View source for 5ckd


==E. coli MazF E24A form III==
<StructureSection load='5ckd' size='340' side='right'caption='[[5ckd]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ckd]] is a 2 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=5CKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CKD 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]] 1.698&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=5ckd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ckd OCA], [https://pdbe.org/5ckd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ckd RCSB], [https://www.ebi.ac.uk/pdbsum/5ckd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ckd ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MAZF_ECOLI MAZF_ECOLI] Toxic component of a type II toxin-antitoxin (TA) module. A sequence-specific endoribonuclease it inhibits protein synthesis by cleaving mRNA and inducing bacterial stasis. It is stable, single-strand specific with mRNA cleavage independent of the ribosome, although translation enhances cleavage for some mRNAs (PubMed:18854355). Cleavage occurs at the 5'-end of ACA sequences, yielding a 2',3'-cyclic phosphate and a free 5'-OH, although cleavage can also occur on the 3'-end of the first A (PubMed:15537630, PubMed:23280569). Digests 16S rRNA in vivo 43 nts upstream of the C-terminus; this removes the anti-Shine-Dalgarno sequence forming a mixed population of wild-type and "stress ribosomes". Stress ribosomes do not translate leader-containing mRNA but are proficient in translation of leaderless mRNA, which alters the protein expression profile of the cell; MazF produces some leaderless mRNA (PubMed:21944167). The toxic endoribonuclease activity is inhibited by its labile cognate antitoxin MazE. Toxicity results when the levels of MazE decrease in the cell, leading to mRNA degradation. This effect can be rescued by expression of MazE, but after 6 hours in rich medium overexpression of MazF leads to programmed cell death (PubMed:8650219, PubMed:11222603). MazF-mediated cell death occurs following a number of stress conditions in a relA-dependent fashion and only when cells are in log phase; sigma factor S (rpoS) protects stationary phase cells from MazF-killing (PubMed:15150257, PubMed:19251848). Cell growth and viability are not affected when MazF and MazE are coexpressed. Both MazE and MazE-MazF bind to the promoter region of the mazE-mazF operon to inhibit their own transcription. MazE has higher affinity for promoter DNA in the presence of MazF (PubMed:25564525). Cross-talk can occur between different TA modules. Ectopic expression of this toxin induces transcription of the relBEF TA module operon with specific cleavage of the mRNA produced (PubMed:23432955).<ref>PMID:11071896</ref> <ref>PMID:11222603</ref> <ref>PMID:15150257</ref> <ref>PMID:15537630</ref> <ref>PMID:18854355</ref> <ref>PMID:19251848</ref> <ref>PMID:21944167</ref> <ref>PMID:23280569</ref> <ref>PMID:23432955</ref> <ref>PMID:25564525</ref> <ref>PMID:8650219</ref>   Might also serve to protect cells against bacteriophage; in the presence of MazE-MazF fewer P1 phage are produced than in a disrupted strain. For strain K38 most wild-type cells are killed but not by phage lysis; it was suggested that MazE-MazF causes P1 phage exclusion from the bacterial population. This phenomenon is strain dependent.<ref>PMID:15316771</ref>   The physiological role of this TA module is debated. Programmed cell death (PCD) occurs when cells are at high density and depends on the presence of MazE-MazF and a quorum sensing pentapeptide, the extracellular death factor (EDF) with sequence Asn-Asn-Trp-Asn-Asn (NNWNN), probably produced from the zwf gene product glucose-6-phosphate 1-dehydrogenase (PubMed:17962566, PubMed:18310334). Cell death governed by the MazE-MazF and DinJ-YafQ TA modules seems to play a role in biofilm formation, while MazE-MazF is also implicated in cell death in liquid media (PubMed:19707553). Implicated in hydroxy radical-mediated cell death induced by hydroxyurea treatment (PubMed:20005847, PubMed:23416055). In conjunction with EDF prevents apoptotic-like death (ALD) in the presence of DNA damaging agents, probably by reducing recA mRNA levels in a non-endonuclease-mediated manner (PubMed:22412352). Other studies (in strains BW25113 and MC4100, the latter makes EDF) demonstrate MazF does not cause PCD but instead bacteriostasis and possibly a dormant state as well as persister cell generation (PubMed:24375411).<ref>PMID:17962566</ref> <ref>PMID:18310334</ref> <ref>PMID:19707553</ref> <ref>PMID:20005847</ref> <ref>PMID:21419338</ref> <ref>PMID:22412352</ref> <ref>PMID:23416055</ref> <ref>PMID:24375411</ref> <ref>PMID:8650219</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Escherichia coli MazF (EcMazF) is the archetype of a large family of ribonucleases involved in bacterial stress response. The crystal structure of EcMazF in complex with a 7 nucleotide substrate mimic explains the relaxed substrate specificity of the E. coli enzyme relative to its Bacillus subtilis counterpart and provides a framework for rationalizing specificity in this enzyme family. In contrast to a conserved mode of substrate recognition and a conserved active site, regulation of enzymatic activity by the antitoxin EcMazE diverges from its B. subtilis homolog. Central in this regulation is a EcMazE-induced double conformational change: a rearangement of a crucial active site loop and a relative rotation of the two monomers in the EcMazF dimer. Both are induced by the C-terminal residues Asp78-Trp82 of EcMazE, which are also responsible for strong negative co-operativity in EcMazE-EcMazF binding. This situation shows unexpected parallels to the regulation of the F-plasmid CcdB activity by CcdA and further supports a common ancestor despite the different activities of the MazF and CcdB toxins. In addition we pinpoint the origin of the lack of activity of the E24A point mutant of EcMazF in its inability to support the substrate binding-competent conformation of EcMazF.

Substrate Recognition and Activity Regulation of the Escherichia coli mRNA Endonuclease MazF.,Zorzini V, Mernik A, Lah J, Sterckx YG, De Jonge N, Garcia-Pino A, De Greve H, Versees W, Loris R J Biol Chem. 2016 Mar 29. pii: jbc.M116.715912. PMID:27026704<ref>PMID:27026704</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5ckd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Loris R]]
[[Category: Zorzini V]]