4q2u: Difference between revisions

Revision as of 07:41, 8 February 2023

Crystal structure of the E. coli DinJ-YafQ toxin-antitoxin complex

Structural highlights

4q2u is a 16 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:	MSE, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DINJ_ECOLI Antitoxin component of a toxin-antitoxin (TA) module. A labile antitoxin that counteracts the effect of the YafQ toxin. YafQ and DinJ together bind their own promoter, and by analogy to other TA modules probably repress its expression.^[1] ^[2] ^[3] Cell death governed by the MazE-MazF and DinJ-YafQ TA modules seems to play a role in biofilm formation.^[4] ^[5] ^[6]

Publication Abstract from PubMed

Bacteria encounter environmental stresses that regulate a gene expression program required for adaptation and survival. Here, we report the 1.8 Angstrom crystal structure of the E. coli toxin-antitoxin complex YafQ-(DinJ)2-YafQ, a key component of the stress response. The antitoxin DinJ dimer adopts a ribbon-helix-helix motif required for transcriptional autorepression while toxin YafQ contains a microbial RNase fold whose proposed active site is concealed by DinJ binding. Contrary to previous reports, our studies indicate that equivalent levels of transcriptional repression occur by direct interaction of either YafQ-(DinJ)2-YafQ or a DinJ dimer at a single inverted repeat of its recognition sequence which overlaps with the -10 promoter region. Surprisingly multiple YafQ-(DinJ)2-YafQ complexes binding to the operator region do not appear to amplify the extent of repression. Our results suggest an alternative model for transcriptional autorepression that may be novel to DinJ-YafQ.

Mechanisms of Toxin Inhibition and Transcriptional Repression by E. coli DinJ-YafQ.,Ruangprasert A, Maehigashi T, Miles SJ, Giridharan N, Liu JX, Dunham CM J Biol Chem. 2014 Jun 4. pii: jbc.M114.573006. PMID:24898247^[7]

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

References

↑ Motiejunaite R, Armalyte J, Markuckas A, Suziedeliene E. Escherichia coli dinJ-yafQ genes act as a toxin-antitoxin module. FEMS Microbiol Lett. 2007 Mar;268(1):112-9. PMID:17263853 doi:https://dx.doi.org/10.1111/j.1574-6968.2006.00563.x
↑ Prysak MH, Mozdzierz CJ, Cook AM, Zhu L, Zhang Y, Inouye M, Woychik NA. Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage. Mol Microbiol. 2009 Mar;71(5):1071-87. doi: 10.1111/j.1365-2958.2008.06572.x., Epub 2009 Jan 30. PMID:19210620 doi:https://dx.doi.org/10.1111/j.1365-2958.2008.06572.x
↑ Kolodkin-Gal I, Verdiger R, Shlosberg-Fedida A, Engelberg-Kulka H. A differential effect of E. coli toxin-antitoxin systems on cell death in liquid media and biofilm formation. PLoS One. 2009 Aug 26;4(8):e6785. doi: 10.1371/journal.pone.0006785. PMID:19707553 doi:10.1371/journal.pone.0006785
↑ Motiejunaite R, Armalyte J, Markuckas A, Suziedeliene E. Escherichia coli dinJ-yafQ genes act as a toxin-antitoxin module. FEMS Microbiol Lett. 2007 Mar;268(1):112-9. PMID:17263853 doi:https://dx.doi.org/10.1111/j.1574-6968.2006.00563.x
↑ Prysak MH, Mozdzierz CJ, Cook AM, Zhu L, Zhang Y, Inouye M, Woychik NA. Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage. Mol Microbiol. 2009 Mar;71(5):1071-87. doi: 10.1111/j.1365-2958.2008.06572.x., Epub 2009 Jan 30. PMID:19210620 doi:https://dx.doi.org/10.1111/j.1365-2958.2008.06572.x
↑ Kolodkin-Gal I, Verdiger R, Shlosberg-Fedida A, Engelberg-Kulka H. A differential effect of E. coli toxin-antitoxin systems on cell death in liquid media and biofilm formation. PLoS One. 2009 Aug 26;4(8):e6785. doi: 10.1371/journal.pone.0006785. PMID:19707553 doi:10.1371/journal.pone.0006785
↑ Ruangprasert A, Maehigashi T, Miles SJ, Giridharan N, Liu JX, Dunham CM. Mechanisms of Toxin Inhibition and Transcriptional Repression by E. coli DinJ-YafQ. J Biol Chem. 2014 Jun 4. pii: jbc.M114.573006. PMID:24898247 doi:https://dx.doi.org/10.1074/jbc.M114.573006

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Motiejunaite R, Armalyte J, Markuckas A, Suziedeliene E. Escherichia coli dinJ-yafQ genes act as a toxin-antitoxin module. FEMS Microbiol Lett. 2007 Mar;268(1):112-9. PMID:17263853 doi:https://dx.doi.org/10.1111/j.1574-6968.2006.00563.x

[2] Prysak MH, Mozdzierz CJ, Cook AM, Zhu L, Zhang Y, Inouye M, Woychik NA. Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage. Mol Microbiol. 2009 Mar;71(5):1071-87. doi: 10.1111/j.1365-2958.2008.06572.x., Epub 2009 Jan 30. PMID:19210620 doi:https://dx.doi.org/10.1111/j.1365-2958.2008.06572.x

[3] Kolodkin-Gal I, Verdiger R, Shlosberg-Fedida A, Engelberg-Kulka H. A differential effect of E. coli toxin-antitoxin systems on cell death in liquid media and biofilm formation. PLoS One. 2009 Aug 26;4(8):e6785. doi: 10.1371/journal.pone.0006785. PMID:19707553 doi:10.1371/journal.pone.0006785

