1o06: Difference between revisions

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New page: left|200px<br /><applet load="1o06" size="450" color="white" frame="true" align="right" spinBox="true" caption="1o06, resolution 1.45Å" /> '''Crystal structure of...
 
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[[Image:1o06.gif|left|200px]]<br /><applet load="1o06" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1o06, resolution 1.45&Aring;" />
'''Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM)'''<br />


==Overview==
==Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM)==
Ubiquitylation is used to target proteins into a large number of different, biological processes including proteasomal degradation, endocytosis, virus, budding, and vacuolar protein sorting (Vps). Ubiquitylated proteins are, typically recognized using one of several different conserved ubiquitin, binding modules. Here, we report the crystal structure and ubiquitin, binding properties of one such module, the ubiquitin-interacting motif, (UIM). We found that UIM peptides from several proteins involved in, endocytosis and vacuolar protein sorting including Hrs, Vps27p, Stam1, and, Eps15 bound specifically, but with modest affinity (Kd = 0.1-1 mm), to, free ubiquitin. Full affinity ubiquitin binding required the presence of, conserved acidic patches at the N and C terminus of the UIM, as well as, highly conserved central alanine and serine residues. NMR chemical shift, perturbation mapping experiments demonstrated that all of these UIM, peptides bind to the I44 surface of ubiquitin. The 1.45 A resolution, crystal structure of the second yeast Vps27p UIM (Vps27p-2) revealed that, the ubiquitin-interacting motif forms an amphipathic helix. Although, Vps27p-2 is monomeric in solution, the motif unexpectedly crystallized as, an antiparallel four-helix bundle, and the potential biological, implications of UIM oligomerization are therefore discussed.
<StructureSection load='1o06' size='340' side='right'caption='[[1o06]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1o06]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O06 FirstGlance]. <br>
1O06 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1O06 OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1o06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o06 OCA], [https://pdbe.org/1o06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o06 RCSB], [https://www.ebi.ac.uk/pdbsum/1o06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o06 ProSAT]</span></td></tr>
Structure and ubiquitin binding of the ubiquitin-interacting motif., Fisher RD, Wang B, Alam SL, Higginson DS, Robinson H, Sundquist WI, Hill CP, J Biol Chem. 2003 Aug 1;278(31):28976-84. Epub 2003 May 14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12750381 12750381]
</table>
[[Category: Single protein]]
== Function ==
[[Category: Alam, S.L.]]
[https://www.uniprot.org/uniprot/VPS27_YEAST VPS27_YEAST] Component of the ESCRT-0 complex which is the sorting receptor for ubiquitinated cargo proteins at the multivesicular body (MVB) and recruits ESCRT-I to the MVB outer membrane. Controls exit from the prevacuolar compartment (PVC) in both the forward direction to the vacuole and the return to the Golgi. Allows VPS10 to return to the (trans-Golgi network) TGN from the PVC. Might also function as an alternate adapter in the COPIb clathrin-like coat.<ref>PMID:3062374</ref> <ref>PMID:1493335</ref> <ref>PMID:8649377</ref> <ref>PMID:9015300</ref> <ref>PMID:9265642</ref> <ref>PMID:11208109</ref> <ref>PMID:11416128</ref> <ref>PMID:12055639</ref> <ref>PMID:11872141</ref> <ref>PMID:12900393</ref> <ref>PMID:14581452</ref> <ref>PMID:15166140</ref> <ref>PMID:15107463</ref> <ref>PMID:15086794</ref> <ref>PMID:17101773</ref> <ref>PMID:17135292</ref>
[[Category: Fisher, R.D.]]
== References ==
[[Category: Higginson, D.S.]]
<references/>
[[Category: Hill, C.P.]]
__TOC__
[[Category: Myszka, D.]]
</StructureSection>
[[Category: Rich, R.]]
[[Category: Large Structures]]
[[Category: Sundquist, W.I.]]
[[Category: Saccharomyces cerevisiae S288C]]
[[Category: Wang, B.]]
[[Category: Alam SL]]
[[Category: ZN]]
[[Category: Fisher RD]]
[[Category: alpha-helix]]
[[Category: Higginson DS]]
[[Category: coiled-coil]]
[[Category: Hill CP]]
[[Category: tetramer]]
[[Category: Myszka D]]
 
[[Category: Rich R]]
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:41:57 2007''
[[Category: Sundquist WI]]
[[Category: Wang B]]

Latest revision as of 11:00, 14 February 2024

Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM)Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM)

Structural highlights

1o06 is a 1 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.45Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VPS27_YEAST Component of the ESCRT-0 complex which is the sorting receptor for ubiquitinated cargo proteins at the multivesicular body (MVB) and recruits ESCRT-I to the MVB outer membrane. Controls exit from the prevacuolar compartment (PVC) in both the forward direction to the vacuole and the return to the Golgi. Allows VPS10 to return to the (trans-Golgi network) TGN from the PVC. Might also function as an alternate adapter in the COPIb clathrin-like coat.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16]

