Editing Proteasome (section)

=== Proteasomal Deubiquitinases ===
Ubiquitin chains conjugated to a protein targeted for proteasomal degradation are normally removed by any one of the three proteasome-associated deubiquitylating enzymes (DUBs), which are Rpn11, Ubp6/USP14 and UCH37.  Rpn11 is the essential DUB responsible for the en block removal of the ubiquitin signal from the substrate, while Ubp6/USP14 and UCH37 have been proposed to edit the ubiquitin code.  Ubp6 knockouts in [[Saccharomyces cerevisiae]] are viable, and there is no homolog of UCH37 in budding yeast, though they exist in [[Schizosaccharomyces pombe]] and higher eukaryotes.  This process recycles ubiquitin and is essential to maintain the ubiquitin reservoir in cells.<ref name=Pickart />

==== Rpn11 (POH1) ====
[[File:Rpn11 crystal structure.jpg|thumb|The crystal structure of yeast Rpn11/8 heterodimer bound to WT Ubiquitin. Rpn11 is in green, Rpn8 is in grey, and Ubiquitin is shown in pink.]]
Rpn11 is an intrinsic, stoichiometric subunit of the 19S regulatory particle and is essential for the function of 26S proteasome.  Rpn11 is a zinc-dependent, metalloprotease of the JAB1/MPN/Mov34 metalloenzyme (JAMM) family of DUBs, that was identified to be the essential DUB responsible for the en block removal of the ubiquitin chain from the protein substrate.<ref>{{cite journal |last1=Verma |first1=Rati |last2=Aravind |first2=L. |last3=Oania |first3=Robert |last4=McDonald |first4=W. Hayes |last5=Yates |first5=John R. |last6=Koonin |first6=Eugene V. |last7=Deshaies |first7=Raymond J. |title=Role of Rpn11 Metalloprotease in Deubiquitination and Degradation by the 26 S Proteasome |journal=Science |date=18 October 2002 |volume=298 |issue=5593 |pages=611–615 |doi=10.1126/science.1075898|pmid=12183636 |bibcode=2002Sci...298..611V }}</ref><ref>{{cite journal |last1=Yao |first1=Tingting |last2=Cohen |first2=Robert E. |title=A cryptic protease couples deubiquitination and degradation by the proteasome |journal=Nature |date=September 2002 |volume=419 |issue=6905 |pages=403–407 |doi=10.1038/nature01071 |pmid=12353037 |bibcode=2002Natur.419..403Y }}</ref>  Rpn11 forms an obligate dimer with Rpn8 forming an active DUB able to cleave all ubiquitin linkages.<ref name="Structure of the Rpn11–Rpn8 dimer r">{{cite journal |last1=Worden |first1=Evan J. |last2=Padovani |first2=Chris |last3=Martin |first3=Andreas |title=Structure of the Rpn11–Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation |journal=Nature Structural & Molecular Biology |date=March 2014 |volume=21 |issue=3 |pages=220–227 |doi=10.1038/nsmb.2771 |pmid=24463465 }}</ref>  The active site of Rpn11 is formed through metal coordination of the catalytic zinc and this site is covered by an Insert-1 loop that covers this active site.<ref name="Structure of the Rpn11–Rpn8 dimer r"/><ref>{{cite journal |last1=Pathare |first1=GR |last2=Nagy |first2=I |last3=Śledź |first3=P |last4=Anderson |first4=DJ |last5=Zhou |first5=HJ |last6=Pardon |first6=E |last7=Steyaert |first7=J |last8=Förster |first8=F |last9=Bracher |first9=A |last10=Baumeister |first10=W |title=Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11. |journal=Proceedings of the National Academy of Sciences of the United States of America |date=25 February 2014 |volume=111 |issue=8 |pages=2984–9 |doi=10.1073/pnas.1400546111 |doi-access=free |pmid=24516147|pmc=3939901 |bibcode=2014PNAS..111.2984P }}</ref> The structure is very similar to that of a related JAMM DUB, AMSH, that is responsible for K63 ubiquitin cleavage, however it lacks the residues that are key for AMSH's linkage specificity. The structure of Rpn11 bound to ubiquitin revealed that the C-terminus of Ubiquitin pushes the insert-1 loop into an beta-sheet providing access to the catalytic zinc.  This structure combined with detailed biochemistry revealed that the DUB activity of Rpn11 was accelerated at least 10-fold by the translocation of the protein substrate, suggesting that the translocation delivered the Ub substrate to the active site of Rpn11.<ref name=":7">{{cite journal |last1=Worden |first1=Evan J. |last2=Dong |first2=Ken C. |last3=Martin |first3=Andreas |title=An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome |journal=Molecular Cell |date=7 September 2017 |volume=67 |issue=5 |pages=799–811.e8 |doi=10.1016/j.molcel.2017.07.023 |pmid=28844860 }}</ref> This model of translocation-dependent deubiquitination was later confirmed by cryoEM of both the yeast and human proteasome bound to a substrate, both of which recapitulated the crystal structure of Ubiquitin bound to Rpn11.<ref name="Substrate-engaged 26 S proteasome s"/><ref>{{cite journal |last1=Dong |first1=Yuanchen |last2=Zhang |first2=Shuwen |last3=Wu |first3=Zhaolong |last4=Li |first4=Xuemei |last5=Wang |first5=Wei Li |last6=Zhu |first6=Yanan |last7=Stoilova-McPhie |first7=Svetla |last8=Lu |first8=Ying |last9=Finley |first9=Daniel |last10=Mao |first10=Youdong |title=Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome |journal=Nature |date=January 2019 |volume=565 |issue=7737 |pages=49–55 |doi=10.1038/s41586-018-0736-4 |pmid=30479383 |pmc=6370054 |bibcode=2019Natur.565...49D }}</ref> Single molecule studies on the yeast proteasome confirmed that the DUB rates measured by biochemistry were indeed stimulated by translocation.<ref>{{cite journal |last1=Jonsson |first1=Erik |last2=Htet |first2=Zaw Min |last3=Bard |first3=Jared A. M. |last4=Dong |first4=Ken C. |last5=Martin |first5=Andreas |title=Ubiquitin modulates 26 S proteasome conformational dynamics and promotes substrate degradation |journal=Science Advances |date=23 December 2022 |volume=8 |issue=51 |pages=eadd9520 |doi=10.1126/sciadv.add9520|pmid=36563145 |pmc=9788759 |bibcode=2022SciA....8D9520J }}</ref> More recent biochemical and single molecule studies have shown that on top of being the essential DUB, Rpn11 is also a ubiquitin receptor that acts as an allosteric sensor to enable proper engagement of a substrate by the proteasome.<ref>{{cite journal |last1=Htet |first1=ZM |last2=Dong |first2=KC |last3=Martin |first3=A |title=The deubiquitinase Rpn11 functions as an allosteric ubiquitin sensor to promote substrate engagement by the 26S proteasome. |journal=bioRxiv: The Preprint Server for Biology |date=24 October 2024 |doi=10.1101/2024.10.24.620116 |pmid=39484543 |pmc=11527175 }}</ref>

