This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3hpw

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 21:41, 5 August 2016

CcdB dimer in complex with one C-terminal CcdA domain

Structural highlights

3hpw is a 3 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	3g7z, 1vub, 2vub, 3vub, 4vub
Gene:	ccdB, ECOK12F043, G, letB ("Bacillus coli" Migula 1895)
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] [CCDA_ECOLI] Antitoxin component of a toxin-antitoxin (TA) module which inhibits the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Labile antitoxin with a half-life of about 1 hour in the presence of CcdB. Binds to and blocks the activity of CcdB; will also remove bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. The N-terminal 36 residues are not required for rejuventation. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdB.^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Toxin-antitoxin modules are small regulatory circuits that ensure survival of bacterial populations under challenging environmental conditions. The ccd toxin-antitoxin module on the F plasmid codes for the toxin CcdB and its antitoxin CcdA. CcdB poisons gyrase while CcdA actively dissociates CcdB:gyrase complexes in a process called rejuvenation. The CcdA:CcdB ratio modulates autorepression of the ccd operon. The mechanisms behind both rejuvenation and regulation of expression are poorly understood. We show that CcdA binds consecutively to two partially overlapping sites on CcdB, which differ in affinity by six orders of magnitude. The first, picomolar affinity interaction triggers a conformational change in CcdB that initiates the dissociation of CcdB:gyrase complexes by an allosteric segmental binding mechanism. The second, micromolar affinity binding event regulates expression of the ccd operon. Both functions of CcdA, rejuvenation and autoregulation, are mechanistically intertwined and depend crucially on the intrinsically disordered nature of the CcdA C-terminal domain.

Rejuvenation of CcdB-poisoned gyrase by an intrinsically disordered protein domain.,De Jonge N, Garcia-Pino A, Buts L, Haesaerts S, Charlier D, Zangger K, Wyns L, De Greve H, Loris R Mol Cell. 2009 Jul 31;35(2):154-63. PMID:19647513^[14]

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
↑ 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
↑ De Jonge N, Garcia-Pino A, Buts L, Haesaerts S, Charlier D, Zangger K, Wyns L, De Greve H, Loris R. Rejuvenation of CcdB-poisoned gyrase by an intrinsically disordered protein domain. Mol Cell. 2009 Jul 31;35(2):154-63. PMID:19647513 doi:10.1016/j.molcel.2009.05.025
↑ De Jonge N, Garcia-Pino A, Buts L, Haesaerts S, Charlier D, Zangger K, Wyns L, De Greve H, Loris R. Rejuvenation of CcdB-poisoned gyrase by an intrinsically disordered protein domain. Mol Cell. 2009 Jul 31;35(2):154-63. PMID:19647513 doi:10.1016/j.molcel.2009.05.025

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3hpw"

@@ Line 1: / Line 1: @@
 ==CcdB dimer in complex with one C-terminal CcdA domain==
 <StructureSection load='3hpw' size='340' side='right' caption='[[3hpw]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3hpw]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HPW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3hpw]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HPW FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3g7z|3g7z]], [[1vub|1vub]], [[2vub|2vub]], [[3vub|3vub]], [[4vub|4vub]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ccdB, ECOK12F043, G, letB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ccdB, ECOK12F043, G, letB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=3hpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hpw RCSB], [http://www.ebi.ac.uk/pdbsum/3hpw 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=3hpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hpw OCA], [http://pdbe.org/3hpw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hpw RCSB], [http://www.ebi.ac.uk/pdbsum/3hpw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hpw ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3hpw ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3hpw" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli]]
+[[Category: Bacillus coli migula 1895]]
 [[Category: Buts, L]]
 [[Category: Garcia-Pino, A]]

3hpw

From Proteopedia

Revision as of 21:41, 5 August 2016

CcdB dimer in complex with one C-terminal CcdA domain

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox