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7p80

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Crystal structure of ClpP from Bacillus subtilis in complex with ADEP2 (compressed state)

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 <StructureSection load='7p80' size='340' side='right'caption='[[7p80]], [[Resolution|resolution]] 2.98&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7p80]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P80 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P80 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7p80]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P80 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P80 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXP:CYCLOHEXANE+PROPIONIC+ACID'>CXP</scene>, <scene name='pdbligand=MP8:(4R)-4-METHYL-L-PROLINE'>MP8</scene>, <scene name='pdbligand=WFP:3,5-DIFLUORO-L-PHENYLALANINE'>WFP</scene>, <scene name='pdbligand=YCP:(2S)-PIPERIDINE-2-CARBOXYLIC+ACID'>YCP</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]] 2.98&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CXP:CYCLOHEXANE+PROPIONIC+ACID'>CXP</scene>, <scene name='pdbligand=MP8:(4R)-4-METHYL-L-PROLINE'>MP8</scene>, <scene name='pdbligand=WFP:3,5-DIFLUORO-L-PHENYLALANINE'>WFP</scene>, <scene name='pdbligand=YCP:(2S)-PIPERIDINE-2-CARBOXYLIC+ACID'>YCP</scene></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=7p80 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p80 OCA], [https://pdbe.org/7p80 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p80 RCSB], [https://www.ebi.ac.uk/pdbsum/7p80 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p80 ProSAT]</span></td></tr>
 </table>
 == 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>
+[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;">
-== Publication Abstract from PubMed ==
-The ClpP serine peptidase is a tetradecameric degradation molecular machine involved in many physiological processes. It becomes a competent ATP-dependent protease when coupled with Clp-ATPases. Small chemical compounds, acyldepsipeptides (ADEPs), are known to cause the dysregulation and activation of ClpP without ATPases and have potential as novel antibiotics. Previously, structural studies of ClpP from various species revealed its structural details, conformational changes, and activation mechanism. Although product release through side exit pores has been proposed, the detailed driving force for product release remains elusive. Herein, we report crystal structures of ClpP from Bacillus subtilis (BsClpP) in unforeseen ADEP-bound states. Cryo-electron microscopy structures of BsClpP revealed various conformational states under different pH conditions. To understand the conformational change required for product release, we investigated the relationship between substrate hydrolysis and the pH-lowering process. The production of hydrolyzed peptides from acidic and basic substrates by proteinase K and BsClpP lowered the pH values. Our data, together with those of previous findings, provide insight into the molecular mechanism of product release by the ClpP self-compartmentalizing protease.
-Structural insights into ClpP protease side exit pore-opening by a pH drop coupled with substrate hydrolysis.,Kim L, Lee BG, Kim M, Kim MK, Kwon DH, Kim H, Brotz-Oesterhelt H, Roh SH, Song HK EMBO J. 2022 Jul 4;41(13):e109755. doi: 10.15252/embj.2021109755. Epub 2022 May, 20. PMID:35593068<ref>PMID:35593068</ref>
+==See Also==
+*[[Clp protease 3D structures|Clp protease 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 7p80" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Endopeptidase Clp]]
+[[Category: Bacillus subtilis subsp. subtilis str. 168]]
 [[Category: Large Structures]]
-[[Category: Kim, L]]
+[[Category: Synthetic construct]]
-[[Category: Kim, M K]]
+[[Category: Kim L]]
-[[Category: Kwon, D H]]
+[[Category: Kim MK]]
-[[Category: Lee, B G]]
+[[Category: Kwon DH]]
-[[Category: Song, H K]]
+[[Category: Lee B-G]]
-[[Category: Acyldepsipeptide]]
+[[Category: Song HK]]
-[[Category: Adep2]]
-[[Category: Antibiotic]]
-[[Category: Clpp]]
-[[Category: Compressed]]
-[[Category: Hydrolase]]

7p80

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Current revision

Crystal structure of ClpP from Bacillus subtilis in complex with ADEP2 (compressed state)

Structural highlights

Function

See Also

References

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