2g4d: Difference between revisions

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-[[Image:2g4d.png|left|200px]]
-<!--
+==Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1==
-The line below this paragraph, containing "STRUCTURE_2g4d", creates the "Structure Box" on the page.
+<StructureSection load='2g4d' size='340' side='right'caption='[[2g4d]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2g4d]] is a 4 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=2G4D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G4D FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2g4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g4d OCA], [https://pdbe.org/2g4d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g4d RCSB], [https://www.ebi.ac.uk/pdbsum/2g4d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g4d ProSAT]</span></td></tr>
-{{STRUCTURE_2g4d|  PDB=2g4d  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SENP1_HUMAN SENP1_HUMAN] Protease that catalyzes two essential functions in the SUMO pathway: processing of full-length SUMO1, SUMO2 and SUMO3 to their mature forms and deconjugation of SUMO1, SUMO2 and SUMO3 from targeted proteins. Deconjugates SUMO1 from HIPK2. Deconjugates SUMO1 from HDAC1, which decreases its transcriptional repression activity.<ref>PMID:10652325</ref> <ref>PMID:15199155</ref> <ref>PMID:16253240</ref> <ref>PMID:16553580</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/g4/2g4d_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=2g4d ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+SUMO (small ubiquitin-related modifier)-specific proteases catalyse the maturation and de-conjugation processes of the sumoylation pathway and modulate various cellular responses including nuclear metabolism and cell cycle progression. The active-site cysteine residue is conserved among all known SUMO-specific proteases and is not substitutable by serine in the hydrolysis reactions demonstrated previously in yeast. We report here that the catalytic domain of human protease SENP1 (SUMO-specific protease 1) mutant SENP1C(C603S) carrying a mutation of cysteine to serine at the active site is inactive in maturation and de-conjugation reactions. To further understand the hydrolytic mechanism catalysed by SENP1, we have determined, at 2.8 A resolution (1 A = 0.1 nm), the X-ray structure of SENP1C(C603S)-SUMO-1 complex. A comparison of the structure of SENP2-SUMO-1 suggests strongly that SUMO-specific proteases require a self-conformational change prior to cleavage of peptide or isopeptide bond in the maturation and de-conjugation processes respectively. Moreover, analysis of the interface of SENP1 and SUMO-1 has led to the identification of four unique amino acids in SENP1 that facilitate the binding of SUMO-1. By means of an in vitro assay, we further demonstrate a novel function of SENP1 in hydrolysing the thioester linkage in E1-SUMO and E2-SUMO complexes. The results disclose a new mechanism of regulation of the sumoylation pathway by the SUMO-specific proteases.
-===Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1===
+Crystal structure of the SENP1 mutant C603S-SUMO complex reveals the hydrolytic mechanism of SUMO-specific protease.,Xu Z, Chau SF, Lam KH, Chan HY, Ng TB, Au SW Biochem J. 2006 Sep 15;398(3):345-52. PMID:16712526<ref>PMID:16712526</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16712526}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2g4d" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16712526 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_16712526}}
-==About this Structure==
-[[2g4d]] is a 4 chain structure of [[SUMO]] with sequence 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=2G4D OCA].
 ==See Also==
-*[[SUMO]]
+*[[SUMO 3D Structures|SUMO 3D Structures]]
+*[[Sentrin-specific protease|Sentrin-specific protease]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:16712526</ref><ref group="xtra">PMID:15487983</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Au, S W.N.]]
+[[Category: Large Structures]]
-[[Category: Chau, S F.]]
+[[Category: Au SWN]]
-[[Category: Lam, K H.]]
+[[Category: Chau SF]]
-[[Category: Xu, Z.]]
+[[Category: Lam KH]]
-[[Category: Hydrolase/protein binding complex]]
+[[Category: Xu Z]]
-[[Category: Protease]]
-[[Category: Sumo deconjugation]]
-[[Category: Sumo maturation]]
-[[Category: Ubiquitin-like protein]]