Proteopedia

5my8

Crystal structure of SRPK1 in complex with SPHINX31Crystal structure of SRPK1 in complex with SPHINX31

Structural highlights

5my8 is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SRPK1_HUMAN Serine/arginine-rich protein-specific kinase which specifically phosphorylates its substrates at serine residues located in regions rich in arginine/serine dipeptides, known as RS domains and is involved in the phosphorylation of SR splicing factors and the regulation of splicing. Plays a central role in the regulatory network for splicing, controlling the intranuclear distribution of splicing factors in interphase cells and the reorganization of nuclear speckles during mitosis. Can influence additional steps of mRNA maturation, as well as other cellular activities, such as chromatin reorganization in somatic and sperm cells and cell cycle progression. Isoform 2 phosphorylates SFRS2, ZRSR2, LBR and PRM1. Isoform 2 phosphorylates SRSF1 using a directional (C-terminal to N-terminal) and a dual-track mechanism incorporating both processive phosphorylation (in which the kinase stays attached to the substrate after each round of phosphorylation) and distributive phosphorylation steps (in which the kinase and substrate dissociate after each phosphorylation event). The RS domain of SRSF1 binds first to a docking groove in the large lobe of the kinase domain of SRPK1. This induces certain structural changes in SRPK1 and/or RRM2 domain of SRSF1, allowing RRM2 to bind the kinase and initiate phosphorylation. The cycles continue for several phosphorylation steps in a processive manner (steps 1-8) until the last few phosphorylation steps (approximately steps 9-12). During that time, a mechanical stress induces the unfolding of the beta-4 motif in RRM2, which then docks at the docking groove of SRPK1. This also signals RRM2 to begin to dissociate, which facilitates SRSF1 dissociation after phosphorylation is completed. Isoform 2 can mediate hepatitis B virus (HBV) core protein phosphorylation. It plays a negative role in the regulation of HBV replication through a mechanism not involving the phosphorylation of the core protein but by reducing the packaging efficiency of the pregenomic RNA (pgRNA) without affecting the formation of the viral core particles. Isoform 1 and isoform 2 can induce splicing of exon 10 in MAPT/TAU. The ratio of isoform 1/isoform 2 plays a decisive role in determining cell fate in K-562 leukaemic cell line: isoform 2 favors proliferation where as isoform 1 favors differentiation.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16]

Publication Abstract from PubMed

Serine/arginine-protein kinase 1 (SRPK1) regulates alternative splicing of VEGF-A to pro-angiogenic isoforms and SRPK1 inhibition can restore the balance of pro/antiangiogenic isoforms to normal physiological levels. The lack of potency and selectivity of available compounds has limited development of SRPK1 inhibitors, with the control of alternative splicing by splicing factor-specific kinases yet to be translated. We present here compounds that occupy a binding pocket created by the unique helical insert of SRPK1, and trigger a backbone flip in the hinge region, that results in potent (<10 nM) and selective inhibition of SRPK1 kinase activity. Treatment with these inhibitors inhibited SRPK1 activity and phosphorylation of serine/arginine splicing factor 1 (SRSF1), resulting in alternative splicing of VEGF-A from pro-angiogenic to antiangiogenic isoforms. This property resulted in potent inhibition of blood vessel growth in models of choroidal angiogenesis in vivo. This work identifies tool compounds for splice isoform selective targeting of pro-angiogenic VEGF, which may lead to new therapeutic strategies for a diversity of diseases where dysfunctional splicing drives disease development.