In addition to binding Ubiquitin, Rpn11 has also recently been shown to be a binding spot for many proteasome associated factors.  Three recent cryo-EM studies have shown that PITHD1 (Proteasome Interacting Thioredoxin Domain 1) and TXNL1 (Thioredoxin-like protein 1) bind the proteasome by binding Rpn2/Rpn10 and making an interaction with the insert-1 loop of Rpn11.<ref name=":1">{{cite journal |title=PITHD1: An Endogenous Inhibitor of the 26S Proteasome During Cellular Dormancy |journal=BioRvix|date=2024 |doi=10.1101/2024.12.04.626795 | vauthors = Amann SJ, Dong K, Roehsner J, Krall D, Grishkovskaya I, Kotisch H, Schleiffer A, Roitinger E, Pauli A, Martin A, Haselbach D }}</ref><ref name=":2">{{cite journal |title=Structure of the TXNL1-bound proteasome |journal=BioRvix |date=2024 |doi=10.1101/2024.11.08.622741 | vauthors = Gao J, Nardone C, Yip MC, Chino H, Gu X, Mirman Z, Rale MJ, Paulo JA, Elledge SJ, Shao S }}</ref><ref name=":3">{{cite journal |title=Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1 |journal=BioRvix |date=2024 |doi=10.1101/2024.11.08.622731 |pmid=39574680 |pmc=11580985 | vauthors = Arkinson C, Gee CL, Zhang Z, Dong KC, Martin A }}</ref>  PITHD1 binds the proteasome in a resting state and has been proposed to be a dormancy factor,<ref name=":1" /> while TXNL1 binds in a processing state, suggesting that it may have an active role in aiding protein degradation.<ref name=":2" /><ref name=":3" />  Cryo-EM has also shown that Rpn11 can bind the Ubiquitin-like domain of midnolin, a protein that enables ubiquitin-independent degradation of transcription factors (see the section on ubiquitin-independent degradation).<ref>{{cite journal |doi=10.1101/2025.02.22.639686 |title=Structural basis for the midnolin-proteasome pathway and its role in suppressing myeloma |date=2025 |pmid=40027645 | vauthors = Nardone C, Gao J, Seo H, Mintseris J, Ort L, Yip MC, Negasi M, Besschetnova AK, Kamitaki N, Gygi SP, Dhe-Paganon S, Munshi N, Fulciniti M, Greenberg ME, Shao S, Elledge SJ, Gu X |journal=bioRxiv: The Preprint Server for Biology |pmc=11870617 }}</ref>

