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<StructureSection load='3nfc' size='340' side='right'caption='[[3nfc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3nfc' size='340' side='right'caption='[[3nfc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3nfc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NFC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NFC FirstGlance]. <br>
<table><tr><td colspan='2'>[[3nfc]] is a 6 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=3NFC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NFC FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ub4|1ub4]]</div></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&#8491;</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=3nfc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nfc OCA], [https://pdbe.org/3nfc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nfc RCSB], [https://www.ebi.ac.uk/pdbsum/3nfc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nfc 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=3nfc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nfc OCA], [https://pdbe.org/3nfc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nfc RCSB], [https://www.ebi.ac.uk/pdbsum/3nfc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nfc ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== 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>
[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>  
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ecoli]]
[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Su, X]]
[[Category: Su X]]
[[Category: Wang, K]]
[[Category: Wang K]]
[[Category: Wang, X]]
[[Category: Wang X]]
[[Category: Zhang, J]]
[[Category: Zhang J]]
[[Category: Mazef system]]
[[Category: Mazf]]
[[Category: Rna cleavage]]
[[Category: Toxin]]

Latest revision as of 19:46, 1 November 2023

Crystal structure of E.coli MazF ToxinCrystal structure of E.coli MazF Toxin

Structural highlights

3nfc is a 6 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 2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] 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.[12] 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).[13] [14] [15] [16] [17] [18] [19] [20] [21]

