1q0w: Difference between revisions

Latest revision as of 09:00, 22 May 2024

Solution structure of Vps27 amino-terminal UIM-ubiquitin complex

Structural highlights

1q0w is a 2 chain structure with sequence from Saccharomyces cerevisiae and Saccharomyces cerevisiae S288C. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Monoubiquitylation is a well-characterized signal for the internalization and sorting of integral membrane proteins to distinct cellular organelles. Recognition and transmission of monoubiquitin signals is mediated by a variety of ubiquitin-binding motifs such as UIM, UBA, UEV, VHS and CUE in endocytic proteins. The yeast Vps27 protein requires two UIMs for efficient interactions with ubiquitin and for sorting cargo into multivesicular bodies. Here we show that the individual UIMs of Vps27 exist as autonomously folded alpha-helices that bind ubiquitin independently, non-cooperatively and with modest affinity. The Vps27 N-terminal UIM engages the Leu8-Ile44-Val70 hydrophobic patch of ubiquitin through a helical surface conserved in UIMs of diverse proteins, including that of the S5a proteasomal regulatory subunit. The Leu8-Ile44-Val70 ubiquitin surface is also the site of interaction for CUE and UBA domains in endocytic proteins, consistent with the view that ubiquitin-binding endocytic proteins act serially on the same monoubiquitylated cargo during transport from cell surface to the lysosome.

Solution structure of Vps27 UIM-ubiquitin complex important for endosomal sorting and receptor downregulation.,Swanson KA, Kang RS, Stamenova SD, Hicke L, Radhakrishnan I EMBO J. 2003 Sep 15;22(18):4597-606. PMID:12970172^[17]

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

References

↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ Prescianotto-Baschong C, Riezman H. Ordering of compartments in the yeast endocytic pathway. Traffic. 2002 Jan;3(1):37-49. PMID:11872141
↑ 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:https://dx.doi.org/10.1083/jcb.200302136
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ Swanson KA, Kang RS, Stamenova SD, Hicke L, Radhakrishnan I. Solution structure of Vps27 UIM-ubiquitin complex important for endosomal sorting and receptor downregulation. EMBO J. 2003 Sep 15;22(18):4597-606. PMID:12970172 doi:https://dx.doi.org/10.1093/emboj/cdg471

Proteopedia Page Contributors and Editors (what is this?)

OCA

[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:https://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

[17] Swanson KA, Kang RS, Stamenova SD, Hicke L, Radhakrishnan I. Solution structure of Vps27 UIM-ubiquitin complex important for endosomal sorting and receptor downregulation. EMBO J. 2003 Sep 15;22(18):4597-606. PMID:12970172 doi:https://dx.doi.org/10.1093/emboj/cdg471

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@@ Line 1: / Line 1: @@
 ==Solution structure of Vps27 amino-terminal UIM-ubiquitin complex==
-<StructureSection load='1q0w' size='340' side='right' caption='[[1q0w]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='1q0w' size='340' side='right'caption='[[1q0w]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1q0w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q0W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1q0w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q0W FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1q0v|1q0v]], [[1o06|1o06]]</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">(UBI1 OR RPL40A OR YIL148W) AND (UBI2 OR RPL40B OR YKR094C) AND (UBI3 OR RPS31 OR YLR167W OR L9470.14) AND (UBI4 OR SCD2 OR YLL039C) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1q0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0w OCA], [https://pdbe.org/1q0w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q0w RCSB], [https://www.ebi.ac.uk/pdbsum/1q0w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q0w ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q0w RCSB], [http://www.ebi.ac.uk/pdbsum/1q0w PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q0/1q0w_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q0/1q0w_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1q0w ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1q0w" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Ubiquitin|Ubiquitin]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Hicke, L.]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Kang, R S.]]
+[[Category: Hicke L]]
-[[Category: Radhakrishnan, I.]]
+[[Category: Kang RS]]
-[[Category: Stamenova, S D.]]
+[[Category: Radhakrishnan I]]
-[[Category: Swanson, K A.]]
+[[Category: Stamenova SD]]
-[[Category: Protein-protein complex]]
+[[Category: Swanson KA]]
-[[Category: Transport protein]]

1q0w: Difference between revisions

Latest revision as of 09:00, 22 May 2024

Solution structure of Vps27 amino-terminal UIM-ubiquitin complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

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