6njg

From Proteopedia

(Difference between revisions)

Current revision

Ubiquitin Variant in Complex with Ubiquitin Interacting Motif

Structural highlights

6njg is a 2 chain structure with sequence from Homo sapiens and Saccharomyces cerevisiae S288C. This structure supersedes the now removed PDB entry 5ucl. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.35Å
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]

Publication Abstract from PubMed

We previously described structural and functional characterization of the first ubiquitin variant (UbV), UbV.v27.1, engineered by phage display to bind with high affinity to a specific ubiquitin interacting motif (UIM). We identified two substitutions relative to ubiquitin (Gly10Val/His68Tyr) that were critical for enhancing binding affinity but could only rationalize the mechanism of action of the Tyr68 substitution. Here we extend our characterization and uncover the mechanism by which the Val10 substitution enhances binding affinity. We show that Val10 in UbV.v27.1 drives UbV dimerization through an intermolecular beta-strand exchange. Dimerization serves to increase the contact surface between the UIM and UbV and also affords direct contacts between two UIMs through an overall 2:2 binding stoichiometry. Our identification of the role of Val10 in UbV dimerization suggests a general means for the development of dimeric UbVs with improved affinity and specificity relative to their monomeric UbV counterparts. This article is protected by copyright. All rights reserved.

Dimerization of a ubiquitin variant leads to high affinity interactions with a ubiquitin interacting motif.,Manczyk N, Veggiani G, Gish GD, Yates BP, Ernst A, Sidhu SS, Sicheri F Protein Sci. 2019 Feb 21. doi: 10.1002/pro.3593. PMID:30793400^[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:http://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
↑ Manczyk N, Veggiani G, Gish GD, Yates BP, Ernst A, Sidhu SS, Sicheri F. Dimerization of a ubiquitin variant leads to high affinity interactions with a ubiquitin interacting motif. Protein Sci. 2019 Feb 21. doi: 10.1002/pro.3593. PMID:30793400 doi:http://dx.doi.org/10.1002/pro.3593

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6njg"

Categories: Homo sapiens | Large Structures | Saccharomyces cerevisiae S288C | Manczyk N | Sicheri F

@@ Line 3: / Line 3: @@
 <StructureSection load='6njg' size='340' side='right'caption='[[6njg]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6njg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5ucl 5ucl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NJG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6njg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5ucl 5ucl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NJG FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35&#8491;</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=6njg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6njg OCA], [http://pdbe.org/6njg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6njg RCSB], [http://www.ebi.ac.uk/pdbsum/6njg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6njg ProSAT]</span></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=6njg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6njg OCA], [https://pdbe.org/6njg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6njg RCSB], [https://www.ebi.ac.uk/pdbsum/6njg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6njg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 18: @@
 </div>
 <div class="pdbe-citations 6njg" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Vacuolar protein sorting-associated protein 3D structures|Vacuolar protein sorting-associated protein 3D structures]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Manczyk, N]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Sicheri, F]]
+[[Category: Manczyk N]]
-[[Category: Protein binding]]
+[[Category: Sicheri F]]
-[[Category: Ubiquitin variant]]
-[[Category: Uim]]

6njg

From Proteopedia

Current revision

Ubiquitin Variant in Complex with Ubiquitin Interacting Motif

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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