5lrv: Difference between revisions

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 ==Structure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diubiquitin==
-<StructureSection load='5lrv' size='340' side='right' caption='[[5lrv]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='5lrv' size='340' side='right'caption='[[5lrv]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5lrv]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LRV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LRV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5lrv]] is a 3 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=5LRV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LRV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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]] 2.8&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ABU:GAMMA-AMINO-BUTANOIC+ACID'>ABU</scene>, <scene name='pdbligand=DAB:2,4-DIAMINOBUTYRIC+ACID'>DAB</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABU:GAMMA-AMINO-BUTANOIC+ACID'>ABU</scene>, <scene name='pdbligand=DAB:2,4-DIAMINOBUTYRIC+ACID'>DAB</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=5lrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lrv OCA], [https://pdbe.org/5lrv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lrv RCSB], [https://www.ebi.ac.uk/pdbsum/5lrv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lrv 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=5lrv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lrv OCA], [http://pdbe.org/5lrv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lrv RCSB], [http://www.ebi.ac.uk/pdbsum/5lrv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lrv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/OTU7B_HUMAN OTU7B_HUMAN]] Negative regulator of the non-canonical NF-kappa-B pathway that acts by mediating deubiquitination of TRAF3, an inhibitor of the NF-kappa-B pathway, thereby acting as a negative regulator of B-cell responses. In response to non-canonical NF-kappa-B stimuli, deubiquitinates 'Lys-48'-linked polyubiquitin chains of TRAF3, preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappa-B. Negatively regulates mucosal immunity against infections. Mediates deubiquitination of EGFR. Has deubiquitinating activity toward 'Lys-11', 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. In vitro, has preference for 'Lys-11'-linked polyubiquitin chains; however such data are unsure in vivo. Hydrolyzes both linear and branched forms of polyubiquitin.<ref>PMID:11463333</ref> <ref>PMID:12682062</ref> <ref>PMID:18178551</ref> <ref>PMID:20622874</ref> <ref>PMID:22179831</ref> <ref>PMID:23827681</ref>  [[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/OTU7B_HUMAN OTU7B_HUMAN] Negative regulator of the non-canonical NF-kappa-B pathway that acts by mediating deubiquitination of TRAF3, an inhibitor of the NF-kappa-B pathway, thereby acting as a negative regulator of B-cell responses. In response to non-canonical NF-kappa-B stimuli, deubiquitinates 'Lys-48'-linked polyubiquitin chains of TRAF3, preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappa-B. Negatively regulates mucosal immunity against infections. Mediates deubiquitination of EGFR. Has deubiquitinating activity toward 'Lys-11', 'Lys-48' or 'Lys-63'-linked polyubiquitin chains. In vitro, has preference for 'Lys-11'-linked polyubiquitin chains; however such data are unsure in vivo. Hydrolyzes both linear and branched forms of polyubiquitin.<ref>PMID:11463333</ref> <ref>PMID:12682062</ref> <ref>PMID:18178551</ref> <ref>PMID:20622874</ref> <ref>PMID:22179831</ref> <ref>PMID:23827681</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Ubiquitinyl hydrolase 1]]
+[[Category: Homo sapiens]]
-[[Category: Akutsu, M]]
+[[Category: Large Structures]]
-[[Category: Burke, J E]]
+[[Category: Akutsu M]]
-[[Category: Elliott, P R]]
+[[Category: Burke JE]]
-[[Category: Freund, S M.V]]
+[[Category: El Oualid F]]
-[[Category: Gersch, M]]
+[[Category: Elliott PR]]
-[[Category: Geurink, P P]]
+[[Category: Freund SMV]]
-[[Category: Kawasaki, M]]
+[[Category: Gersch M]]
-[[Category: Komander, D]]
+[[Category: Geurink PP]]
-[[Category: Kulathu, Y]]
+[[Category: Kawasaki M]]
-[[Category: Maslen, S L]]
+[[Category: Komander D]]
-[[Category: Mevissen, T E.T]]
+[[Category: Kulathu Y]]
-[[Category: Mulder, M P.C]]
+[[Category: Maslen SL]]
-[[Category: Oualid, F El]]
+[[Category: Mevissen TET]]
-[[Category: Ovaa, H]]
+[[Category: Mulder MPC]]
-[[Category: Tol, B D.M van]]
+[[Category: Ovaa H]]
-[[Category: Deubiquitinase]]
+[[Category: Van Tol BDM]]
-[[Category: Hydrolase]]
-[[Category: Otu domain]]
-[[Category: Protease]]