7dft - Revision history

OCA at 16:32, 29 November 2023

OCA — Wed, 29 Nov 2023 16:32:33 GMT

←Older revision		Revision as of 16:32, 29 November 2023
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	<StructureSection load='7dft' size='340' side='right'caption='[[7dft]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='7dft' size='340' side='right'caption='[[7dft]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7dft]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"pseudomonas_oryzae"_uyeda_and_ishiyama_in_ishiyama_1926 "pseudomonas~~ oryzae~~" uyeda and ishiyama in ishiyama 1926~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DFT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DFT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dft]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_oryzae Xanthomonas oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DFT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DFT FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>clpP, ADT25_23080, ADT27_15185, EYR26_04825 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~347~~ "~~Pseudomonas oryzae~~" ~~Uyeda and Ishiyama in Ishiyama 1926])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7dft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dft OCA], [https://pdbe.org/7dft PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dft RCSB], [https://www.ebi.ac.uk/pdbsum/7dft PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dft 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=7dft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dft OCA], [https://pdbe.org/7dft PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dft RCSB], [https://www.ebi.ac.uk/pdbsum/7dft PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dft ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~A0A0M1K022_9XANT A0A0M1K022_9XANT]~~] 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.[HAMAP-Rule:MF_00444~~][RuleBase:RU000550~~]	+	[https://www.uniprot.org/uniprot/CLPP_XANOR CLPP_XANOR] 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.[HAMAP-Rule:MF_00444]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7dft" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7dft" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Clp protease 3D structures\|Clp protease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pseudomonas oryzae uyeda and ishiyama in ishiyama 1926]]
-	[[Category: Endopeptidase Clp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Yang, C G~~]]	+	[[Category: Xanthomonas oryzae]]
-	[[Category: Yang~~, T~~]]	+	[[Category: Yang C-G]]
-	[[Category: ~~Caseinolytic protease p]]~~	+	[[Category: Yang T]]
-	~~[[Category: Clp protease]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:47, 28 July 2021

OCA — Wed, 28 Jul 2021 10:47:29 GMT

←Older revision		Revision as of 10:47, 28 July 2021
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	==Crystal structure of Xanthomonas oryzae ClpP==		==Crystal structure of Xanthomonas oryzae ClpP==
-	<StructureSection load='7dft' size='340' side='right'caption='[[7dft]]' scene=''>	+	<StructureSection load='7dft' size='340' side='right'caption='[[7dft]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DFT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DFT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7dft]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/"pseudomonas_oryzae"_uyeda_and_ishiyama_in_ishiyama_1926 "pseudomonas oryzae" uyeda and ishiyama in ishiyama 1926]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DFT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DFT FirstGlance]. <br>
-	</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=7dft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dft OCA], [https://pdbe.org/7dft PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dft RCSB], [https://www.ebi.ac.uk/pdbsum/7dft PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dft ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">clpP, ADT25_23080, ADT27_15185, EYR26_04825 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=347 "Pseudomonas oryzae" Uyeda and Ishiyama in Ishiyama 1926])</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7dft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dft OCA], [https://pdbe.org/7dft PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dft RCSB], [https://www.ebi.ac.uk/pdbsum/7dft PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dft ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A0A0M1K022_9XANT A0A0M1K022_9XANT]] 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.[HAMAP-Rule:MF_00444][RuleBase:RU000550]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Rice bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is considered a destructive plant bacterial disease. The looming crisis of antibiotic resistance necessitates the discovery of antibiotics with new modes of action. Activated caseinolytic protease P (ClpP) can degrade bacterial FtsZ proteins that are essential for cell division; thus, we hypothesized that small-molecule-induced dysregulation of XooClpP may result in degradation of XooFtsZ to treat leaf blight diseases. In this work, we have determined the crystal structures of XooClpP, and its mutant bound with ADEP4, which revealed the action modes of XooClpP assemblies and XooFtsZ degradation by dysregulated XooClpP in the presence of small-molecule activators, such as ONC212 and ADEP4. Additionally, an antibacterial assessment demonstrated that ONC212 displays excellent activity against Xoo and prevents rice bacterial leaf blight in vivo. Thus, these unique antibacterial effects of small-molecule activators of XooClpP represent a potential strategy for the development of agricultural antibiotics by targeting bacterial ClpP.
		+
		+	Dysregulation of ClpP by Small-Molecule Activators Used Against Xanthomonas oryzae pv. oryzae Infections.,Yang T, Zhang T, Zhou X, Wang P, Gan J, Song B, Yang S, Yang CG J Agric Food Chem. 2021 Jul 14;69(27):7545-7553. doi: 10.1021/acs.jafc.1c01470., Epub 2021 Jul 3. PMID:34218658<ref>PMID:34218658</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7dft" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pseudomonas oryzae uyeda and ishiyama in ishiyama 1926]]
		+	[[Category: Endopeptidase Clp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Yang C-G]]	+	[[Category: Yang, C G]]
-	[[Category: Yang T]]	+	[[Category: Yang, T]]
		+	[[Category: Caseinolytic protease p]]
		+	[[Category: Clp protease]]
		+	[[Category: Hydrolase]]

OCA at 10:09, 19 May 2021

OCA — Wed, 19 May 2021 10:09:04 GMT

←Older revision		Revision as of 10:09, 19 May 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7dft ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of Xanthomonas oryzae ClpP==
-		+	<StructureSection load='7dft' size='340' side='right'caption='[[7dft]]' scene=''>
-	~~Authors~~: ~~Yang~~, C.-G., ~~Yang~~, T.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DFT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DFT FirstGlance]. <br>
-	~~Description: Crystal structure of Xanthomonas oryzae ClpP~~	+	</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=7dft FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dft OCA], [https://pdbe.org/7dft PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dft RCSB], [https://www.ebi.ac.uk/pdbsum/7dft PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dft ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Yang, C.-G]]	+	__TOC__
-	[[Category: Yang, T]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Yang C-G]]
		+	[[Category: Yang T]]

OCA at 05:20, 30 December 2020

OCA — Wed, 30 Dec 2020 05:20:46 GMT

←Older revision		Revision as of 05:20, 30 December 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7dft is ON HOLD	+	The entry 7dft is ON HOLD until Paper Publication

	Authors: Yang, C.-G., Yang, T.		Authors: Yang, C.-G., Yang, T.
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	Description: Crystal structure of Xanthomonas oryzae ClpP		Description: Crystal structure of Xanthomonas oryzae ClpP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Yang, T]]
	[[Category: Yang, C.-G]]		[[Category: Yang, C.-G]]
		+	[[Category: Yang, T]]

OCA: Protected "7dft" [edit=sysop:move=sysop]

OCA — Wed, 18 Nov 2020 08:02:22 GMT

Protected "7dft" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:02, 18 November 2020

OCA: New page: '''Unreleased structure''' The entry 7dft is ON HOLD Authors: Yang, C.-G., Yang, T. Description: Crystal structure of Xanthomonas oryzae ClpP Category: Unreleased Structures [[Cate...

OCA — Wed, 18 Nov 2020 08:02:21 GMT

New page: '''Unreleased structure''' The entry 7dft is ON HOLD Authors: Yang, C.-G., Yang, T. Description: Crystal structure of Xanthomonas oryzae ClpP Category: Unreleased Structures [[Cate...

New page

'''Unreleased structure'''

The entry 7dft is ON HOLD

Authors: Yang, C.-G., Yang, T.

Description: Crystal structure of Xanthomonas oryzae ClpP
[[Category: Unreleased Structures]]
[[Category: Yang, T]]
[[Category: Yang, C.-G]]