3tt7: Difference between revisions
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==Structure of ClpP from Bacillus subtilis in complex with DFP== | ==Structure of ClpP from Bacillus subtilis in complex with DFP== | ||
<StructureSection load='3tt7' size='340' side='right' caption='[[3tt7]], [[Resolution|resolution]] 2.56Å' scene=''> | <StructureSection load='3tt7' size='340' side='right'caption='[[3tt7]], [[Resolution|resolution]] 2.56Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3tt7]] is a 7 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3tt7]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TT7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TT7 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.558Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DFP:DIISOPROPYL+PHOSPHONATE'>DFP</scene></td></tr> | |||
<tr id=' | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3tt7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tt7 OCA], [https://pdbe.org/3tt7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tt7 RCSB], [https://www.ebi.ac.uk/pdbsum/3tt7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tt7 ProSAT]</span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/CLPP_BACSU CLPP_BACSU] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins (By similarity). ClpXP is involved in the complete degradation of the Site-2 clipped anti-sigma-W factor RsiW. This results in the release of SigW and the transcription activation of the genes under the control of the sigma-W factor.<ref>PMID:16899079</ref> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[Clp | *[[Clp protease 3D structures|Clp protease 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus | [[Category: Bacillus subtilis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Kim | [[Category: Kim MK]] | ||
[[Category: Lee | [[Category: Lee B-G]] | ||
[[Category: Song | [[Category: Song HK]] | ||
Latest revision as of 20:33, 1 November 2023
Structure of ClpP from Bacillus subtilis in complex with DFPStructure of ClpP from Bacillus subtilis in complex with DFP
Structural highlights
FunctionCLPP_BACSU Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins (By similarity). ClpXP is involved in the complete degradation of the Site-2 clipped anti-sigma-W factor RsiW. This results in the release of SigW and the transcription activation of the genes under the control of the sigma-W factor.[1] Publication Abstract from PubMedClpP is a cylindrical protease that is tightly regulated by Clp-ATPases. The activation mechanism of ClpP using acyldepsipeptide antibiotics as mimics of natural activators showed enlargement of the axial entrance pore for easier processing of incoming substrates. However, the elimination of degradation products from inside the ClpP chamber remains unclear since there is no exit pore for releasing these products in all determined ClpP structures. Here we report a new crystal structure of ClpP from Bacillus subtilis, which shows a significantly compressed shape along the axial direction. A portion of the handle regions comprising the heptameric ring-ring contacts shows structural transition from an ordered to a disordered state, which triggers the large conformational change from an extended to an overall compressed structure. Along with this structural change, 14 side pores are generated for product release and the catalytic triad adopts an inactive orientation. We have also determined B. subtilis ClpP inhibited by diisopropylfluoro-phosphate and analyzed the active site in detail. Structural information pertaining to several different conformational steps such as those related to extended, ADEP-activated, DFP-inhibited and compressed forms of ClpP from B. subtilis is available. Structural comparisons suggest that functionally important regions in the ClpP-family such as N-terminal segments for the axial pore, catalytic triads, and handle domains for the product releasing pore exhibit intrinsically dynamic and unique structural features. This study provides valuable insights for understanding the enigmatic cylindrical degradation machinery of ClpP as well as other related proteases such as HslV and the 20S proteasome. Structural insights into the conformational diversity of ClpP from Bacillus subtilis.,Lee BG, Kim MK, Song HK Mol Cells. 2011 Nov 9. PMID:22080375[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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