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.

2nbu

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Solution structure of the Rad23 ubiquitin-like (UBL) domain

Structural highlights

2nbu is a 1 chain structure with sequence from Saccharomyces cerevisiae S288C. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RAD23_YEAST Plays a central role both in proteasomal degradation of misfolded proteins and DNA repair. Central component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in DNA excision repair. May play a part in DNA damage recognition and/or in altering chromatin structure to allow access by damage-processing enzymes.

Publication Abstract from PubMed

Three receptors (Rpn1/S2/PSMD2, Rpn10/S5a, Rpn13/Adrm1) in the proteasome bind substrates by interacting with conjugated ubiquitin chains and/or shuttle factors (Rad23/HR23, Dsk2/PLIC/ubiquilin, Ddi1) that carry ubiquitinated substrates to proteasomes. We solved the structure of two such receptors with their preferred shuttle factor, namely hRpn13Pru:hPLIC2UBL and scRpn1 T1:scRad23UBL. We find that ubiquitin folds in Rad23 and Dsk2 are fine-tuned by residue substitutions to achieve high affinity for Rpn1 and Rpn13, respectively. A single substitution in hPLIC2 yields enhanced interactions with the Rpn13 ubiquitin contact surface and sterically blocks hRpn13 binding to its preferred ubiquitin chain type, K48-linked chains. Rpn1 T1 binds two ubiquitins in tandem and we find that Rad23 binds exclusively to the higher-affinity Helix28/Helix30 site. Rad23 contacts at Helix28/Helix30 are optimized compared to ubiquitin by multiple conservative amino acid substitutions. Thus, shuttle factors deliver substrates to proteasomes through fine-tuned ubiquitin-like surfaces.

Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome.,Chen X, Randles L, Shi K, Tarasov SG, Aihara H, Walters KJ Structure. 2016 Jul 6. pii: S0969-2126(16)30125-3. doi:, 10.1016/j.str.2016.05.018. PMID:27396824^[1]

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

References

↑ Chen X, Randles L, Shi K, Tarasov SG, Aihara H, Walters KJ. Structures of Rpn1 T1:Rad23 and hRpn13:hPLIC2 Reveal Distinct Binding Mechanisms between Substrate Receptors and Shuttle Factors of the Proteasome. Structure. 2016 Jul 6. pii: S0969-2126(16)30125-3. doi:, 10.1016/j.str.2016.05.018. PMID:27396824 doi:http://dx.doi.org/10.1016/j.str.2016.05.018

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/2nbu"

Categories: Large Structures | Saccharomyces cerevisiae S288C | Chen X | Walters KJ

@@ Line 1: / Line 1: @@
 ==Solution structure of the Rad23 ubiquitin-like (UBL) domain==
-<StructureSection load='2nbu' size='340' side='right'caption='[[2nbu]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2nbu' size='340' side='right'caption='[[2nbu]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2nbu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NBU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2nbu]] is a 1 chain structure with sequence from [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=2NBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NBU FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nbv|2nbv]], [[2nbw|2nbw]]</div></td></tr>
+</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=2nbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nbu OCA], [https://pdbe.org/2nbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nbu RCSB], [https://www.ebi.ac.uk/pdbsum/2nbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nbu ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RAD23, YEL037C, SYGP-ORF29 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=2nbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nbu OCA], [https://pdbe.org/2nbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nbu RCSB], [https://www.ebi.ac.uk/pdbsum/2nbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nbu ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RAD23_YEAST RAD23_YEAST]] Plays a central role both in proteasomal degradation of misfolded proteins and DNA repair. Central component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in DNA excision repair. May play a part in DNA damage recognition and/or in altering chromatin structure to allow access by damage-processing enzymes.
+[https://www.uniprot.org/uniprot/RAD23_YEAST RAD23_YEAST] Plays a central role both in proteasomal degradation of misfolded proteins and DNA repair. Central component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in DNA excision repair. May play a part in DNA damage recognition and/or in altering chromatin structure to allow access by damage-processing enzymes.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 24: @@
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Chen, X]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Walters, K J]]
+[[Category: Chen X]]
-[[Category: Dna binding protein]]
+[[Category: Walters KJ]]

2nbu

From Proteopedia

Current revision

Solution structure of the Rad23 ubiquitin-like (UBL) domain

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox