Cell. 2004 Jun 11;117(6):693-7 PMID: 15186771
  15. The GTPase-activating protein Rap1GAP uses a catalytic asparagine.
    Nature. 2004 May 13;429(6988):197-201 PMID: 15141215
  16. A motility in the eukaryotic flagellum unrelated to flagellar beating.
    Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5519-23 PMID: 8516294
  17. Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis.
    EMBO J. 1990 Aug;9(8):2351-9 PMID: 2196171
  18. Chlamydomonas IFT70/CrDYF-1 is a core component of IFT particle complex B and is required for flagellar assembly.
    Mol Biol Cell. 2010 Aug 1;21(15):2696-706 PMID: 20534810
  19. A core complex of BBS proteins cooperates with the GTPase Rab8 to promote ciliary membrane biogenesis.
    Cell. 2007 Jun 15;129(6):1201-13 PMID: 17574030
  20. The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants.
    Science. 1997 Jul 18;277(5324):333-8 PMID: 9219684
  21. HA-tagging of putative flagellar proteins in Chlamydomonas reinhardtii identifies a novel protein of intraflagellar transport complex B.
    Cell Motil Cytoskeleton. 2009 Aug;66(8):469-82 PMID: 19382199
  22. PDGFRalphaalpha signaling is regulated through the primary cilium in fibroblasts.
    Curr Biol. 2005 Oct 25;15(20):1861-6 PMID: 16243034
  23. Crystal structure of IIGP1: a paradigm for interferon-inducible p47 resistance GTPases.
    Mol Cell. 2004 Sep 10;15(5):727-39 PMID: 15350217
  24. Intraflagellar transport is required in Drosophila to differentiate sensory cilia but not sperm.
    Curr Biol. 2003 Sep 30;13(19):1679-86 PMID: 14521833
  25. Chlamydomonas kinesin-II-dependent intraflagellar transport (IFT): IFT particles contain proteins required for ciliary assembly in Caenorhabditis elegans sensory neurons.
    J Cell Biol. 1998 May 18;141(4):993-1008 PMID: 9585417
  26. Intraflagellar transport (IFT) cargo: IFT transports flagellar precursors to the tip and turnover products to the cell body.
    J Cell Biol. 2004 Jan 19;164(2):255-66 PMID: 14718520
  27. On flagellar structure in certain flagellates.
    J Biophys Biochem Cytol. 1960 Jul;7:697-716 PMID: 13827900
  28. Direct interactions of intraflagellar transport complex B proteins IFT88, IFT52, and IFT46.
    J Biol Chem. 2010 Jul 9;285(28):21508-18 PMID: 20435895
  29. IIGP1, an interferon-gamma-inducible 47-kDa GTPase of the mouse, showing cooperative enzymatic activity and GTP-dependent multimerization.
    J Biol Chem. 2003 Aug 1;278(31):29336-43 PMID: 12732635
  30. Guidelines for the nomenclature of the human heat shock proteins.
    Cell Stress Chaperones. 2009 Jan;14(1):105-11 PMID: 18663603
  31. RhoBTB3: a Rho GTPase-family ATPase required for endosome to Golgi transport.
    Cell. 2009 May 29;137(5):938-48 PMID: 19490898
  32. Vps9, Rabex-5 and DSS4: proteins with weak but distinct nucleotide-exchange activities for Rab proteins.
    J Mol Biol. 2001 Jun 29;310(1):141-56 PMID: 11419942
  33. The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll.
    Structure. 1995 Nov 15;3(11):1197-205 PMID: 8591030
  34. Why proteins without an alpha-crystallin domain should not be included in the human small heat shock protein family HSPB.
    Cell Stress Chaperones. 2010 Jul;15(4):457-61 PMID: 19921466
  35. Carbohydrate recognition by a large sialidase toxin from Clostridium perfringens.
    Biochemistry. 2007 Oct 9;46(40):11352-60 PMID: 17850114
  36. Localization of 5-HT(6) receptors at the plasma membrane of neuronal cilia in the rat brain.
    Brain Res. 2000 Jul 28;872(1-2):271-5 PMID: 10924708
  37. Proteomic analysis of a eukaryotic cilium.
    J Cell Biol. 2005 Jul 4;170(1):103-13 PMID: 15998802
  38. Mutant sensory cilia in the nematode Caenorhabditis elegans.
    Dev Biol. 1986 Oct;117(2):456-87 PMID: 2428682
  39. Molecular mechanisms of protein and lipid targeting to ciliary membranes.
    J Cell Sci. 2010 Feb 15;123(Pt 4):529-36 PMID: 20145001
  40. Kinetics of interaction of Rab5 and Rab7 with nucleotides and magnesium ions.
    J Biol Chem. 1996 Aug 23;271(34):20470-8 PMID: 8702787
  41. Preventing apoptotic cell death by a novel small heat shock protein.
    Eur J Cell Biol. 2007 Mar;86(3):161-71 PMID: 17275951
  42. Crystal structures of alpha-crystallin domain dimers of alphaB-crystallin and Hsp20.
    J Mol Biol. 2009 Oct 9;392(5):1242-52 PMID: 19646995
  43. Intraflagellar transport (IFT) protein IFT25 is a phosphoprotein component of IFT complex B and physically interacts with IFT27 in Chlamydomonas.