References

  1. ↑ Marianovsky I, Aizenman E, Engelberg-Kulka H, Glaser G. The regulation of the Escherichia coli mazEF promoter involves an unusual alternating palindrome. J Biol Chem. 2001 Feb 23;276(8):5975-84. Epub 2000 Nov 8. PMID:11071896 doi:http://dx.doi.org/10.1074/jbc.M008832200
  2. ↑ Sat B, Hazan R, Fisher T, Khaner H, Glaser G, Engelberg-Kulka H. Programmed cell death in Escherichia coli: some antibiotics can trigger mazEF lethality. J Bacteriol. 2001 Mar;183(6):2041-5. PMID:11222603 doi:http://dx.doi.org/10.1128/JB.183.6.2041-2045.2001
  3. ↑ Hazan R, Sat B, Engelberg-Kulka H. Escherichia coli mazEF-mediated cell death is triggered by various stressful conditions. J Bacteriol. 2004 Jun;186(11):3663-9. PMID:15150257 doi:10.1128/JB.186.11.3663-3669.2004
  4. ↑ Zhang Y, Zhang J, Hara H, Kato I, Inouye M. Insights into the mRNA cleavage mechanism by MazF, an mRNA interferase. J Biol Chem. 2005 Feb 4;280(5):3143-50. Epub 2004 Nov 10. PMID:15537630 doi:10.1074/jbc.M411811200
  5. ↑ Christensen-Dalsgaard M, Gerdes K. Translation affects YoeB and MazF messenger RNA interferase activities by different mechanisms. Nucleic Acids Res. 2008 Nov;36(20):6472-81. doi: 10.1093/nar/gkn667. Epub 2008, Oct 14. PMID:18854355 doi:http://dx.doi.org/10.1093/nar/gkn667
  6. ↑ Kolodkin-Gal I, Engelberg-Kulka H. The stationary-phase sigma factor sigma(S) is responsible for the resistance of Escherichia coli stationary-phase cells to mazEF-mediated cell death. J Bacteriol. 2009 May;191(9):3177-82. doi: 10.1128/JB.00011-09. Epub 2009 Feb 27. PMID:19251848 doi:http://dx.doi.org/10.1128/JB.00011-09
  7. ↑ Vesper O, Amitai S, Belitsky M, Byrgazov K, Kaberdina AC, Engelberg-Kulka H, Moll I. Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli. Cell. 2011 Sep 30;147(1):147-57. doi: 10.1016/j.cell.2011.07.047. Epub 2011 Sep, 22. PMID:21944167 doi:http://dx.doi.org/10.1016/j.cell.2011.07.047
  8. ↑ Park JH, Yoshizumi S, Yamaguchi Y, Wu KP, Inouye M. ACA-specific RNA sequence recognition is acquired via the loop 2 region of MazF mRNA interferase. Proteins. 2013 May;81(5):874-83. doi: 10.1002/prot.24246. Epub 2013 Feb 25. PMID:23280569 doi:http://dx.doi.org/10.1002/prot.24246
  9. ↑ Kasari V, Mets T, Tenson T, Kaldalu N. Transcriptional cross-activation between toxin-antitoxin systems of Escherichia coli. BMC Microbiol. 2013 Feb 21;13:45. doi: 10.1186/1471-2180-13-45. PMID:23432955 doi:http://dx.doi.org/10.1186/1471-2180-13-45
  10. ↑ Zorzini V, Buts L, Schrank E, Sterckx YG, Respondek M, Engelberg-Kulka H, Loris R, Zangger K, van Nuland NA. Escherichia coli antitoxin MazE as transcription factor: insights into MazE-DNA binding. Nucleic Acids Res. 2015 Jan 30;43(2):1241-56. doi: 10.1093/nar/gku1352. Epub 2015, Jan 6. PMID:25564525 doi:http://dx.doi.org/10.1093/nar/gku1352
  11. ↑ Aizenman E, Engelberg-Kulka H, Glaser G. An Escherichia coli chromosomal "addiction module" regulated by guanosine [corrected] 3',5'-bispyrophosphate: a model for programmed bacterial cell death. Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):6059-63. PMID:8650219
  12. ↑ Hazan R, Engelberg-Kulka H. Escherichia coli mazEF-mediated cell death as a defense mechanism that inhibits the spread of phage P1. Mol Genet Genomics. 2004 Sep;272(2):227-34. Epub 2004 Aug 14. PMID:15316771 doi:10.1007/s00438-004-1048-y
  13. ↑ Kolodkin-Gal I, Hazan R, Gaathon A, Carmeli S, Engelberg-Kulka H. A linear pentapeptide is a quorum-sensing factor required for mazEF-mediated cell death in Escherichia coli. Science. 2007 Oct 26;318(5850):652-5. PMID:17962566 doi:http://dx.doi.org/10.1126/science.1147248
  14. ↑ Kolodkin-Gal I, Engelberg-Kulka H. The extracellular death factor: physiological and genetic factors influencing its production and response in Escherichia coli. J Bacteriol. 2008 May;190(9):3169-75. doi: 10.1128/JB.01918-07. Epub 2008 Feb 29. PMID:18310334 doi:http://dx.doi.org/10.1128/JB.01918-07
  15. ↑ 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
  16. ↑ Davies BW, Kohanski MA, Simmons LA, Winkler JA, Collins JJ, Walker GC. Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli. Mol Cell. 2009 Dec 11;36(5):845-60. doi: 10.1016/j.molcel.2009.11.024. PMID:20005847 doi:http://dx.doi.org/10.1016/j.molcel.2009.11.024
  17. ↑ Belitsky M, Avshalom H, Erental A, Yelin I, Kumar S, London N, Sperber M, Schueler-Furman O, Engelberg-Kulka H. The Escherichia coli extracellular death factor EDF induces the endoribonucleolytic activities of the toxins MazF and ChpBK. Mol Cell. 2011 Mar 18;41(6):625-35. doi: 10.1016/j.molcel.2011.02.023. PMID:21419338 doi:http://dx.doi.org/10.1016/j.molcel.2011.02.023
  18. ↑ Erental A, Sharon I, Engelberg-Kulka H. Two programmed cell death systems in Escherichia coli: an apoptotic-like death is inhibited by the mazEF-mediated death pathway. PLoS Biol. 2012;10(3):e1001281. doi: 10.1371/journal.pbio.1001281. Epub 2012 Mar , 6. PMID:22412352 doi:http://dx.doi.org/10.1371/journal.pbio.1001281
  19. ↑ Dorsey-Oresto A, Lu T, Mosel M, Wang X, Salz T, Drlica K, Zhao X. YihE kinase is a central regulator of programmed cell death in bacteria. Cell Rep. 2013 Feb 21;3(2):528-37. doi: 10.1016/j.celrep.2013.01.026. Epub 2013, Feb 14. PMID:23416055 doi:http://dx.doi.org/10.1016/j.celrep.2013.01.026
  20. ↑ Tripathi A, Dewan PC, Siddique SA, Varadarajan R. MazF-induced growth inhibition and persister generation in Escherichia coli. J Biol Chem. 2014 Feb 14;289(7):4191-205. doi: 10.1074/jbc.M113.510511. Epub 2013, Dec 27. PMID:24375411 doi:http://dx.doi.org/10.1074/jbc.M113.510511
  21. ↑ Aizenman E, Engelberg-Kulka H, Glaser G. An Escherichia coli chromosomal "addiction module" regulated by guanosine [corrected] 3',5'-bispyrophosphate: a model for programmed bacterial cell death. Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):6059-63. PMID:8650219

3nfc, resolution 2.00Å

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