==== USP14/UBP6 ====
In contrast to Rpn11, USP14 and UCH37 are the DUBs that do not always associated with the proteasome and are not essential for ubiquitin dependent degradation.  Instead, these DUBs are proposed to "edit" the ubiquitin code of a substrate that is already engaged with the proteasome. In cells, about 10-40% of the proteasomes were found to have USP14 associated. Ubp6/USP14 is a member of the Ubiquitin Specific Protease (USP) family, utilizing a catalytic cysteine to cleave ubiquitin.  Along with the USP, Ubp6/USP14 contains a [[Ubiquitin-like protein]] (UBL) that binds the proteasome.  Ubp6/USP14 is largely activated by the proteasome and exhibit a very low DUB activity alone.<ref name="Ubp6 deubiquitinase controls confor">{{cite journal |last1=Bashore |first1=Charlene |last2=Dambacher |first2=Corey M. |last3=Goodall |first3=Ellen A. |last4=Matyskiela |first4=Mary E. |last5=Lander |first5=Gabriel C. |last6=Martin |first6=Andreas |title=Ubp6 deubiquitinase controls conformational dynamics and substrate degradation of the 26S proteasome |journal=Nature Structural & Molecular Biology |date=September 2015 |volume=22 |issue=9 |pages=712–719 |doi=10.1038/nsmb.3075 |pmid=26301997 |pmc=4560640 }}</ref><ref>{{cite journal |last1=Aufderheide |first1=Antje |last2=Beck |first2=Florian |last3=Stengel |first3=Florian |last4=Hartwig |first4=Michaela |last5=Schweitzer |first5=Andreas |last6=Pfeifer |first6=Günter |last7=Goldberg |first7=Alfred L. |last8=Sakata |first8=Eri |last9=Baumeister |first9=Wolfgang |last10=Förster |first10=Friedrich |title=Structural characterization of the interaction of Ubp6 with the 26S proteasome |journal=Proceedings of the National Academy of Sciences |date=14 July 2015 |volume=112 |issue=28 |pages=8626–8631 |doi=10.1073/pnas.1510449112 |doi-access=free |pmid=26130806 |pmc=4507206 |bibcode=2015PNAS..112.8626A }}</ref> Once activated, USP14 was found to suppress proteasome function by its DUB activity and by inducing parallel pathways of proteasome conformational transitions, one of which turned out to directly prohibit substrate insertion into the AAA-ATPase, as first observed biochemically <ref name="Ubp6 deubiquitinase controls confor"/> and later confirmed by time-resolved cryogenic electron microscopy.<ref name=Zhang0>{{cite journal | vauthors = Zhang S, Zou S, Yin D, Zhao L, Finley D, Wu Z, Mao Y | title = USP14-regulated allostery of the human proteasome by time-resolved cryo-EM | journal = Nature | volume = 605 | issue = 7910 | pages = 567–574 | date = April 2022 | pmid = 35477760 | doi = 10.1038/s41586-022-04671-8| pmc = 9117149 | bibcode = 2022Natur.605..567Z }}</ref> It appears that USP14 regulates proteasome function at multiple checkpoints by both catalytically competing with Rpn11 and allosterically reprogramming the AAA-ATPase states, which is rather unexpected for a DUB.<ref name=Zhang0 /> These observations imply that the proteasome regulation may depend on its dynamic transitions of conformational states.

==== UCH37 ====
UCH37 is a Ubiquitin C-terminal hydrolase that activated upon binding the 26S proteasome through the ubiquitin receptor Rpn13.<ref>{{cite journal |last1=Yao |first1=Tingting |last2=Song |first2=Ling |last3=Xu |first3=Wei |last4=DeMartino |first4=George N. |last5=Florens |first5=Laurence |last6=Swanson |first6=Selene K. |last7=Washburn |first7=Michael P. |last8=Conaway |first8=Ronald C. |last9=Conaway |first9=Joan Weliky |last10=Cohen |first10=Robert E. |title=Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1 |journal=Nature Cell Biology |date=September 2006 |volume=8 |issue=9 |pages=994–1002 |doi=10.1038/ncb1460 |pmid=16906146 }}</ref>  UCH37 is activated upon binding the proteasome through the C-terminal DEUBAD (DUB adaptor) domain that binds Rpn2.<ref>{{cite journal |last1=VanderLinden |first1=Ryan T. |last2=Hemmis |first2=Casey W. |last3=Schmitt |first3=Benjamin |last4=Ndoja |first4=Ada |last5=Whitby |first5=Frank G. |last6=Robinson |first6=Howard |last7=Cohen |first7=Robert E. |last8=Yao |first8=Tingting |last9=Hill |first9=Christopher P. |title=Structural Basis for the Activation and Inhibition of the UCH37 Deubiquitylase |journal=Molecular Cell |date=5 March 2015 |volume=57 |issue=5 |pages=901–911 |doi=10.1016/j.molcel.2015.01.016 |pmid=25702872 |pmc=4355076 }}</ref><ref>{{cite journal |last1=Sahtoe |first1=DD |last2=van Dijk |first2=WJ |last3=El Oualid |first3=F |last4=Ekkebus |first4=R |last5=Ovaa |first5=H |last6=Sixma |first6=TK |title=Mechanism of UCH-L5 activation and inhibition by DEUBAD domains in RPN13 and INO80G. |journal=Molecular Cell |date=5 March 2015 |volume=57 |issue=5 |pages=887–900 |doi=10.1016/j.molcel.2014.12.039 |pmid=25702870|pmc=4352763 }}</ref>