4ml2

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of wild-type YafQ

Structural highlights

4ml2 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.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3] ^[4] Cell death governed by the MazE-MazF and DinJ-YafQ TA modules seems to play a role in biofilm formation.^[5] ^[6] ^[7] ^[8]

Publication Abstract from PubMed

Toxin YafQ functions as a ribonuclease in the dinJ-yafQ toxin-antitoxin system of Escherichia coli. Antitoxin DinJ neutralizes YafQ-mediated toxicity by forming a stable protein complex. Here, crystal structures of the (DinJ)2-(YafQ)2 complex and the isolated YafQ toxin have been determined. The structure of the heterotetrameric complex (DinJ)2-(YafQ)2 revealed that the N-terminal region of DinJ folds into a ribbon-helix-helix motif and dimerizes for DNA recognition, and the C-terminal portion of each DinJ exclusively wraps around a YafQ molecule. Upon incorporation into the heterotetrameric complex, a conformational change of YafQ in close proximity to the catalytic site of the typical microbial ribonuclease fold was observed and validated. Mutagenesis experiments revealed that a DinJ mutant restored YafQ RNase activity in a tetramer complex in vitro, but not in vivo. An electrophoretic mobility shift assay showed that one of the palindromic sequences present in the upstream intergenic region of DinJ served as a binding sequences for both the DinJ-YafQ complex and the antitoxin DinJ alone. Based on structure-guided and site-directed mutagenesis of DinJ-YafQ, we showed that two pairs of amino acids in DinJ were important for DNA binding: The R8A and K16A, and S31A and R35A substitutions in DinJ abolished the DNA binding ability of the DinJ-YafQ complex.

Structural and Functional Characterization of Escherichia coli Toxin-antitoxin Complex DinJ-YafQ.,Liang Y, Gao Z, Wang F, Zhang Y, Dong Y, Liu Q J Biol Chem. 2014 Jun 12. pii: jbc.M114.559773. PMID:24923448^[9]

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:http://dx.doi.org/10.1111/j.1574-6968.2006.00563.x
↑ Harrison JJ, Wade WD, Akierman S, Vacchi-Suzzi C, Stremick CA, Turner RJ, Ceri H. The chromosomal toxin gene yafQ is a determinant of multidrug tolerance for Escherichia coli growing in a biofilm. Antimicrob Agents Chemother. 2009 Jun;53(6):2253-8. doi: 10.1128/AAC.00043-09., Epub 2009 Mar 23. PMID:19307375 doi:http://dx.doi.org/10.1128/AAC.00043-09
↑ 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:http://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:http://dx.doi.org/10.1111/j.1574-6968.2006.00563.x
↑ Harrison JJ, Wade WD, Akierman S, Vacchi-Suzzi C, Stremick CA, Turner RJ, Ceri H. The chromosomal toxin gene yafQ is a determinant of multidrug tolerance for Escherichia coli growing in a biofilm. Antimicrob Agents Chemother. 2009 Jun;53(6):2253-8. doi: 10.1128/AAC.00043-09., Epub 2009 Mar 23. PMID:19307375 doi:http://dx.doi.org/10.1128/AAC.00043-09
↑ 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:http://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
↑ Liang Y, Gao Z, Wang F, Zhang Y, Dong Y, Liu Q. Structural and Functional Characterization of Escherichia coli Toxin-antitoxin Complex DinJ-YafQ. J Biol Chem. 2014 Jun 12. pii: jbc.M114.559773. PMID:24923448 doi:http://dx.doi.org/10.1074/jbc.M114.559773

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/4ml2"

@@ Line 1: / Line 1: @@
 ==Crystal structure of wild-type YafQ==
-<StructureSection load='4ml2' size='340' side='right' caption='[[4ml2]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+<StructureSection load='4ml2' size='340' side='right'caption='[[4ml2]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ml2]] is a 1 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=4ML2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ML2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ml2]] 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=4ML2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ML2 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ml0|4ml0]], [[4mmj|4mmj]], [[4mmg|4mmg]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">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'>[https://proteopedia.org/fgij/fg.htm?mol=4ml2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ml2 OCA], [https://pdbe.org/4ml2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ml2 RCSB], [https://www.ebi.ac.uk/pdbsum/4ml2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ml2 ProSAT]</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=4ml2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ml2 OCA], [http://pdbe.org/4ml2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ml2 RCSB], [http://www.ebi.ac.uk/pdbsum/4ml2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ml2 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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/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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Dong, Y H]]
+[[Category: Large Structures]]
-[[Category: Gao, Z Q]]
+[[Category: Dong YH]]
-[[Category: Liang, Y J]]
+[[Category: Gao ZQ]]
-[[Category: Liu, Q S]]
+[[Category: Liang YJ]]
-[[Category: Antitoxin]]
+[[Category: Liu QS]]
-[[Category: Toxin]]

4ml2

From Proteopedia

Current revision

Crystal structure of wild-type YafQ

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox