7epg

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Revision as of 10:06, 21 December 2022

Crystal structure of E.coli CcdB mutant S12G

Structural highlights

7epg is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

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^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Miki T, Yoshioka K, Horiuchi T. Control of cell division by sex factor F in Escherichia coli. I. The 42.84-43.6 F segment couples cell division of the host bacteria with replication of plasmid DNA. J Mol Biol. 1984 Apr 25;174(4):605-25. PMID:6327993
↑ Tam JE, Kline BC. Control of the ccd operon in plasmid F. J Bacteriol. 1989 May;171(5):2353-60. PMID:2651399
↑ Ogura T, Hiraga S. Mini-F plasmid genes that couple host cell division to plasmid proliferation. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4784-8. PMID:6308648
↑ Tam JE, Kline BC. The F plasmid ccd autorepressor is a complex of CcdA and CcdB proteins. Mol Gen Genet. 1989 Oct;219(1-2):26-32. PMID:2615761
↑ Bernard P, Couturier M. Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes. J Mol Biol. 1992 Aug 5;226(3):735-45. PMID:1324324
↑ Maki S, Takiguchi S, Horiuchi T, Sekimizu K, Miki T. Partner switching mechanisms in inactivation and rejuvenation of Escherichia coli DNA gyrase by F plasmid proteins LetD (CcdB) and LetA (CcdA). J Mol Biol. 1996 Mar 1;256(3):473-82. PMID:8604132 doi:http://dx.doi.org/10.1006/jmbi.1996.0102
↑ Chattopadhyay G, Bhowmick J, Manjunath K, Ahmed S, Goyal P, Varadarajan R. Mechanistic insights into global suppressors of protein folding defects. PLoS Genet. 2022 Aug 29;18(8):e1010334. doi: 10.1371/journal.pgen.1010334. , eCollection 2022 Aug. PMID:36037221 doi:http://dx.doi.org/10.1371/journal.pgen.1010334

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7epg"

Categories: Escherichia coli K-12 | Large Structures | Manjunath K | Varadarajan R

@@ Line 1: / Line 1: @@
 ==Crystal structure of E.coli CcdB mutant S12G==
-<StructureSection load='7epg' size='340' side='right'caption='[[7epg]]' scene=''>
+<StructureSection load='7epg' size='340' side='right'caption='[[7epg]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EPG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7epg]] 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=7EPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EPG 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=7epg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7epg OCA], [https://pdbe.org/7epg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7epg RCSB], [https://www.ebi.ac.uk/pdbsum/7epg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7epg 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=7epg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7epg OCA], [https://pdbe.org/7epg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7epg RCSB], [https://www.ebi.ac.uk/pdbsum/7epg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7epg ProSAT]</span></td></tr>
 </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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 7epg" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
 [[Category: Manjunath K]]
 [[Category: Varadarajan R]]

7epg

From Proteopedia

Revision as of 10:06, 21 December 2022

Crystal structure of E.coli CcdB mutant S12G

Structural highlights

Function

Publication Abstract from PubMed

References

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