4ml0: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4ml0]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_B_str._REL606 Escherichia coli B str. REL606]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ML0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ML0 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4ml0]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_B_str._REL606 Escherichia coli B str. REL606]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ML0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ML0 FirstGlance]. <br>
</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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</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=4ml0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ml0 OCA], [https://pdbe.org/4ml0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ml0 RCSB], [https://www.ebi.ac.uk/pdbsum/4ml0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ml0 ProSAT]</span></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=4ml0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ml0 OCA], [https://pdbe.org/4ml0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ml0 RCSB], [https://www.ebi.ac.uk/pdbsum/4ml0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ml0 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/DINJ_ECOBD DINJ_ECOBD] Antitoxin component of a type II toxin-antitoxin (TA) system (PubMed:24923448). A labile antitoxin that counteracts the effect of cognate toxin YafQ (PubMed:24923448). The YafQ-DinJ heterotetramer binds the consensus sequence 5'-TTTGAGCTACA-3' in the dinJ promoter; DinJ also binds DNA but not as well as the YafQ-DinJ complex (PubMed:24923448). Binding to the dinJ represses expression of the promoter (By similarity).[UniProtKB:Q47150]<ref>PMID:24923448</ref>  
[https://www.uniprot.org/uniprot/DINJ_ECOBD DINJ_ECOBD] Antitoxin component of a type II toxin-antitoxin (TA) system (PubMed:24923448). A labile antitoxin that counteracts the effect of cognate toxin YafQ (PubMed:24923448). The YafQ-DinJ heterotetramer binds the consensus sequence 5'-TTTGAGCTACA-3' in the dinJ promoter; DinJ also binds DNA but not as well as the YafQ-DinJ complex (PubMed:24923448). Binding to the dinJ represses expression of the promoter (By similarity).[UniProtKB:Q47150]<ref>PMID:24923448</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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4ml0" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 08:56, 20 March 2024

Crystal structure of E.coli DinJ-YafQ complex

4ml0, resolution 2.10Å

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