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2lbc

From Proteopedia

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solution structure of tandem UBA of USP13

Structural highlights

2lbc is a 1 chain structure with sequence from Homo sapiens. 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

UBP13_HUMAN Deubiquitinase that mediates deubiquitination of target proteins such as BECN1, MITF, SKP2 and USP10 and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD). Component of a regulatory loop that controls autophagy and p53/TP53 levels: mediates deubiquitination of BECN1, a key regulator of autophagy, leading to stabilize the PIK3C3/VPS34-containing complexes. Also deubiquitinates USP10, an essential regulator of p53/TP53 stability. In turn, PIK3C3/VPS34-containing complexes regulate USP13 stability, suggesting the existence of a regulatory system by which PIK3C3/VPS34-containing complexes regulate p53/TP53 protein levels via USP10 and USP13. Recruited by nuclear UFD1 and mediates deubiquitination of SKP2, thereby regulating endoplasmic reticulum-associated degradation (ERAD). Mediates stabilization of SIAH2 independently of deubiquitinase activity: binds ubiquitinated SIAH2 and acts by impairing SIAH2 autoubiquitination. Has a weak deubiquitinase activity in vitro and preferentially cleaves 'Lys-63'-linked polyubiquitin chains. In contrast to USP5, it is not able to mediate unanchored polyubiquitin disassembly. Able to cleave ISG15 in vitro; however, additional experiments are required to confirm such data.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

Deubiquitination is a reverse process of cellular ubiquitination important for many biological events. Ubiquitin (Ub)-specific protease 13 (USP13) is an ortholog of USP5 implicated in catalyzing hydrolysis of various Ub chains, but its enzymatic properties and catalytic regulation remain to be explored. Here we report studies of the roles of the Ub-binding domains of USP13 in regulatory catalysis by biochemical and NMR structural approaches. Our data demonstrate that USP13, distinct from USP5, exhibits a weak deubiquitinating activity preferring to Lys63-linked polyubiquitin (K63-polyUb) in a non-activation manner. The zinc finger (ZnF) domain of USP13 shares a similar fold with that of USP5, but it cannot bind with Ub, so that USP13 has lost its ability to be activated by free Ub. Substitution of the ZnF domain with that of USP5 confers USP13 the property of catalytic activation. The tandem Ub-associated (UBA) domains of USP13 can bind with different types of diUb but preferentially with K63-linked, providing a possible explanation for the weak activity preferring to K63-polyUb. USP13 can also regulate the protein level of CD3delta in cells, probably depending on its weak deubiquitinating activity and the Ub-binding properties of the UBA domains. Thus, the non-activating catalysis of USP13 for K63-polyUb chains implies that it may function differently from USP5 in cellular deubiquitination processes.

Domain analysis reveals that a deubiquitinating enzyme USP13 performs non-activating catalysis for Lys63-linked polyubiquitin.,Zhang YH, Zhou CJ, Zhou ZR, Song AX, Hu HY PLoS One. 2011;6(12):e29362. Epub 2011 Dec 28. PMID:22216260^[7]

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

References

↑ Catic A, Fiebiger E, Korbel GA, Blom D, Galardy PJ, Ploegh HL. Screen for ISG15-crossreactive deubiquitinases. PLoS One. 2007 Jul 25;2(7):e679. PMID:17653289 doi:http://dx.doi.org/10.1371/journal.pone.0000679
↑ Liu J, Xia H, Kim M, Xu L, Li Y, Zhang L, Cai Y, Norberg HV, Zhang T, Furuya T, Jin M, Zhu Z, Wang H, Yu J, Li Y, Hao Y, Choi A, Ke H, Ma D, Yuan J. Beclin1 controls the levels of p53 by regulating the deubiquitination activity of USP10 and USP13. Cell. 2011 Sep 30;147(1):223-34. doi: 10.1016/j.cell.2011.08.037. PMID:21962518 doi:http://dx.doi.org/10.1016/j.cell.2011.08.037
↑ Scortegagna M, Subtil T, Qi J, Kim H, Zhao W, Gu W, Kluger H, Ronai ZA. USP13 enzyme regulates Siah2 ligase stability and activity via noncatalytic ubiquitin-binding domains. J Biol Chem. 2011 Aug 5;286(31):27333-41. doi: 10.1074/jbc.M111.218214. Epub 2011, Jun 9. PMID:21659512 doi:http://dx.doi.org/10.1074/jbc.M111.218214
↑ Zhao X, Fiske B, Kawakami A, Li J, Fisher DE. Regulation of MITF stability by the USP13 deubiquitinase. Nat Commun. 2011 Aug 2;2:414. doi: 10.1038/ncomms1421. PMID:21811243 doi:http://dx.doi.org/10.1038/ncomms1421
↑ Chen M, Gutierrez GJ, Ronai ZA. Ubiquitin-recognition protein Ufd1 couples the endoplasmic reticulum (ER) stress response to cell cycle control. Proc Natl Acad Sci U S A. 2011 May 31;108(22):9119-24. doi:, 10.1073/pnas.1100028108. Epub 2011 May 13. PMID:21571647 doi:http://dx.doi.org/10.1073/pnas.1100028108
↑ Zhang YH, Zhou CJ, Zhou ZR, Song AX, Hu HY. Domain analysis reveals that a deubiquitinating enzyme USP13 performs non-activating catalysis for Lys63-linked polyubiquitin. PLoS One. 2011;6(12):e29362. Epub 2011 Dec 28. PMID:22216260 doi:10.1371/journal.pone.0029362
↑ Zhang YH, Zhou CJ, Zhou ZR, Song AX, Hu HY. Domain analysis reveals that a deubiquitinating enzyme USP13 performs non-activating catalysis for Lys63-linked polyubiquitin. PLoS One. 2011;6(12):e29362. Epub 2011 Dec 28. PMID:22216260 doi:10.1371/journal.pone.0029362

