4ml2
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 4ml2 is ON HOLD until Paper Publication Authors: Liang, Y.J., Gao, Z.Q., Liu, Q.S., Dong, Y.H. Description: Crystal structure of wild-type YafQ) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of wild-type YafQ== | |
| + | <StructureSection load='4ml2' size='340' side='right'caption='[[4ml2]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</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='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> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [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 == | ||
| + | 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<ref>PMID:24923448</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 4ml2" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Escherichia coli K-12]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Dong YH]] | ||
| + | [[Category: Gao ZQ]] | ||
| + | [[Category: Liang YJ]] | ||
| + | [[Category: Liu QS]] | ||
Current revision
Crystal structure of wild-type YafQ
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