References

  1. ↑ Robinson JS, Klionsky DJ, Banta LM, Emr SD. Protein sorting in Saccharomyces cerevisiae: isolation of mutants defective in the delivery and processing of multiple vacuolar hydrolases. Mol Cell Biol. 1988 Nov;8(11):4936-48. PMID:3062374
  2. ↑ Raymond CK, Howald-Stevenson I, Vater CA, Stevens TH. Morphological classification of the yeast vacuolar protein sorting mutants: evidence for a prevacuolar compartment in class E vps mutants. Mol Biol Cell. 1992 Dec;3(12):1389-402. PMID:1493335
  3. ↑ Nothwehr SF, Bryant NJ, Stevens TH. The newly identified yeast GRD genes are required for retention of late-Golgi membrane proteins. Mol Cell Biol. 1996 Jun;16(6):2700-7. PMID:8649377
  4. ↑ Bryant NJ, Stevens TH. Two separate signals act independently to localize a yeast late Golgi membrane protein through a combination of retrieval and retention. J Cell Biol. 1997 Jan 27;136(2):287-97. PMID:9015300
  5. ↑ Luo W, Chang A. Novel genes involved in endosomal traffic in yeast revealed by suppression of a targeting-defective plasma membrane ATPase mutant. J Cell Biol. 1997 Aug 25;138(4):731-46. PMID:9265642
  6. ↑ Gerrard SR, Levi BP, Stevens TH. Pep12p is a multifunctional yeast syntaxin that controls entry of biosynthetic, endocytic and retrograde traffic into the prevacuolar compartment. Traffic. 2000 Mar;1(3):259-69. PMID:11208109
  7. ↑ Dupre S, Haguenauer-Tsapis R. Deubiquitination step in the endocytic pathway of yeast plasma membrane proteins: crucial role of Doa4p ubiquitin isopeptidase. Mol Cell Biol. 2001 Jul;21(14):4482-94. PMID:11416128 doi:10.1128/MCB.21.14.4482-4494.2001
  8. ↑ Bilodeau PS, Urbanowski JL, Winistorfer SC, Piper RC. The Vps27p Hse1p complex binds ubiquitin and mediates endosomal protein sorting. Nat Cell Biol. 2002 Jul;4(7):534-9. PMID:12055639 doi:10.1038/ncb815
  9. ↑ Prescianotto-Baschong C, Riezman H. Ordering of compartments in the yeast endocytic pathway. Traffic. 2002 Jan;3(1):37-49. PMID:11872141
  10. ↑ Katzmann DJ, Stefan CJ, Babst M, Emr SD. Vps27 recruits ESCRT machinery to endosomes during MVB sorting. J Cell Biol. 2003 Aug 4;162(3):413-23. PMID:12900393 doi:http://dx.doi.org/10.1083/jcb.200302136
  11. ↑ Bilodeau PS, Winistorfer SC, Kearney WR, Robertson AD, Piper RC. Vps27-Hse1 and ESCRT-I complexes cooperate to increase efficiency of sorting ubiquitinated proteins at the endosome. J Cell Biol. 2003 Oct 27;163(2):237-43. PMID:14581452 doi:10.1083/jcb.200305007
  12. ↑ Eguez L, Chung YS, Kuchibhatla A, Paidhungat M, Garrett S. Yeast Mn2+ transporter, Smf1p, is regulated by ubiquitin-dependent vacuolar protein sorting. Genetics. 2004 May;167(1):107-17. PMID:15166140
  13. ↑ Eugster A, Pecheur EI, Michel F, Winsor B, Letourneur F, Friant S. Ent5p is required with Ent3p and Vps27p for ubiquitin-dependent protein sorting into the multivesicular body. Mol Biol Cell. 2004 Jul;15(7):3031-41. Epub 2004 Apr 23. PMID:15107463 doi:10.1091/mbc.E03-11-0793
  14. ↑ Bowers K, Lottridge J, Helliwell SB, Goldthwaite LM, Luzio JP, Stevens TH. Protein-protein interactions of ESCRT complexes in the yeast Saccharomyces cerevisiae. Traffic. 2004 Mar;5(3):194-210. PMID:15086794 doi:10.1111/j.1600-0854.2004.00169.x
  15. ↑ Gabriely G, Kama R, Gerst JE. Involvement of specific COPI subunits in protein sorting from the late endosome to the vacuole in yeast. Mol Cell Biol. 2007 Jan;27(2):526-40. Epub 2006 Nov 13. PMID:17101773 doi:MCB.00577-06
  16. ↑ Curtiss M, Jones C, Babst M. Efficient cargo sorting by ESCRT-I and the subsequent release of ESCRT-I from multivesicular bodies requires the subunit Mvb12. Mol Biol Cell. 2007 Feb;18(2):636-45. Epub 2006 Nov 29. PMID:17135292 doi:E06-07-0588

1o06, resolution 1.45Å

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