Development of Potent, Selective SRPK1 Inhibitors as Potential Topical Therapeutics for Neovascular Eye Disease.,Batson J, Toop HD, Redondo C, Babaei-Jadidi R, Chaikuad A, Wearmouth SF, Gibbons B, Allen C, Tallant C, Zhang J, Du C, Hancox JC, Hawtrey T, Da Rocha J, Griffith R, Knapp S, Bates DO, Morris JC ACS Chem Biol. 2017 Mar 17;12(3):825-832. doi: 10.1021/acschembio.6b01048. Epub, 2017 Feb 6. PMID:28135068[17]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Gui JF, Lane WS, Fu XD. A serine kinase regulates intracellular localization of splicing factors in the cell cycle. Nature. 1994 Jun 23;369(6482):678-82. PMID:8208298 doi:http://dx.doi.org/10.1038/369678a0
  2. ↑ Nikolakaki E, Kohen R, Hartmann AM, Stamm S, Georgatsou E, Giannakouros T. Cloning and characterization of an alternatively spliced form of SR protein kinase 1 that interacts specifically with scaffold attachment factor-B. J Biol Chem. 2001 Oct 26;276(43):40175-82. Epub 2001 Aug 16. PMID:11509566 doi:http://dx.doi.org/10.1074/jbc.M104755200
  3. ↑ Daub H, Blencke S, Habenberger P, Kurtenbach A, Dennenmoser J, Wissing J, Ullrich A, Cotten M. Identification of SRPK1 and SRPK2 as the major cellular protein kinases phosphorylating hepatitis B virus core protein. J Virol. 2002 Aug;76(16):8124-37. PMID:12134018
  4. ↑ Lee CG, Hague LK, Li H, Donnelly R. Identification of toposome, a novel multisubunit complex containing topoisomerase IIalpha. Cell Cycle. 2004 May;3(5):638-47. Epub 2004 May 4. PMID:15034300
  5. ↑ Tronchere H, Wang J, Fu XD. A protein related to splicing factor U2AF35 that interacts with U2AF65 and SR proteins in splicing of pre-mRNA. Nature. 1997 Jul 24;388(6640):397-400. PMID:9237760 doi:http://dx.doi.org/10.1038/41137
  6. ↑ Papoutsopoulou S, Nikolakaki E, Giannakouros T. SRPK1 and LBR protein kinases show identical substrate specificities. Biochem Biophys Res Commun. 1999 Feb 24;255(3):602-7. PMID:10049757 doi:http://dx.doi.org/10.1006/bbrc.1999.0249
  7. ↑ Papoutsopoulou S, Nikolakaki E, Chalepakis G, Kruft V, Chevaillier P, Giannakouros T. SR protein-specific kinase 1 is highly expressed in testis and phosphorylates protamine 1. Nucleic Acids Res. 1999 Jul 15;27(14):2972-80. PMID:10390541
  8. ↑ Aubol BE, Chakrabarti S, Ngo J, Shaffer J, Nolen B, Fu XD, Ghosh G, Adams JA. Processive phosphorylation of alternative splicing factor/splicing factor 2. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12601-6. Epub 2003 Oct 10. PMID:14555757 doi:http://dx.doi.org/10.1073/pnas.1635129100
  9. ↑ Zheng Y, Fu XD, Ou JH. Suppression of hepatitis B virus replication by SRPK1 and SRPK2 via a pathway independent of the phosphorylation of the viral core protein. Virology. 2005 Nov 10;342(1):150-8. Epub 2005 Aug 24. PMID:16122776 doi:http://dx.doi.org/10.1016/j.virol.2005.07.030
  10. ↑ Ma CT, Velazquez-Dones A, Hagopian JC, Ghosh G, Fu XD, Adams JA. Ordered multi-site phosphorylation of the splicing factor ASF/SF2 by SRPK1. J Mol Biol. 2008 Feb 8;376(1):55-68. Epub 2007 Aug 21. PMID:18155240 doi:http://dx.doi.org/10.1016/j.jmb.2007.08.029
  11. ↑ Hagopian JC, Ma CT, Meade BR, Albuquerque CP, Ngo JC, Ghosh G, Jennings PA, Fu XD, Adams JA. Adaptable molecular interactions guide phosphorylation of the SR protein ASF/SF2 by SRPK1. J Mol Biol. 2008 Oct 17;382(4):894-909. doi: 10.1016/j.jmb.2008.07.055. Epub 2008, Jul 26. PMID:18687337 doi:http://dx.doi.org/10.1016/j.jmb.2008.07.055
  12. ↑ Huynh N, Ma CT, Giang N, Hagopian J, Ngo J, Adams J, Ghosh G. Allosteric interactions direct binding and phosphorylation of ASF/SF2 by SRPK1. Biochemistry. 2009 Dec 8;48(48):11432-40. doi: 10.1021/bi901107q. PMID:19886675 doi:http://dx.doi.org/10.1021/bi901107q
  13. ↑ Zhong XY, Ding JH, Adams JA, Ghosh G, Fu XD. Regulation of SR protein phosphorylation and alternative splicing by modulating kinetic interactions of SRPK1 with molecular chaperones. Genes Dev. 2009 Feb 15;23(4):482-95. doi: 10.1101/gad.1752109. PMID:19240134 doi:http://dx.doi.org/10.1101/gad.1752109
  14. ↑ Ma CT, Hagopian JC, Ghosh G, Fu XD, Adams JA. Regiospecific phosphorylation control of the SR protein ASF/SF2 by SRPK1. J Mol Biol. 2009 Jul 24;390(4):618-34. Epub 2009 May 27. PMID:19477182 doi:http://dx.doi.org/S0022-2836(09)00623-8
  15. ↑ Sanidas I, Kotoula V, Ritou E, Daans J, Lenz C, Mairhofer M, Daniilidou M, Kolbus A, Kruft V, Ponsaerts P, Nikolakaki E. The ratio of SRPK1/SRPK1a regulates erythroid differentiation in K562 leukaemic cells. Biochim Biophys Acta. 2010 Dec;1803(12):1319-31. doi:, 10.1016/j.bbamcr.2010.07.008. Epub 2010 Aug 12. PMID:20708644 doi:http://dx.doi.org/10.1016/j.bbamcr.2010.07.008
  16. ↑ Ngo JC, Chakrabarti S, Ding JH, Velazquez-Dones A, Nolen B, Aubol BE, Adams JA, Fu XD, Ghosh G. Interplay between SRPK and Clk/Sty kinases in phosphorylation of the splicing factor ASF/SF2 is regulated by a docking motif in ASF/SF2. Mol Cell. 2005 Oct 7;20(1):77-89. PMID:16209947 doi:10.1016/j.molcel.2005.08.025
  17. ↑ Batson J, Toop HD, Redondo C, Babaei-Jadidi R, Chaikuad A, Wearmouth SF, Gibbons B, Allen C, Tallant C, Zhang J, Du C, Hancox JC, Hawtrey T, Da Rocha J, Griffith R, Knapp S, Bates DO, Morris JC. Development of Potent, Selective SRPK1 Inhibitors as Potential Topical Therapeutics for Neovascular Eye Disease. ACS Chem Biol. 2017 Mar 17;12(3):825-832. doi: 10.1021/acschembio.6b01048. Epub, 2017 Feb 6. PMID:28135068 doi:http://dx.doi.org/10.1021/acschembio.6b01048

5my8, resolution 1.70Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=5my8&oldid=3947246"