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/2lbc"

@@ Line 1: / Line 1: @@
 ==solution structure of tandem UBA of USP13==
-<StructureSection load='2lbc' size='340' side='right' caption='[[2lbc]], [[NMR_Ensembles_of_Models | 15 NMR models]]' scene=''>
+<StructureSection load='2lbc' size='340' side='right'caption='[[2lbc]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2lbc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LBC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LBC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2lbc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LBC FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">USP13, ISOT3 ([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">Solution NMR</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </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=2lbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lbc OCA], [https://pdbe.org/2lbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lbc RCSB], [https://www.ebi.ac.uk/pdbsum/2lbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lbc ProSAT]</span></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=2lbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lbc OCA], [http://pdbe.org/2lbc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lbc RCSB], [http://www.ebi.ac.uk/pdbsum/2lbc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lbc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/UBP13_HUMAN UBP13_HUMAN]] Deubiquitinase that mediates deubiquitination of target proteins such as BECN1, MITF, SKP2 and USP10 and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD). Component of a regulatory loop that controls autophagy and p53/TP53 levels: mediates deubiquitination of BECN1, a key regulator of autophagy, leading to stabilize the PIK3C3/VPS34-containing complexes. Also deubiquitinates USP10, an essential regulator of p53/TP53 stability. In turn, PIK3C3/VPS34-containing complexes regulate USP13 stability, suggesting the existence of a regulatory system by which PIK3C3/VPS34-containing complexes regulate p53/TP53 protein levels via USP10 and USP13. Recruited by nuclear UFD1 and mediates deubiquitination of SKP2, thereby regulating endoplasmic reticulum-associated degradation (ERAD). Mediates stabilization of SIAH2 independently of deubiquitinase activity: binds ubiquitinated SIAH2 and acts by impairing SIAH2 autoubiquitination. Has a weak deubiquitinase activity in vitro and preferentially cleaves 'Lys-63'-linked polyubiquitin chains. In contrast to USP5, it is not able to mediate unanchored polyubiquitin disassembly. Able to cleave ISG15 in vitro; however, additional experiments are required to confirm such data.<ref>PMID:17653289</ref> <ref>PMID:21962518</ref> <ref>PMID:21659512</ref> <ref>PMID:21811243</ref> <ref>PMID:21571647</ref> <ref>PMID:22216260</ref>
+[https://www.uniprot.org/uniprot/UBP13_HUMAN UBP13_HUMAN] Deubiquitinase that mediates deubiquitination of target proteins such as BECN1, MITF, SKP2 and USP10 and is involved in various processes such as autophagy and endoplasmic reticulum-associated degradation (ERAD). Component of a regulatory loop that controls autophagy and p53/TP53 levels: mediates deubiquitination of BECN1, a key regulator of autophagy, leading to stabilize the PIK3C3/VPS34-containing complexes. Also deubiquitinates USP10, an essential regulator of p53/TP53 stability. In turn, PIK3C3/VPS34-containing complexes regulate USP13 stability, suggesting the existence of a regulatory system by which PIK3C3/VPS34-containing complexes regulate p53/TP53 protein levels via USP10 and USP13. Recruited by nuclear UFD1 and mediates deubiquitination of SKP2, thereby regulating endoplasmic reticulum-associated degradation (ERAD). Mediates stabilization of SIAH2 independently of deubiquitinase activity: binds ubiquitinated SIAH2 and acts by impairing SIAH2 autoubiquitination. Has a weak deubiquitinase activity in vitro and preferentially cleaves 'Lys-63'-linked polyubiquitin chains. In contrast to USP5, it is not able to mediate unanchored polyubiquitin disassembly. Able to cleave ISG15 in vitro; however, additional experiments are required to confirm such data.<ref>PMID:17653289</ref> <ref>PMID:21962518</ref> <ref>PMID:21659512</ref> <ref>PMID:21811243</ref> <ref>PMID:21571647</ref> <ref>PMID:22216260</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 20: @@
 ==See Also==
-*[[Thioesterase|Thioesterase]]
+*[[Thioesterase 3D structures|Thioesterase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Ubiquitinyl hydrolase 1]]
+[[Category: Large Structures]]
-[[Category: Hu, H]]
+[[Category: Hu H]]
-[[Category: Song, A]]
+[[Category: Song A]]
-[[Category: Zhang, Y]]
+[[Category: Zhang Y]]
-[[Category: Zhou, C]]
+[[Category: Zhou C]]
-[[Category: Zhou, Z]]
+[[Category: Zhou Z]]
-[[Category: Hydrolase]]
-[[Category: Tandem uba of usp13]]

2lbc

From Proteopedia

Current revision

solution structure of tandem UBA of USP13

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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