2gwf: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2gwf.gif|left|200px]]<br />
-<applet load="2gwf" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2gwf, resolution 2.30&Aring;" />
-'''Structure of a USP8-NRDP1 complex'''<br />
-==Overview==
+==Structure of a USP8-NRDP1 complex==
-Ubiquitin-specific protease 8 (USP8) hydrolyzes mono and polyubiquitylated, targets such as epidermal growth factor receptors and is involved in, clathrin-mediated internalization. In 1182 residues, USP8 contains, multiple domains, including coiled-coil, rhodanese, and catalytic domains., We report the first high-resolution crystal structures of these domains, and discuss their implications for USP8 function. The amino-terminal, domain is a homodimer with a novel fold. It is composed of two five-helix, bundles, where the first helices are swapped, and carboxyl-terminal, helices are extended in an antiparallel fashion. The structure of the, rhodanese domain, determined in complex with the E3 ligase NRDP1, reveals, the canonical rhodanese fold but with a distorted primordial active site., The USP8 recognition domain of NRDP1 has a novel protein fold that, interacts with a conserved peptide loop of the rhodanese domain. A, consensus sequence of this loop is found in other NRDP1 targets, suggesting a common mode of interaction. The structure of the, carboxyl-terminal catalytic domain of USP8 exhibits the conserved, tripartite architecture but shows unique traits. Notably, the active site, including the ubiquitin binding pocket, is in a closed conformation, incompatible with substrate binding. The presence of a zinc ribbon, subdomain near the ubiquitin binding site further suggests a, polyubiquitin-specific binding site and a mechanism for substrate induced, conformational changes.
+<StructureSection load='2gwf' size='340' side='right'caption='[[2gwf]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2gwf]] 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=2GWF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GWF FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</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=2gwf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gwf OCA], [https://pdbe.org/2gwf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gwf RCSB], [https://www.ebi.ac.uk/pdbsum/2gwf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gwf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UBP8_HUMAN UBP8_HUMAN] Hydrolase that can remove conjugated ubiquitin from proteins and therefore plays an important regulatory role at the level of protein turnover by preventing degradation. Converts both 'Lys-48' an 'Lys-63'-linked ubiquitin chains. Catalytic activity is enhanced in the M phase. Involved in cell proliferation. Required to enter into S phase in response to serum stimulation. May regulate T-cell anergy mediated by RNF128 via the formation of a complex containing RNF128 and OTUB1. Probably regulates the stability of STAM2 and RASGRF1. Regulates endosomal ubiquitin dynamics, cargo sorting, membrane traffic at early endosomes, and maintenance of ESCRT-0 stability. The level of protein ubiquitination on endosomes is essential for maintaining the morphology of the organelle. Deubiquitinates EPS15 and controles tyrosine kinase stability. Removes conjugated ubiquitin from EGFR thus regulating EGFR degradation and downstream MAPK signaling. Involved in acrosome biogenesis through interaction with the spermatid ESCRT-0 complex and microtubules. Deubiquitinates BIRC6/bruce and KIF23/MKLP1.<ref>PMID:9628861</ref> <ref>PMID:16520378</ref> <ref>PMID:17711858</ref> <ref>PMID:18329369</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gw/2gwf_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2gwf ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-GWF is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Active as [http://en.wikipedia.org/wiki/Ubiquitin_thiolesterase Ubiquitin thiolesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.2.15 3.1.2.15] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2GWF OCA].
+*[[Thioesterase 3D structures|Thioesterase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8)., Avvakumov GV, Walker JR, Xue S, Finerty PJ Jr, Mackenzie F, Newman EM, Dhe-Paganon S, J Biol Chem. 2006 Dec 8;281(49):38061-70. Epub 2006 Oct 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17035239 17035239]
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Ubiquitin thiolesterase]]
+[[Category: Arrowsmith CH]]
-[[Category: Arrowsmith, C.H.]]
+[[Category: Avvakumov GV]]
-[[Category: Avvakumov, G.V.]]
+[[Category: Bochkarev A]]
-[[Category: Bochkarev, A.]]
+[[Category: Butler-Cole C]]
-[[Category: Butler-Cole, C.]]
+[[Category: Dhe-Paganon S]]
-[[Category: Dhe-Paganon, S.]]
+[[Category: Edwards AM]]
-[[Category: Edwards, A.M.]]
+[[Category: Finerty Jr PJ]]
-[[Category: Jr., P.J.Finerty.]]
+[[Category: Newman EM]]
-[[Category: Newman, E.M.]]
+[[Category: Sundstrom M]]
-[[Category: SGC, Structural.Genomics.Consortium.]]
+[[Category: Walker JR]]
-[[Category: Sundstrom, M.]]
+[[Category: Weigelt J]]
-[[Category: Walker, J.R.]]
+[[Category: Xue S]]
-[[Category: Weigelt, J.]]
-[[Category: Xue, S.]]
-[[Category: e3 ligase]]
-[[Category: hydrolase]]
-[[Category: protease]]
-[[Category: protein ubiquitination]]
-[[Category: protein-protein complex]]
-[[Category: sgc]]
-[[Category: structural genomics]]
-[[Category: structural genomics consortium]]
-[[Category: ubl conjugation pathway]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 22:23:24 2007''