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Solution structure of human peptidyl prolyl isomerase-like protein 1 and insights into its interaction with SKIP.

Xu C, Zhang J, Huang X, Sun J, Xu Y, Tang Y, Wu J, Shi Y, Huang Q, Zhang Q
J Biol Chem 281 15900-8 (2006)
Cited: 31 times
EuropePMC logo PMID: 16595688

Abstract

The human PPIL1 (peptidyl prolyl isomerase-like protein 1) is a specific component of human 35 S U5 small nuclear ribonucleoprotein particle and 45 S activated spliceosome. It is recruited by SKIP, another essential component of 45 S activated spliceosome, into spliceosome just before the catalytic step 1. It stably associates with SKIP, which also exists in 35 S and activated spliceosome as a nuclear matrix protein. We report here the solution structure of PPIL1 determined by NMR spectroscopy. The structure of PPIL1 resembles other members of the cyclophilin family and exhibits PPIase activity. To investigate its interaction with SKIP in vitro, we identified the SKIP contact region by GST pulldown experiments and surface plasmon resonance. We provide direct evidence of PPIL1 stably associated with SKIP. The dissociation constant is 1.25 x 10(-7) M for the N-terminal peptide of SKIP-(59-129) with PPIL1. We also used chemical shift perturbation experiments to show the possible SKIP binding interface on PPIL1. These results illustrated that a novel cyclophilin-protein contact mode exists in the PPIL1-SKIP complex during activation of the spliceosome. The biological implication of this binding with spliceosome rearrangement during activation is discussed.

Reviews - 1xwn mentioned but not cited (2)

  1. Roles of Prolyl Isomerases in RNA-Mediated Gene Expression. Thapar R. Biomolecules 5 974-999 (2015)
  2. Structural and Functional Insights into Human Nuclear Cyclophilins. Rajiv C, Davis TL. Biomolecules 8 (2018)

Articles - 1xwn mentioned but not cited (1)

  1. Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases. Davis TL, Walker JR, Campagna-Slater V, Finerty PJ, Paramanathan R, Bernstein G, MacKenzie F, Tempel W, Ouyang H, Lee WH, Eisenmesser EZ, Dhe-Paganon S. PLoS Biol 8 e1000439 (2010)


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  1. Structural mechanisms of cyclophilin D-dependent control of the mitochondrial permeability transition pore. Gutiérrez-Aguilar M, Baines CP. Biochim Biophys Acta 1850 2041-2047 (2015)
  2. Cyclophilins as modulators of viral replication. Frausto SD, Lee E, Tang H. Viruses 5 1684-1701 (2013)
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  5. From Drosophila to humans: reflections on the roles of the prolyl isomerases and chaperones, cyclophilins, in cell function and disease. Ferreira PA, Orry A. J Neurogenet 26 132-143 (2012)
  6. Structural basis of protein-protein interaction studied by NMR. Shi Y, Wu J. J Struct Funct Genomics 8 67-72 (2007)

