This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5jiu

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:51, 10 June 2020

The crystal structure of RanBPM/9 IUS-SPRY domain in complex with DDX-4 peptide

Structural highlights

5jiu is a 4 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	5ji7, 5ji9, 5jia
Gene:	RANBP9, RANBPM (HUMAN)
Activity:	RNA helicase, with EC number 3.6.4.13
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RANB9_HUMAN] May act as an adapter protein to couple membrane receptors to intracellular signaling pathways. May be involved in signaling of ITGB2/LFA-1 and other integrins. Enhances HGF-MET signaling by recruiting Sos and activating the Ras pathway. Enhances dihydrotestosterone-induced transactivation activity of AR, as well as dexamethasone-induced transactivation activity of NR3C1, but not affect estrogen-induced transactivation. Stabilizes TP73 isoform Alpha, probably by inhibiting its ubiquitination, and increases its proapoptotic activity. Inhibits the kinase activity of DYRK1A and DYRK1B. Inhibits FMR1 binding to RNA (By similarity).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] [DDX4_MOUSE] Probable ATP-dependent RNA helicase required during spermatogenesis to repress transposable elements and preventing their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons. Involved in the secondary piRNAs metabolic process, the production of piRNAs in fetal male germ cells through a ping-pong amplification cycle.^[8]

Publication Abstract from PubMed

RanBPM and RanBP10 are non-canonical members of the Ran binding protein family that lack the Ran binding domain and do not associate with Ran GTPase in vivo. Rather, they have been shown to be scaffolding proteins that are important for a variety of cellular processes, and both of these proteins contain a SPRY domain, which has been implicated in mediating protein-protein interactions with a variety of targets including the DEAD-box containing ATP-dependent RNA helicase (DDX-4). In this study, we have determined the crystal structures of the SPIa and the ryanodine receptor domain and of approximately 70 upstream residues (immediate upstream to SPRY motif) of both RanBPM and RanBP10. They are almost identical, composed of a beta-sandwich fold with a set of two helices on each side located at the edge of the sheets. A unique shallow binding surface is formed by highly conserved loops on the surface of the beta-sheet with two aspartates on one end, a positive patch on the opposite end, and a tryptophan lining at the bottom of the surface. The 20-mer peptide (residues 228-247) of human DDX-4, an ATP-dependent RNA helicase known to regulate germ cell development, binds to this surface with a KD of ~13muM. The crystal structure of the peptide complex and the mutagenesis studies elucidate how RanBPM can recognize its interaction partners to function in gametogenesis.

Structural Basis for the Interaction between the IUS-SPRY Domain of RanBPM and DDX-4 in Germ Cell Development.,Hong SK, Kim KH, Song EJ, Kim EE J Mol Biol. 2016 Oct 23;428(21):4330-4344. doi: 10.1016/j.jmb.2016.09.004. Epub, 2016 Sep 10. PMID:27622290^[9]

