4zm0: Difference between revisions

Revision as of 07:32, 18 May 2023

Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat

Structural highlights

4zm0 is a 8 chain structure with sequence from Escherichia virus P1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	144, NA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PHD_BPP1 Antitoxin component of a toxin-antitoxin (TA) module. A labile antitoxin that binds to the doc toxin and neutralizes its toxic effect. Bacteriophage P1 lysogenizes bacteria as a low-copy number plasmid. Phd and doc proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss.^[1] ^[2] Binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.^[3] ^[4]

Publication Abstract from PubMed

Conditional cooperativity is a common mechanism involved in transcriptional regulation of prokaryotic type II toxin-antitoxin operons and is intricately related to bacterial persistence. It allows the toxin component of a toxin-antitoxin module to act as a co-repressor at low doses of toxin as compared to antitoxin. When toxin level exceeds a certain threshold, however, the toxin becomes a de-repressor. Most antitoxins contain an intrinsically disordered region (IDR) that typically is involved in toxin neutralization and repressor complex formation. To address how the antitoxin IDR is involved in transcription regulation, we studied the phd-doc operon from bacteriophage P1. We provide evidence that the IDR of Phd provides an entropic barrier precluding full operon repression in the absence of Doc. Binding of Doc results in a cooperativity switch and consequent strong operon repression, enabling context-specific modulation of the regulatory process. Variations of this theme are likely to be a common mechanism in the autoregulation of bacterial operons that involve intrinsically disordered regions.

An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation.,Garcia-Pino A, De Gieter S, Talavera A, De Greve H, Efremov RG, Loris R Nat Chem Biol. 2016 May 2. doi: 10.1038/nchembio.2078. PMID:27159580^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Magnuson R, Yarmolinsky MB. Corepression of the P1 addiction operon by Phd and Doc. J Bacteriol. 1998 Dec;180(23):6342-51. PMID:9829946
↑ Liu M, Zhang Y, Inouye M, Woychik NA. Bacterial addiction module toxin Doc inhibits translation elongation through its association with the 30S ribosomal subunit. Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5885-90. doi:, 10.1073/pnas.0711949105. Epub 2008 Apr 8. PMID:18398006 doi:10.1073/pnas.0711949105
↑ Magnuson R, Yarmolinsky MB. Corepression of the P1 addiction operon by Phd and Doc. J Bacteriol. 1998 Dec;180(23):6342-51. PMID:9829946
↑ Liu M, Zhang Y, Inouye M, Woychik NA. Bacterial addiction module toxin Doc inhibits translation elongation through its association with the 30S ribosomal subunit. Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5885-90. doi:, 10.1073/pnas.0711949105. Epub 2008 Apr 8. PMID:18398006 doi:10.1073/pnas.0711949105
↑ Garcia-Pino A, De Gieter S, Talavera A, De Greve H, Efremov RG, Loris R. An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation. Nat Chem Biol. 2016 May 2. doi: 10.1038/nchembio.2078. PMID:27159580 doi:https://dx.doi.org/10.1038/nchembio.2078

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Magnuson R, Yarmolinsky MB. Corepression of the P1 addiction operon by Phd and Doc. J Bacteriol. 1998 Dec;180(23):6342-51. PMID:9829946

[2] Liu M, Zhang Y, Inouye M, Woychik NA. Bacterial addiction module toxin Doc inhibits translation elongation through its association with the 30S ribosomal subunit. Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5885-90. doi:, 10.1073/pnas.0711949105. Epub 2008 Apr 8. PMID:18398006 doi:10.1073/pnas.0711949105

[3] Magnuson R, Yarmolinsky MB. Corepression of the P1 addiction operon by Phd and Doc. J Bacteriol. 1998 Dec;180(23):6342-51. PMID:9829946

[4] Liu M, Zhang Y, Inouye M, Woychik NA. Bacterial addiction module toxin Doc inhibits translation elongation through its association with the 30S ribosomal subunit. Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5885-90. doi:, 10.1073/pnas.0711949105. Epub 2008 Apr 8. PMID:18398006 doi:10.1073/pnas.0711949105

[5] Garcia-Pino A, De Gieter S, Talavera A, De Greve H, Efremov RG, Loris R. An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation. Nat Chem Biol. 2016 May 2. doi: 10.1038/nchembio.2078. PMID:27159580 doi:https://dx.doi.org/10.1038/nchembio.2078

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[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
 ==Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat==
-<StructureSection load='4zm0' size='340' side='right' caption='[[4zm0]], [[Resolution|resolution]] 3.17&Aring;' scene=''>
+<StructureSection load='4zm0' size='340' side='right'caption='[[4zm0]], [[Resolution|resolution]] 3.17&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4zm0]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpp1 Bpp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZM0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZM0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4zm0]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_P1 Escherichia virus P1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZM0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4zlx|4zlx]]</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=4zm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zm0 OCA], [https://pdbe.org/4zm0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zm0 RCSB], [https://www.ebi.ac.uk/pdbsum/4zm0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zm0 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">phd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10678 BPP1])</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=4zm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zm0 OCA], [http://pdbe.org/4zm0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zm0 RCSB], [http://www.ebi.ac.uk/pdbsum/4zm0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zm0 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PHD_BPP1 PHD_BPP1]] Antitoxin component of a toxin-antitoxin (TA) module. A labile antitoxin that binds to the doc toxin and neutralizes its toxic effect. Bacteriophage P1 lysogenizes bacteria as a low-copy number plasmid. Phd and doc proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref>   Binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref>
+[https://www.uniprot.org/uniprot/PHD_BPP1 PHD_BPP1] Antitoxin component of a toxin-antitoxin (TA) module. A labile antitoxin that binds to the doc toxin and neutralizes its toxic effect. Bacteriophage P1 lysogenizes bacteria as a low-copy number plasmid. Phd and doc proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref>   Binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Bpp1]]
+[[Category: Escherichia virus P1]]
-[[Category: Garcia-Pino, A]]
+[[Category: Large Structures]]
-[[Category: Loris, R]]
+[[Category: Garcia-Pino A]]
-[[Category: Conditional cooperativity]]
+[[Category: Loris R]]
-[[Category: Dna binding]]
-[[Category: Intrinsic disorder]]
-[[Category: Protein-dna complex]]
-[[Category: Toxin-antitoxin]]
-[[Category: Transcription]]
-[[Category: Transcription factor]]

4zm0: Difference between revisions

Revision as of 07:32, 18 May 2023

Antitoxin Phd from phage P1 in complex with its operator DNA inverted repeat

Structural highlights

Function

Publication Abstract from PubMed

References

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