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  2. Cryo-EM structure of a human spliceosome activated for step 2 of splicing. Bertram K, Agafonov DE, Liu WT, Dybkov O, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Lührmann R. Nature 542 318-323 (2017)
  3. Structure of a human catalytic step I spliceosome. Zhan X, Yan C, Zhang X, Zhang X, Lei J, Shi Y. Science 359 537-545 (2018)
  4. Survey of the year 2006 commercial optical biosensor literature. Rich RL, Myszka DG. J Mol Recognit 20 300-366 (2007)
  5. Regulation of intestinal epithelial cells transcriptome by enteric glial cells: impact on intestinal epithelial barrier functions. Van Landeghem L, Mahé MM, Teusan R, Léger J, Guisle I, Houlgatte R, Neunlist M. BMC Genomics 10 507 (2009)
  6. SKIP counteracts p53-mediated apoptosis via selective regulation of p21Cip1 mRNA splicing. Chen Y, Zhang L, Jones KA. Genes Dev 25 701-716 (2011)
  7. SWATH analysis of the synaptic proteome in Alzheimer's disease. Chang RY, Etheridge N, Nouwens AS, Dodd PR. Neurochem Int 87 1-12 (2015)
  8. A large intrinsically disordered region in SKIP and its disorder-order transition induced by PPIL1 binding revealed by NMR. Wang X, Zhang S, Zhang J, Huang X, Xu C, Wang W, Liu Z, Wu J, Shi Y. J Biol Chem 285 4951-4963 (2010)
  9. In silico analysis of the cyclophilin repertoire of apicomplexan parasites. Krücken J, Greif G, von Samson-Himmelstjerna G. Parasit Vectors 2 27 (2009)
  10. The crystal structure of PPIL1 bound to cyclosporine A suggests a binding mode for a linear epitope of the SKIP protein. Stegmann CM, Lührmann R, Wahl MC. PLoS One 5 e10013 (2010)
  11. Rice cyclophilin OsCYP18-2 is translocated to the nucleus by an interaction with SKIP and enhances drought tolerance in rice and Arabidopsis. Lee SS, Park HJ, Yoon DH, Kim BG, Ahn JC, Luan S, Cho HS. Plant Cell Environ 38 2071-2087 (2015)
  12. The crystal structure of human WD40 repeat-containing peptidylprolyl isomerase (PPWD1). Davis TL, Walker JR, Ouyang H, MacKenzie F, Butler-Cole C, Newman EM, Eisenmesser EZ, Dhe-Paganon S. FEBS J 275 2283-2295 (2008)
  13. Structure and evolution of the spliceosomal peptidyl-prolyl cis-trans isomerase Cwc27. Ulrich A, Wahl MC. Acta Crystallogr D Biol Crystallogr 70 3110-3123 (2014)
  14. Nuclear cyclophilins affect spliceosome assembly and function in vitro. Adams BM, Coates MN, Jackson SR, Jurica MS, Davis TL. Biochem J 469 223-233 (2015)
  15. Transmembrane helix 1 contributes to substrate translocation and protein stability of bile acid transporter SLC10A2. da Silva TC, Hussainzada N, Khantwal CM, Polli JE, Swaan PW. J Biol Chem 286 27322-27332 (2011)
  16. Congress Visualization and orchestration of the dynamic molecular society in cells. Yao X, Fang G. Cell Res 19 152-155 (2009)
  17. High SKIP expression is correlated with poor prognosis and cell proliferation of hepatocellular carcinoma. Liu G, Huang X, Cui X, Zhang J, Wei L, Ni R, Lu C. Med Oncol 30 537 (2013)
  18. Targeting the cyclophilin domain of Ran-binding protein 2 (Ranbp2) with novel small molecules to control the proteostasis of STAT3, hnRNPA2B1 and M-opsin. Cho KI, Orry A, Park SE, Ferreira PA. ACS Chem Neurosci 6 1476-1485 (2015)
  19. Compound Interaction Screen on a Photoactivatable Cellulose Membrane (CISCM) Identifies Drug Targets. Melder FTI, Lindemann P, Welle A, Trouillet V, Heißler S, Nazaré M, Selbach M. ChemMedChem 17 e202200346 (2022)
  20. Nineteen complex-related factor Prp45 is required for the early stages of cotranscriptional spliceosome assembly. Hálová M, Gahura O, Převorovský M, Cit Z, Novotný M, Valentová A, Abrhámová K, Půta F, Folk P. RNA 23 1512-1524 (2017)
  21. Mutations in Spliceosomal Genes PPIL1 and PRP17 Cause Neurodegenerative Pontocerebellar Hypoplasia with Microcephaly. Chai G, Webb A, Li C, Antaki D, Lee S, Breuss MW, Lang N, Stanley V, Anzenberg P, Yang X, Marshall T, Gaffney P, Wierenga KJ, Chung BH, Tsang MH, Pais LS, Lovgren AK, VanNoy GE, Rehm HL, Mirzaa G, Leon E, Diaz J, Neumann A, Kalverda AP, Manfield IW, Parry DA, Logan CV, Johnson CA, Bonthron DT, Valleley EMA, Issa MY, Abdel-Ghafar SF, Abdel-Hamid MS, Jennings P, Zaki MS, Sheridan E, Gleeson JG. Neuron 109 241-256.e9 (2021)
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