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

References

↑ Wang D, Li Z, Messing EM, Wu G. Activation of Ras/Erk pathway by a novel MET-interacting protein RanBPM. J Biol Chem. 2002 Sep 27;277(39):36216-22. Epub 2002 Jul 29. PMID:12147692 doi:http://dx.doi.org/10.1074/jbc.M205111200
↑ Rao MA, Cheng H, Quayle AN, Nishitani H, Nelson CC, Rennie PS. RanBPM, a nuclear protein that interacts with and regulates transcriptional activity of androgen receptor and glucocorticoid receptor. J Biol Chem. 2002 Dec 13;277(50):48020-7. Epub 2002 Oct 1. PMID:12361945 doi:http://dx.doi.org/10.1074/jbc.M209741200
↑ Zou Y, Lim S, Lee K, Deng X, Friedman E. Serine/threonine kinase Mirk/Dyrk1B is an inhibitor of epithelial cell migration and is negatively regulated by the Met adaptor Ran-binding protein M. J Biol Chem. 2003 Dec 5;278(49):49573-81. Epub 2003 Sep 18. PMID:14500717 doi:http://dx.doi.org/10.1074/jbc.M307556200
↑ Denti S, Sirri A, Cheli A, Rogge L, Innamorati G, Putignano S, Fabbri M, Pardi R, Bianchi E. RanBPM is a phosphoprotein that associates with the plasma membrane and interacts with the integrin LFA-1. J Biol Chem. 2004 Mar 26;279(13):13027-34. Epub 2004 Jan 13. PMID:14722085 doi:http://dx.doi.org/10.1074/jbc.M313515200
↑ Menon RP, Gibson TJ, Pastore A. The C terminus of fragile X mental retardation protein interacts with the multi-domain Ran-binding protein in the microtubule-organising centre. J Mol Biol. 2004 Oct 8;343(1):43-53. PMID:15381419 doi:http://dx.doi.org/10.1016/j.jmb.2004.08.024
↑ Kramer S, Ozaki T, Miyazaki K, Kato C, Hanamoto T, Nakagawara A. Protein stability and function of p73 are modulated by a physical interaction with RanBPM in mammalian cultured cells. Oncogene. 2005 Jan 27;24(5):938-44. PMID:15558019 doi:http://dx.doi.org/1208257
↑ Harada N, Yokoyama T, Yamaji R, Nakano Y, Inui H. RanBP10 acts as a novel coactivator for the androgen receptor. Biochem Biophys Res Commun. 2008 Mar 28;368(1):121-5. doi:, 10.1016/j.bbrc.2008.01.072. Epub 2008 Jan 24. PMID:18222118 doi:http://dx.doi.org/10.1016/j.bbrc.2008.01.072
↑ Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Takamatsu K, Chuma S, Kojima-Kita K, Shiromoto Y, Asada N, Toyoda A, Fujiyama A, Totoki Y, Shibata T, Kimura T, Nakatsuji N, Noce T, Sasaki H, Nakano T. MVH in piRNA processing and gene silencing of retrotransposons. Genes Dev. 2010 May;24(9):887-92. doi: 10.1101/gad.1902110. PMID:20439430 doi:http://dx.doi.org/10.1101/gad.1902110
↑ Hong SK, Kim KH, Song EJ, Kim EE. Structural Basis for the Interaction between the IUS-SPRY Domain of RanBPM and DDX-4 in Germ Cell Development. J Mol Biol. 2016 Oct 23;428(21):4330-4344. doi: 10.1016/j.jmb.2016.09.004. Epub, 2016 Sep 10. PMID:27622290 doi:http://dx.doi.org/10.1016/j.jmb.2016.09.004

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5jiu"

@@ Line 1: / Line 1: @@
 ==The crystal structure of RanBPM/9 IUS-SPRY domain in complex with DDX-4 peptide==
-<StructureSection load='5jiu' size='340' side='right' caption='[[5jiu]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+<StructureSection load='5jiu' size='340' side='right'caption='[[5jiu]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5jiu]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JIU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JIU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5jiu]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JIU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JIU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ji7|5ji7]], [[5ji9|5ji9]], [[5jia|5jia]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RANBP9, RANBPM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA_helicase RNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.13 3.6.4.13] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jiu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jiu OCA], [http://pdbe.org/5jiu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jiu RCSB], [http://www.ebi.ac.uk/pdbsum/5jiu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jiu ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5jiu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jiu OCA], [http://pdbe.org/5jiu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jiu RCSB], [http://www.ebi.ac.uk/pdbsum/5jiu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jiu ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 24: / Line 25: @@
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: RNA helicase]]
 [[Category: Hong, S K]]

5jiu

From Proteopedia

Revision as of 07:51, 10 June 2020

The crystal structure of RanBPM/9 IUS-SPRY domain in complex with DDX-4 peptide

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox