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1xt9

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[[Image:1xt9.gif|left|200px]]
 
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==Crystal Structure of Den1 in complex with Nedd8==
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The line below this paragraph, containing "STRUCTURE_1xt9", creates the "Structure Box" on the page.
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<StructureSection load='1xt9' size='340' side='right'caption='[[1xt9]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1xt9]] is a 2 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=1XT9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XT9 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xt9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xt9 OCA], [https://pdbe.org/1xt9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xt9 RCSB], [https://www.ebi.ac.uk/pdbsum/1xt9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xt9 ProSAT]</span></td></tr>
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{{STRUCTURE_1xt9| PDB=1xt9 | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SENP8_HUMAN SENP8_HUMAN] Protease that catalyzes two essential functions in the NEDD8 pathway: processing of full-length NEDD8 to its mature form and deconjugation of NEDD8 from targeted proteins such as cullins or p53.<ref>PMID:12730221</ref> <ref>PMID:12759363</ref> <ref>PMID:12759362</ref> <ref>PMID:15242646</ref> <ref>PMID:15775960</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xt/1xt9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1xt9 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The Nedd8 conjugation pathway is conserved from yeast to humans and is essential in many organisms. Nedd8 is conjugated to cullin proteins in a process that alters SCF E3 ubiquitin ligase activity, and it is presumed that Nedd8 deconjugation would reverse these effects. We now report the X-ray structures of the human Nedd8-specific protease, Den1, in a complex with the inhibitor Nedd8 aldehyde, thus revealing a model for the tetrahedral transition state intermediate generated during proteolysis. Although Den1 is closely related to the SUMO-specific protease family (Ulp/Senp family), structural analysis of the interface suggests determinants involved in Nedd8 selectivity by Den1 over other ubiquitin-like family members and suggests how the Ulp/Senp architecture has been modified to interact with different ubiquitin-like modifiers.
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'''Crystal Structure of Den1 in complex with Nedd8'''
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Structure of a complex between Nedd8 and the Ulp/Senp protease family member Den1.,Reverter D, Wu K, Erdene TG, Pan ZQ, Wilkinson KD, Lima CD J Mol Biol. 2005 Jan 7;345(1):141-51. PMID:15567417<ref>PMID:15567417</ref>
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==Overview==
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The Nedd8 conjugation pathway is conserved from yeast to humans and is essential in many organisms. Nedd8 is conjugated to cullin proteins in a process that alters SCF E3 ubiquitin ligase activity, and it is presumed that Nedd8 deconjugation would reverse these effects. We now report the X-ray structures of the human Nedd8-specific protease, Den1, in a complex with the inhibitor Nedd8 aldehyde, thus revealing a model for the tetrahedral transition state intermediate generated during proteolysis. Although Den1 is closely related to the SUMO-specific protease family (Ulp/Senp family), structural analysis of the interface suggests determinants involved in Nedd8 selectivity by Den1 over other ubiquitin-like family members and suggests how the Ulp/Senp architecture has been modified to interact with different ubiquitin-like modifiers.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1XT9 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XT9 OCA].
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</div>
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<div class="pdbe-citations 1xt9" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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Structure of a complex between Nedd8 and the Ulp/Senp protease family member Den1., Reverter D, Wu K, Erdene TG, Pan ZQ, Wilkinson KD, Lima CD, J Mol Biol. 2005 Jan 7;345(1):141-51. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15567417 15567417]
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*[[NEDD8|NEDD8]]
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*[[Sentrin-specific protease|Sentrin-specific protease]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Erdene, T G.]]
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[[Category: Erdene TG]]
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[[Category: Lima, C D.]]
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[[Category: Lima CD]]
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[[Category: Pan, Z Q.]]
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[[Category: Pan ZQ]]
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[[Category: Reverter, D.]]
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[[Category: Reverter D]]
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[[Category: Wilkinson, K D.]]
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[[Category: Wilkinson KD]]
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[[Category: Wu, K.]]
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[[Category: Wu K]]
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[[Category: Cysteine protease]]
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[[Category: Ubiquitin-like]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 15:29:03 2008''
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Current revision

Crystal Structure of Den1 in complex with Nedd8

PDB ID 1xt9

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