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.

5v1y

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex

Structural highlights

5v1y is a 6 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.421Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ADRM1_HUMAN Functions as a proteasomal ubiquitin receptor. Recruits the deubiquitinating enzyme UCHL5 at the 26S proteasome and promotes its activity.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

The 26S proteasome is a large cellular assembly that mediates the selective degradation of proteins in the nucleus and cytosol and is an established target for anti-cancer therapeutics. Protein substrates are typically targeted to the proteasome through modification with a polyubiquitin chain, which can be recognized by several proteasome-associated ubiquitin receptors. One of these receptors, RPN13/ADRM1, is recruited to the proteasome through direct interaction with the large scaffolding protein RPN2 within the 19S regulatory particle. To better understand the interactions between RPN13, RPN2, and ubiquitin, we used human proteins to map the RPN13-binding epitope to the C-terminal 14 residues of RPN2, which, like ubiquitin, binds the N-terminal PRU domain of RPN13. We also report crystal structures of the RPN13 PRU domain in complex with peptides corresponding to the RPN2 C-terminus and ubiquitin. Through mutational analysis, we validated the RPN2 binding interface revealed by our structures and quantified binding interactions with surface plasmon resonance and fluorescence polarization. In contrast to a previous report, we find that RPN13 binds ubiquitin with an affinity similar to that of other proteasome-associated ubiquitin receptors and that RPN2, ubiquitin, and the deubiquitylase UCH37 bind to RPN13 with independent energetics. These findings provide a detailed characterization of interactions that are important for proteasome function, indicate ubiquitin affinities that are consistent with the role of RPN13 as a proteasomal ubiquitin receptor, and have major implications for the development of novel anticancer therapeutics.

Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism.,VanderLinden RT, Hemmis CW, Yao T, Robinson H, Hill CP J Biol Chem. 2017 Apr 25. pii: jbc.M117.785287. doi: 10.1074/jbc.M117.785287. PMID:28442575^[6]

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

References

↑ Hamazaki J, Iemura S, Natsume T, Yashiroda H, Tanaka K, Murata S. A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes. EMBO J. 2006 Oct 4;25(19):4524-36. Epub 2006 Sep 21. PMID:16990800 doi:http://dx.doi.org/10.1038/sj.emboj.7601338
↑ Qiu XB, Ouyang SY, Li CJ, Miao S, Wang L, Goldberg AL. hRpn13/ADRM1/GP110 is a novel proteasome subunit that binds the deubiquitinating enzyme, UCH37. EMBO J. 2006 Dec 13;25(24):5742-53. Epub 2006 Nov 30. PMID:17139257 doi:http://dx.doi.org/7601450
↑ Jorgensen JP, Lauridsen AM, Kristensen P, Dissing K, Johnsen AH, Hendil KB, Hartmann-Petersen R. Adrm1, a putative cell adhesion regulating protein, is a novel proteasome-associated factor. J Mol Biol. 2006 Jul 28;360(5):1043-52. Epub 2006 Jun 21. PMID:16815440 doi:http://dx.doi.org/S0022-2836(06)00703-0
↑ Yao T, Song L, Xu W, DeMartino GN, Florens L, Swanson SK, Washburn MP, Conaway RC, Conaway JW, Cohen RE. Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1. Nat Cell Biol. 2006 Sep;8(9):994-1002. Epub 2006 Aug 13. PMID:16906146 doi:ncb1460
↑ Husnjak K, Elsasser S, Zhang N, Chen X, Randles L, Shi Y, Hofmann K, Walters KJ, Finley D, Dikic I. Proteasome subunit Rpn13 is a novel ubiquitin receptor. Nature. 2008 May 22;453(7194):481-8. PMID:18497817 doi:10.1038/nature06926
↑ VanderLinden RT, Hemmis CW, Yao T, Robinson H, Hill CP. Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism. J Biol Chem. 2017 Apr 25. pii: jbc.M117.785287. doi: 10.1074/jbc.M117.785287. PMID:28442575 doi:http://dx.doi.org/10.1074/jbc.M117.785287

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/5v1y"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex==
-<StructureSection load='5v1y' size='340' side='right' caption='[[5v1y]], [[Resolution|resolution]] 1.42&Aring;' scene=''>
+<StructureSection load='5v1y' size='340' side='right'caption='[[5v1y]], [[Resolution|resolution]] 1.42&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5v1y]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V1Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V1Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5v1y]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V1Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V1Y FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5v1z|5v1z]]</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]] 1.421&#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=5v1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1y OCA], [http://pdbe.org/5v1y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v1y RCSB], [http://www.ebi.ac.uk/pdbsum/5v1y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1y 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=5v1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1y OCA], [https://pdbe.org/5v1y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v1y RCSB], [https://www.ebi.ac.uk/pdbsum/5v1y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1y ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ADRM1_HUMAN ADRM1_HUMAN]] Functions as a proteasomal ubiquitin receptor. Recruits the deubiquitinating enzyme UCHL5 at the 26S proteasome and promotes its activity.<ref>PMID:16990800</ref> <ref>PMID:17139257</ref> <ref>PMID:16815440</ref> <ref>PMID:16906146</ref> <ref>PMID:18497817</ref>  [[http://www.uniprot.org/uniprot/PSMD1_HUMAN PSMD1_HUMAN]] Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. [[http://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>
+[https://www.uniprot.org/uniprot/ADRM1_HUMAN ADRM1_HUMAN] Functions as a proteasomal ubiquitin receptor. Recruits the deubiquitinating enzyme UCHL5 at the 26S proteasome and promotes its activity.<ref>PMID:16990800</ref> <ref>PMID:17139257</ref> <ref>PMID:16815440</ref> <ref>PMID:16906146</ref> <ref>PMID:18497817</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 18: @@
 </div>
 <div class="pdbe-citations 5v1y" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Hemmis, C W]]
+[[Category: Homo sapiens]]
-[[Category: Hill, C P]]
+[[Category: Large Structures]]
-[[Category: Robinson, H]]
+[[Category: Hemmis CW]]
-[[Category: VanderLinden, R T]]
+[[Category: Hill CP]]
-[[Category: Yao, T]]
+[[Category: Robinson H]]
-[[Category: Proteasome]]
+[[Category: VanderLinden RT]]
-[[Category: Protein binding]]
+[[Category: Yao T]]
-[[Category: Rpn13]]
-[[Category: Rpn2]]
-[[Category: Ubiquitin]]

5v1y

From Proteopedia

Current revision

Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex

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