4mxi - Revision history

OCA at 16:44, 20 September 2023

OCA — Wed, 20 Sep 2023 16:44:21 GMT

←Older revision		Revision as of 16:44, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4mxi]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_NCTC_8325 Staphylococcus aureus subsp. aureus NCTC 8325]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MXI FirstGlance]. <br>		<table><tr><td colspan='2'>[[4mxi]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_NCTC_8325 Staphylococcus aureus subsp. aureus NCTC 8325]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MXI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</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]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</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=4mxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxi OCA], [https://pdbe.org/4mxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mxi RCSB], [https://www.ebi.ac.uk/pdbsum/4mxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mxi 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=4mxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxi OCA], [https://pdbe.org/4mxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mxi RCSB], [https://www.ebi.ac.uk/pdbsum/4mxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mxi ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:16, 28 December 2022

OCA — Wed, 28 Dec 2022 10:16:56 GMT

←Older revision		Revision as of 10:16, 28 December 2022
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	==ClpP Ser98dhA==		==ClpP Ser98dhA==
-	<StructureSection load='4mxi' size='340' side='right' caption='[[4mxi]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4mxi' size='340' side='right'caption='[[4mxi]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4mxi]] is a 7 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Staa8 Staa8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4MXI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4mxi]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_NCTC_8325 Staphylococcus aureus subsp. aureus NCTC 8325]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MXI FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qwd\|3qwd]], [[3v5i\|3v5i]], [[3v5e\|3v5e]]</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=4mxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxi OCA], [https://pdbe.org/4mxi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mxi RCSB], [https://www.ebi.ac.uk/pdbsum/4mxi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mxi ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, SAOUHSC_00790 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93061 STAA8])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4mxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxi OCA], [~~http~~://pdbe.org/4mxi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4mxi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4mxi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4mxi ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CLPP_STAA8 CLPP_STAA8]] 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).	+	[https://www.uniprot.org/uniprot/CLPP_STAA8 CLPP_STAA8] 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).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 20:

	==See Also==		==See Also==
-	*[[Clp ~~Protease~~\|Clp ~~Protease~~]]	+	*[[Clp protease 3D structures\|Clp protease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Endopeptidase Clp~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Staa8~~]]	+	[[Category: Staphylococcus aureus subsp. aureus NCTC 8325]]
-	[[Category: Alte, F]]	+	[[Category: Alte F]]
-	[[Category: Gersch, M]]	+	[[Category: Gersch M]]
-	[[Category: Groll, M]]	+	[[Category: Groll M]]
-	[[Category: Kolb, R]]	+	[[Category: Kolb R]]
-	[[Category: Sieber~~, S A]]~~	+	[[Category: Sieber SA]]
-	~~[[Category: Clpp]]~~	+
-	~~[[Category: Complex disassembly]]~~	+
-	~~[[Category: Dehydroalanine]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibition]]~~	+
-	~~[[Category: Serine protease~~]]	+

OCA at 14:48, 5 August 2016

OCA — Fri, 05 Aug 2016 14:48:17 GMT

←Older revision		Revision as of 14:48, 5 August 2016
Line 1:		Line 1:
		+
	==ClpP Ser98dhA==		==ClpP Ser98dhA==
	<StructureSection load='4mxi' size='340' side='right' caption='[[4mxi]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='4mxi' size='340' side='right' caption='[[4mxi]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, SAOUHSC_00790 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93061 STAA8])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, SAOUHSC_00790 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93061 STAA8])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4mxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mxi RCSB], [http://www.ebi.ac.uk/pdbsum/4mxi PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4mxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxi OCA], [http://pdbe.org/4mxi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mxi RCSB], [http://www.ebi.ac.uk/pdbsum/4mxi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mxi ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4mxi" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 03:23, 25 December 2014

OCA — Thu, 25 Dec 2014 03:23:25 GMT

←Older revision		Revision as of 03:23, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4mxi~~\| ~~PDB~~=4mxi \| ~~SCENE~~= }}	+	==ClpP Ser98dhA==
-	===~~ClpP Ser98dhA~~===	+	<StructureSection load='4mxi' size='340' side='right' caption='[[4mxi]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24106749}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4mxi]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Staa8 Staa8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MXI FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3qwd\|3qwd]], [[3v5i\|3v5i]], [[3v5e\|3v5e]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, SAOUHSC_00790 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93061 STAA8])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4mxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mxi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mxi RCSB], [http://www.ebi.ac.uk/pdbsum/4mxi PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/CLPP_STAA8 CLPP_STAA8]] 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).		[[http://www.uniprot.org/uniprot/CLPP_STAA8 CLPP_STAA8]] 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).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Over 100 protease inhibitors are currently used in the clinics and most of them use blockage of the active site for their mode of inhibition. Among the protease drug targets are several enzymes for which the correct multimeric assembly is crucial to their activity such as the proteasome and the HIV protease. Here, we present a novel mechanism of protease inhibition that relies on active-site-directed small molecules that disassemble the protease complex. We show the applicability of this mechanism within the ClpP protease family, whose members are tetradecameric serine proteases and serve as regulators of several cellular processes including homeostasis and virulence. Compound-binding to ClpP in substochiometric fashion triggers the formation of completely inactive heptamers. Moreover, we report the selective beta-sultam-induced dehydroalanine formation of the active site serine. This reaction proceeds through sulfonylation and subsequent elimination thereby obliterating the catalytic charge relay system. The identity of the dehydroalanine was confirmed by mass-spectrometry and crystallography. Activity-based protein profiling experiments suggest the formation of a dehydroalanine moiety in living S. aureus cells upon beta-sultam treatment. Collectively, these findings extend our view on multicomponent protease inhibition that until now has mainly relied on blockage of the active site or occupation of a regulatory allosteric site.
		+
		+	Disruption of oligomerization and dehydroalanine formation as mechanisms for ClpP protease inhibition.,Gersch M, Kolb R, Alte F, Groll M, Sieber SA J Am Chem Soc. 2013 Oct 9. PMID:24106749<ref>PMID:24106749</ref>

