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4mem

From Proteopedia

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Crystal Structure of the rat USP11 DUSP-UBL domains

Structural highlights

4mem is a 2 chain structure with sequence from Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.34Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UBP11_RAT Protease that can remove conjugated ubiquitin from target proteins and polyubiquitin chains. Inhibits the degradation of target proteins by the proteasome. Cleaves preferentially 'Lys-6' and 'Lys-63'-linked ubiquitin chains. Has lower activity with 'Lys-11' and 'Lys-33'-linked ubiquitin chains, and extremely low activity with 'Lys-27', 'Lys-29' and 'Lys-48'-linked ubiquitin chains (in vitro). Plays a role in the regulation of pathways leading to NF-kappa-B activation. Plays a role in the regulation of DNA repair after double-stranded DNA breaks. Acts as a chromatin regulator via its association with the Polycomb group (PcG) multiprotein PRC1-like complex; may act by deubiquitinating components of the PRC1-like comple. Promotes cell proliferation by deubiquitinating phosphorylated E2F1x.[UniProtKB:P51784]

Publication Abstract from PubMed

The ubiquitin specific protease 11 (USP11) is implicated in DNA repair, viral RNA replication, and TGFbeta signaling. We report the first characterization of the USP11 domain architecture and its role in regulating the enzymatic activity. USP11 consists of an N-terminal "domain present in USPs" (DUSP) and "ubiquitin-like" (UBL) domain, together referred to as DU domains, and the catalytic domain harboring a second UBL domain. Crystal structures of the DU domains show a tandem arrangement with a shortened beta-hairpin at the two-domain interface and altered surface characteristics compared to the homologues USP4 and USP15. A conserved VEVY motif is a signature feature at the two-domain interface that shapes a potential protein interaction site. Small angle X-ray scattering and gel filtration experiments are consistent with the USP11DU domains and full-length USP11 being monomeric. Unexpectedly, we reveal, through kinetic assays of a series of deletion mutants, that the catalytic activity of USP11 is not regulated through intramolecular autoinhibition or activation by the N-terminal DU or UBL domains. Moreover, ubiquitin chain cleavage assays with all eight linkages reveal a preference for Lys63-, Lys6-, Lys33-, and Lys11-linked chains over Lys27-, Lys29-, and Lys48-linked and linear chains consistent with USP11's function in DNA repair pathways that is mediated by the protease domain. Our data support a model whereby USP11 domains outside the catalytic core domain serve as protein interaction or trafficking modules rather than a direct regulatory function of the proteolytic activity. This highlights the diversity of USPs in substrate recognition and regulation of ubiquitin deconjugation.

Structure and Catalytic Regulatory Function of Ubiquitin Specific Protease 11 N-Terminal and Ubiquitin-like Domains.,Harper S, Gratton HE, Cornaciu I, Oberer M, Scott DJ, Emsley J, Dreveny I Biochemistry. 2014 Apr 29. PMID:24724799^[1]

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

References

↑ Harper S, Gratton HE, Cornaciu I, Oberer M, Scott DJ, Emsley J, Dreveny I. Structure and Catalytic Regulatory Function of Ubiquitin Specific Protease 11 N-Terminal and Ubiquitin-like Domains. Biochemistry. 2014 Apr 29. PMID:24724799 doi:http://dx.doi.org/10.1021/bi500116x

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/4mem"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the rat USP11 DUSP-UBL domains==
-<StructureSection load='4mem' size='340' side='right' caption='[[4mem]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
+<StructureSection load='4mem' size='340' side='right'caption='[[4mem]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4mem]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MEM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4mem]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MEM FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4mel|4mel]]</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]] 2.34&#8491;</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=4mem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mem OCA], [https://pdbe.org/4mem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mem RCSB], [https://www.ebi.ac.uk/pdbsum/4mem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mem 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=4mem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mem OCA], [http://pdbe.org/4mem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mem RCSB], [http://www.ebi.ac.uk/pdbsum/4mem PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mem ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/UBP11_RAT UBP11_RAT] Protease that can remove conjugated ubiquitin from target proteins and polyubiquitin chains. Inhibits the degradation of target proteins by the proteasome. Cleaves preferentially 'Lys-6' and 'Lys-63'-linked ubiquitin chains. Has lower activity with 'Lys-11' and 'Lys-33'-linked ubiquitin chains, and extremely low activity with 'Lys-27', 'Lys-29' and 'Lys-48'-linked ubiquitin chains (in vitro). Plays a role in the regulation of pathways leading to NF-kappa-B activation. Plays a role in the regulation of DNA repair after double-stranded DNA breaks. Acts as a chromatin regulator via its association with the Polycomb group (PcG) multiprotein PRC1-like complex; may act by deubiquitinating components of the PRC1-like comple. Promotes cell proliferation by deubiquitinating phosphorylated E2F1x.[UniProtKB:P51784]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 20: @@
 ==See Also==
-*[[Thioesterase|Thioesterase]]
+*[[Thioesterase 3D structures|Thioesterase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ubiquitinyl hydrolase 1]]
+[[Category: Large Structures]]
-[[Category: Cornaciu, I]]
+[[Category: Rattus norvegicus]]
-[[Category: Dreveny, I]]
+[[Category: Cornaciu I]]
-[[Category: Emsley, J]]
+[[Category: Dreveny I]]
-[[Category: Gratton, H E]]
+[[Category: Emsley J]]
-[[Category: Harper, S]]
+[[Category: Gratton HE]]
-[[Category: Oberer, M]]
+[[Category: Harper S]]
-[[Category: Scott, D J]]
+[[Category: Oberer M]]
-[[Category: Du finger]]
+[[Category: Scott DJ]]
-[[Category: Hydrolase]]
-[[Category: Ubiquitin thiolesterase]]

4mem

From Proteopedia

Current revision

Crystal Structure of the rat USP11 DUSP-UBL domains

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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