7epj - Revision history

OCA at 16:59, 29 November 2023

OCA — Wed, 29 Nov 2023 16:59:24 GMT

←Older revision		Revision as of 16:59, 29 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7epj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EPJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[7epj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EPJ 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]] 1.354Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7epj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7epj OCA], [https://pdbe.org/7epj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7epj RCSB], [https://www.ebi.ac.uk/pdbsum/7epj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7epj 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=7epj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7epj OCA], [https://pdbe.org/7epj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7epj RCSB], [https://www.ebi.ac.uk/pdbsum/7epj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7epj ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:06, 21 December 2022

OCA — Wed, 21 Dec 2022 10:06:33 GMT

←Older revision		Revision as of 10:06, 21 December 2022
Line 1:		Line 1:

	==Crystal structure of E.coli CcdB mutant V46L==		==Crystal structure of E.coli CcdB mutant V46L==
-	<StructureSection load='7epj' size='340' side='right'caption='[[7epj]]' scene=''>	+	<StructureSection load='7epj' size='340' side='right'caption='[[7epj]], [[Resolution\|resolution]] 1.35Å' 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=7EPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EPJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7epj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EPJ 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=7epj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7epj OCA], [https://pdbe.org/7epj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7epj RCSB], [https://www.ebi.ac.uk/pdbsum/7epj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7epj 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7epj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7epj OCA], [https://pdbe.org/7epj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7epj RCSB], [https://www.ebi.ac.uk/pdbsum/7epj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7epj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CCDB_ECOLI CCDB_ECOLI] Toxic component of a toxin-antitoxin (TA) module, functioning in plasmid maintainence. Responsible for the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Half-life of over 2 hours. Cell killing by CcdB is accompanied by filamentation, defects in chromosome and plasmid segregation, defects in cell division, formation of anucleate cells, decreased DNA synthesis and plasmid loss. Interferes with the activity of DNA gyrase, inducing it to form a covalent GyrA-DNA complex that cannot be resolved, thus promoting breakage of plasmid and chromosomal DNA. DNA breakage requires hydrolyzable ATP. Toxicity is inhibited by labile antitoxin CcdA, which blocks the activity of CcdB; CcdA also removes bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Also acts to inhibit partitioning of the chromosomal DNA. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdA.<ref>PMID:6327993</ref> <ref>PMID:2651399</ref> <ref>PMID:6308648</ref> <ref>PMID:2615761</ref> <ref>PMID:1324324</ref> <ref>PMID:8604132</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Most amino acid substitutions in a protein either lead to partial loss-of-function or are near neutral. Several studies have shown the existence of second-site mutations that can rescue defects caused by diverse loss-of-function mutations. Such global suppressor mutations are key drivers of protein evolution. However, the mechanisms responsible for such suppression remain poorly understood. To address this, we characterized multiple suppressor mutations both in isolation and in combination with inactive mutants. We examined six global suppressors of the bacterial toxin CcdB, the known M182T global suppressor of TEM-1 beta-lactamase, the N239Y global suppressor of p53-DBD and three suppressors of the SARS-CoV-2 spike Receptor Binding Domain. When coupled to inactive mutants, they promote increased in-vivo solubilities as well as regain-of-function phenotypes. In the case of CcdB, where novel suppressors were isolated, we determined the crystal structures of three such suppressors to obtain insight into the specific molecular interactions responsible for the observed effects. While most individual suppressors result in small stability enhancements relative to wildtype, which can be combined to yield significant stability increments, thermodynamic stabilisation is neither necessary nor sufficient for suppressor action. Instead, in diverse systems, we observe that individual global suppressors greatly enhance the foldability of buried site mutants, primarily through increase in refolding rate parameters measured in vitro. In the crowded intracellular environment, mutations that slow down folding likely facilitate off-pathway aggregation. We suggest that suppressor mutations that accelerate refolding can counteract this, enhancing the yield of properly folded, functional protein in vivo.
		+
		+	Mechanistic insights into global suppressors of protein folding defects.,Chattopadhyay G, Bhowmick J, Manjunath K, Ahmed S, Goyal P, Varadarajan R PLoS Genet. 2022 Aug 29;18(8):e1010334. doi: 10.1371/journal.pgen.1010334. , eCollection 2022 Aug. PMID:36037221<ref>PMID:36037221</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7epj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Goyal P]]		[[Category: Goyal P]]
	[[Category: Manjunath K]]		[[Category: Manjunath K]]
	[[Category: Varadarajan R]]		[[Category: Varadarajan R]]

OCA at 05:27, 8 June 2022

OCA — Wed, 08 Jun 2022 05:27:49 GMT

←Older revision		Revision as of 05:27, 8 June 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7epj ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of E.coli CcdB mutant V46L==
-		+	<StructureSection load='7epj' size='340' side='right'caption='[[7epj]]' scene=''>
-	~~Authors~~: ~~Manjunath~~, K., ~~Goyal~~, P., ~~Varadarajan~~, R.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EPJ FirstGlance]. <br>
-	~~Description: Crystal structure of E.coli CcdB mutant V46L~~	+	</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=7epj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7epj OCA], [https://pdbe.org/7epj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7epj RCSB], [https://www.ebi.ac.uk/pdbsum/7epj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7epj ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Manjunath, K~~]]	+	__TOC__
-	[[Category: ~~Goyal, P~~]]	+	</StructureSection>
-	[[Category: Varadarajan, R]]	+	[[Category: Large Structures]]
		+	[[Category: Goyal P]]
		+	[[Category: Manjunath K]]
		+	[[Category: Varadarajan R]]

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

OCA — Wed, 05 May 2021 07:19:16 GMT

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

←Older revision

Revision as of 07:19, 5 May 2021

OCA: New page: '''Unreleased structure''' The entry 7epj is ON HOLD until Paper Publication Authors: Manjunath, K., Goyal, P., Varadarajan, R. Description: Crystal structure of E.coli CcdB mutant V46...

OCA — Wed, 05 May 2021 07:19:15 GMT

New page: '''Unreleased structure''' The entry 7epj is ON HOLD until Paper Publication Authors: Manjunath, K., Goyal, P., Varadarajan, R. Description: Crystal structure of E.coli CcdB mutant V46...

New page

'''Unreleased structure'''

The entry 7epj is ON HOLD until Paper Publication

Authors: Manjunath, K., Goyal, P., Varadarajan, R.

Description: Crystal structure of E.coli CcdB mutant V46L
[[Category: Unreleased Structures]]
[[Category: Manjunath, K]]
[[Category: Goyal, P]]
[[Category: Varadarajan, R]]