1ky9: Difference between revisions

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-[[Image:1ky9.gif|left|200px]]
-<!--
+==Crystal Structure of DegP (HtrA)==
-The line below this paragraph, containing "STRUCTURE_1ky9", creates the "Structure Box" on the page.
+<StructureSection load='1ky9' size='340' side='right'caption='[[1ky9]], [[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'>[[1ky9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KY9 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_1ky9|  PDB=1ky9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ky9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ky9 OCA], [https://pdbe.org/1ky9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ky9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ky9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ky9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DEGP_ECOLI DEGP_ECOLI] DegP acts as a chaperone at low temperatures but switches to a peptidase (heat shock protein) at higher temperatures. It degrades transiently denatured and unfolded proteins which accumulate in the periplasm following heat shock or other stress conditions. DegP is efficient with Val-Xaa and Ile-Xaa peptide bonds, suggesting a preference for beta-branched side chain amino acids. Only unfolded proteins devoid of disulfide bonds appear capable of being cleaved, thereby preventing non-specific proteolysis of folded proteins. Its proteolytic activity is essential for the survival of cells at elevated temperatures. It can degrade IciA, ada, casein, globin and PapA. DegP shares specificity with DegQ. DegP is also involved in the biogenesis of partially folded outer-membrane proteins (OMP).<ref>PMID:2180903</ref> <ref>PMID:8830688</ref> <ref>PMID:10319814</ref> <ref>PMID:18505836</ref> <ref>PMID:12730160</ref> <ref>PMID:18496527</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/ky/1ky9_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=1ky9 ConSurf].
+<div style="clear:both"></div>
-'''Crystal Structure of DegP (HtrA)'''
+==See Also==
+*[[Heat Shock Protein structures|Heat Shock Protein structures]]
+== References ==
-==Overview==
+<references/>
-Molecular chaperones and proteases monitor the folded state of other proteins. In addition to recognizing non-native conformations, these quality control factors distinguish substrates that can be refolded from those that need to be degraded. To investigate the molecular basis of this process, we have solved the crystal structure of DegP (also known as HtrA), a widely conserved heat shock protein that combines refolding and proteolytic activities. The DegP hexamer is formed by staggered association of trimeric rings. The proteolytic sites are located in a central cavity that is only accessible laterally. The mobile side-walls are constructed by twelve PDZ domains, which mediate the opening and closing of the particle and probably the initial binding of substrate. The inner cavity is lined by several hydrophobic patches that may act as docking sites for unfolded polypeptides. In the chaperone conformation, the protease domain of DegP exists in an inactive state, in which substrate binding in addition to catalysis is abolished.
+__TOC__
+</StructureSection>
-==About this Structure==
-KY9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KY9 OCA].
-==Reference==
-Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine., Krojer T, Garrido-Franco M, Huber R, Ehrmann M, Clausen T, Nature. 2002 Mar 28;416(6879):455-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11919638 11919638]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Clausen, T.]]
+[[Category: Clausen T]]
-[[Category: Ehrmann, M.]]
+[[Category: Ehrmann M]]
-[[Category: Garrido-Franco, M.]]
+[[Category: Garrido-Franco M]]
-[[Category: Huber, R.]]
+[[Category: Huber R]]
-[[Category: Krojer, T.]]
+[[Category: Krojer T]]
-[[Category: Atp-independent]]
-[[Category: Cage-forming protein]]
-[[Category: Chaperone]]
-[[Category: Pdz]]
-[[Category: Periplasm]]
-[[Category: Protein quality control]]
-[[Category: Serine protease]]
-[[Category: Temperature-regulated]]
-[[Category: Trypsin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 23:19:12 2008''