3kh2

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:20, 30 October 2024) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3kh2.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of the P1 bacteriophage Doc toxin (F68S) in complex with the Phd antitoxin (L17M/V39A). Northeast Structural Genomics targets ER385-ER386==
-
The line below this paragraph, containing "STRUCTURE_3kh2", creates the "Structure Box" on the page.
+
<StructureSection load='3kh2' size='340' side='right'caption='[[3kh2]], [[Resolution|resolution]] 2.71&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[3kh2]] 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=3KH2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KH2 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.71&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-
{{STRUCTURE_3kh2| PDB=3kh2 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kh2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kh2 OCA], [https://pdbe.org/3kh2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kh2 RCSB], [https://www.ebi.ac.uk/pdbsum/3kh2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kh2 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DOC_BPP1 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.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref> 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.<ref>PMID:9829946</ref> <ref>PMID:18398006</ref>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/3kh2_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
 +
<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/main_output.php?pdb_ID=3kh2 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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 structure of the P1 bacteriophage Doc toxin (F68S) in complex with the Phd antitoxin (L17M/V39A). Northeast Structural Genomics targets ER385-ER386===
+
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<ref>PMID:20696400</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_20696400}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3kh2" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 20696400 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_20696400}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Escherichia virus P1]]
-
3KH2 is a 8 chains structure with sequences 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].
+
[[Category: Large Structures]]
-
 
+
[[Category: Abashidze M]]
-
==Reference==
+
[[Category: Acton T]]
-
<ref group="xtra">PMID:20696400</ref><references group="xtra"/>
+
[[Category: Arbing MA]]
-
[[Category: Enterobacteria phage p1]]
+
[[Category: Hunt JF]]
-
[[Category: Abashidze, M.]]
+
[[Category: Inouye M]]
-
[[Category: Acton, T.]]
+
[[Category: Kuzin AP]]
-
[[Category: Arbing, M A.]]
+
[[Category: Liu M]]
-
[[Category: Hunt, J F.]]
+
[[Category: Montelione GT]]
-
[[Category: Inouye, M.]]
+
[[Category: Su M]]
-
[[Category: Kuzin, A P.]]
+
[[Category: Verdon G]]
-
[[Category: Liu, M.]]
+
[[Category: Woychik NA]]
-
[[Category: Montelione, G T.]]
+
[[Category: Xiao R]]
-
[[Category: NESG, Northeast Structural Genomics Consortium.]]
+
-
[[Category: Su, M.]]
+
-
[[Category: Verdon, G.]]
+
-
[[Category: Woychik, N A.]]
+
-
[[Category: Xiao, R.]]
+
-
[[Category: Antitoxin]]
+
-
[[Category: Protein structure initiative]]
+
-
[[Category: Psi-2]]
+
-
[[Category: Structural genomic]]
+
-
[[Category: Toxin]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 18 11:42:44 2010''
+

Current revision

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

PDB ID 3kh2

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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