7p81

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<StructureSection load='7p81' size='340' side='right'caption='[[7p81]], [[Resolution|resolution]] 2.79&Aring;' scene=''>
<StructureSection load='7p81' size='340' side='right'caption='[[7p81]], [[Resolution|resolution]] 2.79&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[7p81]] is a 48 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7P81 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P81 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[7p81]] is a 48 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=7P81 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7P81 FirstGlance]. <br>
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</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>
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</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>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7p80|7p80]]</div></td></tr>
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<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>
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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=7p81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p81 OCA], [https://pdbe.org/7p81 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p81 RCSB], [https://www.ebi.ac.uk/pdbsum/7p81 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p81 ProSAT]</span></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=7p81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7p81 OCA], [https://pdbe.org/7p81 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7p81 RCSB], [https://www.ebi.ac.uk/pdbsum/7p81 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7p81 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[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>
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[[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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 7p81" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Endopeptidase Clp]]
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[[Category: Bacillus subtilis subsp. subtilis str. 168]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Kim, L]]
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[[Category: Synthetic construct]]
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[[Category: Kim, M K]]
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[[Category: Kim L]]
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[[Category: Kwon, D H]]
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[[Category: Kim MK]]
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[[Category: Lee, B G]]
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[[Category: Kwon DH]]
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[[Category: Song, H K]]
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[[Category: Lee B-G]]
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[[Category: Acyldepsipeptide]]
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[[Category: Song HK]]
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[[Category: Adep2]]
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[[Category: Antibiotic]]
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[[Category: Clpp]]
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[[Category: Compressed]]
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[[Category: Hydrolase]]
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Revision as of 05:25, 8 September 2022

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

PDB ID 7p81

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