[4] Motiejunaite R, Armalyte J, Markuckas A, Suziedeliene E. Escherichia coli dinJ-yafQ genes act as a toxin-antitoxin module. FEMS Microbiol Lett. 2007 Mar;268(1):112-9. PMID:17263853 doi:https://dx.doi.org/10.1111/j.1574-6968.2006.00563.x

[5] Prysak MH, Mozdzierz CJ, Cook AM, Zhu L, Zhang Y, Inouye M, Woychik NA. Bacterial toxin YafQ is an endoribonuclease that associates with the ribosome and blocks translation elongation through sequence-specific and frame-dependent mRNA cleavage. Mol Microbiol. 2009 Mar;71(5):1071-87. doi: 10.1111/j.1365-2958.2008.06572.x., Epub 2009 Jan 30. PMID:19210620 doi:https://dx.doi.org/10.1111/j.1365-2958.2008.06572.x

[6] Kolodkin-Gal I, Verdiger R, Shlosberg-Fedida A, Engelberg-Kulka H. A differential effect of E. coli toxin-antitoxin systems on cell death in liquid media and biofilm formation. PLoS One. 2009 Aug 26;4(8):e6785. doi: 10.1371/journal.pone.0006785. PMID:19707553 doi:10.1371/journal.pone.0006785

[7] Ruangprasert A, Maehigashi T, Miles SJ, Giridharan N, Liu JX, Dunham CM. Mechanisms of Toxin Inhibition and Transcriptional Repression by E. coli DinJ-YafQ. J Biol Chem. 2014 Jun 4. pii: jbc.M114.573006. PMID:24898247 doi:https://dx.doi.org/10.1074/jbc.M114.573006

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[5]

[6]

[7]

@@ Line 3: / Line 3: @@
 <StructureSection load='4q2u' size='340' side='right'caption='[[4q2u]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4q2u]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q2U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q2U FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4q2u]] is a 16 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=4Q2U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q2U FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4q2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q2u OCA], [https://pdbe.org/4q2u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q2u RCSB], [https://www.ebi.ac.uk/pdbsum/4q2u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q2u ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dinJ, b0226, JW0216 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), yafQ, b0225, JW0215 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4q2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q2u OCA], [http://pdbe.org/4q2u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q2u RCSB], [http://www.ebi.ac.uk/pdbsum/4q2u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q2u ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DINJ_ECOLI DINJ_ECOLI]] Antitoxin component of a toxin-antitoxin (TA) module. A labile antitoxin that counteracts the effect of the YafQ toxin. YafQ and DinJ together bind their own promoter, and by analogy to other TA modules probably repress its expression.<ref>PMID:17263853</ref> <ref>PMID:19210620</ref> <ref>PMID:19707553</ref>   Cell death governed by the MazE-MazF and DinJ-YafQ TA modules seems to play a role in biofilm formation.<ref>PMID:17263853</ref> <ref>PMID:19210620</ref> <ref>PMID:19707553</ref>  [[http://www.uniprot.org/uniprot/YAFQ_ECOLI YAFQ_ECOLI]] Toxic component of a toxin-antitoxin (TA) module. A sequence-specific mRNA endoribonuclease that inhibits translation elongation and induces bacterial stasis. Cleavage occurs between the second and third residue of the Lys codon followed by a G or A (5'AAA(G/A)3'), is reading-frame dependent and occurs within the 5' end of most mRNAs. Ribosome-binding confers the sequence specificity and reading frame-dependence. When overexpressed in liquid media YafQ partially inhibits protein synthesis, with a reduction in growth rate and colony growth rate. This effect is counteracted by coexpression with DinJ, the YafQ antitoxin. YafQ and DinJ together bind their own promoter, and by analogy to other TA modules probably repress its expression.<ref>PMID:17263853</ref> <ref>PMID:19307375</ref> <ref>PMID:19210620</ref> <ref>PMID:19707553</ref>   Cell death governed by the MazE-MazF and DinJ-YafQ TA modules seems to play a role in biofilm formation.<ref>PMID:17263853</ref> <ref>PMID:19307375</ref> <ref>PMID:19210620</ref> <ref>PMID:19707553</ref>
+[https://www.uniprot.org/uniprot/DINJ_ECOLI DINJ_ECOLI] Antitoxin component of a toxin-antitoxin (TA) module. A labile antitoxin that counteracts the effect of the YafQ toxin. YafQ and DinJ together bind their own promoter, and by analogy to other TA modules probably repress its expression.<ref>PMID:17263853</ref> <ref>PMID:19210620</ref> <ref>PMID:19707553</ref>   Cell death governed by the MazE-MazF and DinJ-YafQ TA modules seems to play a role in biofilm formation.<ref>PMID:17263853</ref> <ref>PMID:19210620</ref> <ref>PMID:19707553</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Dunham, C M]]
+[[Category: Dunham CM]]
-[[Category: Maehigashi, T]]
+[[Category: Maehigashi T]]
-[[Category: Ruangprasert, A]]
+[[Category: Ruangprasert A]]
-[[Category: Bacterial toxin-antitoxin complex]]
-[[Category: Dna binding]]
-[[Category: Rhh motif]]
-[[Category: Ribonuclease]]
-[[Category: Ribosome binding]]
-[[Category: Toxin-toxin repressor complex]]
-[[Category: Translation control]]

4q2u: Difference between revisions

Revision as of 07:41, 8 February 2023

Crystal structure of the E. coli DinJ-YafQ toxin-antitoxin complex

Structural highlights

Function

Publication Abstract from PubMed

References

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