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4mxi]] is~~ a ~~7 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Staa8 Staa8]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4MXI OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:024106749</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Clp Protease\|Clp Protease]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Endopeptidase Clp]]		[[Category: Endopeptidase Clp]]
	[[Category: Staa8]]		[[Category: Staa8]]
-	[[Category: Alte, F.]]	+	[[Category: Alte, F]]
-	[[Category: Gersch, M.]]	+	[[Category: Gersch, M]]
-	[[Category: Groll, M.]]	+	[[Category: Groll, M]]
-	[[Category: Kolb, R.]]	+	[[Category: Kolb, R]]
-	[[Category: Sieber, S A.]]	+	[[Category: Sieber, S A]]
	[[Category: Clpp]]		[[Category: Clpp]]
	[[Category: Complex disassembly]]		[[Category: Complex disassembly]]

OCA at 04:34, 13 February 2014

OCA — Thu, 13 Feb 2014 04:34:35 GMT

←Older revision		Revision as of 04:34, 13 February 2014
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[4mxi]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Xenopus_itombwensis Xenopus itombwensis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXI OCA].	+	[[4mxi]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Staa8 Staa8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXI OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:024106749</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:024106749</ref><references group="xtra"/><references/>
	[[Category: Endopeptidase Clp]]		[[Category: Endopeptidase Clp]]
-	[[Category: ~~Xenopus itombwensis~~]]	+	[[Category: Staa8]]
	[[Category: Alte, F.]]		[[Category: Alte, F.]]
	[[Category: Gersch, M.]]		[[Category: Gersch, M.]]

OCA at 06:46, 23 October 2013

OCA — Wed, 23 Oct 2013 06:46:21 GMT

←Older revision		Revision as of 06:46, 23 October 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4mxi\| PDB=4mxi \| SCENE= }}
		+	===ClpP Ser98dhA===
		+	{{ABSTRACT_PUBMED_24106749}}

-	~~The entry 4mxi is ON HOLD~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/CLPP_STAA8 CLPP_STAA8]] 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).

-	~~Authors~~: ~~Gersch, M~~.~~, Kolb, R~~.~~, Alte, F~~.~~, Groll, M~~.~~, Sieber, S~~.A.	+	==About this Structure==
		+	[[4mxi]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Xenopus_itombwensis Xenopus itombwensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MXI OCA].

-	~~Description~~: ~~ClpP Ser98dhA~~	+	==Reference==
		+	<ref group="xtra">PMID:024106749</ref><references group="xtra"/><references/>
		+	[[Category: Endopeptidase Clp]]
		+	[[Category: Xenopus itombwensis]]
		+	[[Category: Alte, F.]]
		+	[[Category: Gersch, M.]]
		+	[[Category: Groll, M.]]
		+	[[Category: Kolb, R.]]
		+	[[Category: Sieber, S A.]]
		+	[[Category: Clpp]]
		+	[[Category: Complex disassembly]]
		+	[[Category: Dehydroalanine]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibition]]
		+	[[Category: Serine protease]]

OCA: Protected "4mxi" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2013 06:58:47 GMT

Protected "4mxi" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:58, 2 October 2013

OCA: New page: '''Unreleased structure''' The entry 4mxi is ON HOLD Authors: Gersch, M., Kolb, R., Alte, F., Groll, M., Sieber, S.A. Description: ClpP Ser98dhA

OCA — Wed, 02 Oct 2013 06:58:46 GMT

New page: '''Unreleased structure''' The entry 4mxi is ON HOLD Authors: Gersch, M., Kolb, R., Alte, F., Groll, M., Sieber, S.A. Description: ClpP Ser98dhA

New page

'''Unreleased structure'''

The entry 4mxi is ON HOLD

Authors: Gersch, M., Kolb, R., Alte, F., Groll, M., Sieber, S.A.

Description: ClpP Ser98dhA