3kh2

From Proteopedia

(Difference between revisions)

Revision as of 01:18, 5 August 2016

Crystal structure of the P1 bacteriophage Doc toxin (F68S) in complex with the Phd antitoxin (L17M/V39A). Northeast Structural Genomics targets ER385-ER386

Structural highlights

3kh2 is a 8 chain structure with sequence from Bpp1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
NonStd Res:
Gene:	doc (BPP1), phd (BPP1)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DOC_BPP1] Toxic component of a toxin-antitoxin (TA) module. Overexpression results in inhibition of growth in liquid cultures and a decrease in colony formation by inhibiting translation, stabilizing mRNA and polysomes; these effects are overcome by concomitant expression of antitoxin phd. Binds 70S ribosomes and the 30S ribosomal subunits, the binding site is the same as for the antibiotic hygromycin B. Bacteriophage P1 lysogenizes bacteria as a low-copy number plasmid. Doc and phd proteins function in unison to stabilize plasmid number by inducing a lethal response to P1 plasmid prophage loss. Overexpression of doc can induce the mRNA interferase activity of RelE in vivo.^[1] ^[2] Antitoxin phd 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] [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.^[5] ^[6] Binds to its own promoter repressing its expression; toxin doc acts as a corepressor or derepressor depending on the ratio, repressing or inducing expression.^[7] ^[8]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Bacterial toxin-antitoxin (TA) systems serve a variety of physiological functions including regulation of cell growth and maintenance of foreign genetic elements. Sequence analyses suggest that TA families are linked by complex evolutionary relationships reflecting likely swapping of functional domains between different TA families. Our crystal structures of Phd-Doc from bacteriophage P1, the HigA antitoxin from Escherichia coli CFT073, and YeeU of the YeeUWV systems from E. coli K12 and Shigella flexneri confirm this inference and reveal additional, unanticipated structural relationships. The growth-regulating Doc toxin exhibits structural similarity to secreted virulence factors that are toxic for eukaryotic target cells. The Phd antitoxin possesses the same fold as both the YefM and NE2111 antitoxins that inhibit structurally unrelated toxins. YeeU, which has an antitoxin-like activity that represses toxin expression, is structurally similar to the ribosome-interacting toxins YoeB and RelE. These observations suggest extensive functional exchanges have occurred between TA systems during bacterial evolution.

Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems.,Arbing MA, Handelman SK, Kuzin AP, Verdon G, Wang C, Su M, Rothenbacher FP, Abashidze M, Liu M, Hurley JM, Xiao R, Acton T, Inouye M, Montelione GT, Woychik NA, Hunt JF Structure. 2010 Aug 11;18(8):996-1010. PMID:20696400^[9]

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
↑ 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
↑ Arbing MA, Handelman SK, Kuzin AP, Verdon G, Wang C, Su M, Rothenbacher FP, Abashidze M, Liu M, Hurley JM, Xiao R, Acton T, Inouye M, Montelione GT, Woychik NA, Hunt JF. Crystal structures of Phd-Doc, HigA, and YeeU establish multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems. Structure. 2010 Aug 11;18(8):996-1010. PMID:20696400 doi:10.1016/j.str.2010.04.018

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3kh2"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the P1 bacteriophage Doc toxin (F68S) in complex with the Phd antitoxin (L17M/V39A). Northeast Structural Genomics targets ER385-ER386==
 <StructureSection load='3kh2' size='340' side='right' caption='[[3kh2]], [[Resolution|resolution]] 2.71&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kh2]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_p1 Enterobacteria phage p1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KH2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KH2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kh2]] 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=3KH2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KH2 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HED:2-HYDROXYETHYL+DISULFIDE'>HED</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">doc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10678 Enterobacteria phage P1]), phd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10678 Enterobacteria phage P1])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">doc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10678 BPP1]), 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=3kh2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kh2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kh2 RCSB], [http://www.ebi.ac.uk/pdbsum/3kh2 PDBsum]</span></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=3kh2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kh2 OCA], [http://pdbe.org/3kh2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kh2 RCSB], [http://www.ebi.ac.uk/pdbsum/3kh2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kh2 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3kh2 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3kh2" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Enterobacteria phage p1]]
+[[Category: Bpp1]]
 [[Category: Abashidze, M]]
 [[Category: Acton, T]]

3kh2

From Proteopedia

Revision as of 01:18, 5 August 2016

Crystal structure of the P1 bacteriophage Doc toxin (F68S) in complex with the Phd antitoxin (L17M/V39A). Northeast Structural Genomics targets ER385-ER386

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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