    PLoS One. 2009;4(5):e5384 PMID: 19412537
  44. A novel function for the atypical small G protein Rab-like 5 in the assembly of the trypanosome flagellum.
    J Cell Sci. 2009 Mar 15;122(Pt 6):834-41 PMID: 19240117
  45. Transport of a novel complex in the cytoplasmic matrix of Chlamydomonas flagella.
    Proc Natl Acad Sci U S A. 1997 Apr 29;94(9):4457-62 PMID: 9114011
  46. Structure at 1.65 A of RhoA and its GTPase-activating protein in complex with a transition-state analogue.
    Nature. 1997 Oct 16;389(6652):758-62 PMID: 9338791
  47. The Rap-RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues.
    EMBO J. 2008 Apr 9;27(7):1145-53 PMID: 18309292
  48. IFT80, which encodes a conserved intraflagellar transport protein, is mutated in Jeune asphyxiating thoracic dystrophy.
    Nat Genet. 2007 Jun;39(6):727-9 PMID: 17468754
  49. Bardet-Biedl syndrome: beyond the cilium.
    Pediatr Nephrol. 2007 Jul;22(7):926-36 PMID: 17357787
  50. Coot: model-building tools for molecular graphics.
    Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32 PMID: 15572765
  51. PHENIX: a comprehensive Python-based system for macromolecular structure solution.
    Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21 PMID: 20124702
  52. Evolution of intraflagellar transport from coated vesicles and autogenous origin of the eukaryotic cilium.
    Bioessays. 2006 Feb;28(2):191-8 PMID: 16435301
  53. Hedgehog signalling in the mouse requires intraflagellar transport proteins.
    Nature. 2003 Nov 6;426(6962):83-7 PMID: 14603322
  54. PKD2 functions as an epidermal growth factor-activated plasma membrane channel.
    Mol Cell Biol. 2005 Sep;25(18):8285-98 PMID: 16135816
  55. Intraflagellar transport genes are essential for differentiation and survival of vertebrate sensory neurons.
    Neuron. 2004 Jun 10;42(5):703-16 PMID: 15182712
  56. Rab GTPases as coordinators of vesicle traffic.
    Nat Rev Mol Cell Biol. 2009 Aug;10(8):513-25 PMID: 19603039
  57. Structure and function of mammalian cilia.
    Histochem Cell Biol. 2008 Jun;129(6):687-93 PMID: 18365235
  58. Electron-tomographic analysis of intraflagellar transport particle trains in situ.
    J Cell Biol. 2009 Oct 5;187(1):135-48 PMID: 19805633
  59. Biological and biochemical properties of human rasH genes mutated at codon 61.
    Cell. 1986 Jan 17;44(1):167-76 PMID: 3510078
  60. Insight into catalysis of a unique GTPase reaction by a combined biochemical and FTIR approach.
    J Mol Biol. 2007 Apr 6;367(4):983-95 PMID: 17300802
  61. Structure of the Sec23/24-Sar1 pre-budding complex of the COPII vesicle coat.
    Nature. 2002 Sep 19;419(6904):271-7 PMID: 12239560
  62. Towards a proteome-scale map of the human protein-protein interaction network.
    Nature. 2005 Oct 20;437(7062):1173-8 PMID: 16189514
  63. Coordination of Rab8 and Rab11 in primary ciliogenesis.
    Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6346-51 PMID: 20308558
  64. The Oak Ridge Polycystic Kidney (orpk) disease gene is required for left-right axis determination.
    Development. 2000 Jun;127(11):2347-55 PMID: 10804177
  65. Protein structure comparison by alignment of distance matrices.
    J Mol Biol. 1993 Sep 5;233(1):123-38 PMID: 8377180
  66. Characterization of mouse IFT complex B.
    Cell Motil Cytoskeleton. 2009 Aug;66(8):457-68 PMID: 19253336
  67. CEP290 tethers flagellar transition zone microtubules to the membrane and regulates flagellar protein content.
    J Cell Biol. 2010 Sep 6;190(5):927-40 PMID: 20819941
  68. Chlamydomonas IFT88 and its mouse homologue, polycystic kidney disease gene tg737, are required for assembly of cilia and flagella.
    J Cell Biol. 2000 Oct 30;151(3):709-18 PMID: 11062270
  69. Distinct mutants of retrograde intraflagellar transport (IFT) share similar morphological and molecular defects.
    J Cell Biol. 1998 Dec 14;143(6):1591-601 PMID: 9852153
  70. Characterization of the intraflagellar transport complex B core: direct interaction of the IFT81 and IFT74/72 subunits.
    J Biol Chem. 2005 Jul 29;280(30):27688-96 PMID: 15955805
  71. The mechanism for activation of GTP hydrolysis on the ribosome.
    Science. 2010 Nov 5;330(6005):835-838 PMID: 21051640
  72. GTPase activating proteins: structural and functional insights 18 years after discovery.
    Cell Mol Life Sci. 2005 Dec;62(24):3014-38 PMID: 16314935
  73. The primary cilium in cell signaling and cancer.
    Cancer Res. 2006 Jul 1;66(13):6463-7 PMID: 16818613
  74. RanGAP mediates GTP hydrolysis without an arginine finger.
    Nature. 2002 Feb 7;415(6872):662-6 PMID: 11832950
Article Info
Journal
The EMBO journal
Abbr.
EMBO J
ISSN
1460-2075
Published
2011-05-18
Epub
2011-00-19
Pages
1907-18
Language
English
Region
England
NLM ID
8208664
PMCID
PMC3098482
Subset
IM
Databases
PDB
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]