2zhg: Difference between revisions

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New page: left|200px {{Structure |PDB= 2zhg |SIZE=350|CAPTION= <scene name='initialview01'>2zhg</scene>, resolution 2.80Å |SITE= <scene name='pdbsite=AC1:Fes+Binding+Site+...
 
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[[Image:2zhg.jpg|left|200px]]


{{Structure
==Crystal structure of SoxR in complex with DNA==
|PDB= 2zhg |SIZE=350|CAPTION= <scene name='initialview01'>2zhg</scene>, resolution 2.80&Aring;
<StructureSection load='2zhg' size='340' side='right'caption='[[2zhg]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Fes+Binding+Site+For+Residue+A+501'>AC1</scene>, <scene name='pdbsite=AC2:Dtt+Binding+Site+For+Residue+A+901'>AC2</scene> and <scene name='pdbsite=AC3:Gol+Binding+Site+For+Residue+A+801'>AC3</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
<table><tr><td colspan='2'>[[2zhg]] 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=2ZHG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZHG FirstGlance]. <br>
|ACTIVITY=
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
|GENE= soxR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd04776 HTH_GnyR], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01110 HTH_SoxR]</span>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zhg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zhg OCA], [https://pdbe.org/2zhg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zhg RCSB], [https://www.ebi.ac.uk/pdbsum/2zhg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zhg ProSAT]</span></td></tr>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zhg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zhg OCA], [http://www.ebi.ac.uk/pdbsum/2zhg PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2zhg RCSB]</span>
</table>
}}
== Function ==
[https://www.uniprot.org/uniprot/SOXR_ECOLI SOXR_ECOLI] Activates the transcription of the soxS gene which itself controls the superoxide response regulon. SoxR contains a 2Fe-2S iron-sulfur cluster that may act as a redox sensor system that recognizes superoxide. The variable redox state of the Fe-S cluster is employed in vivo to modulate the transcriptional activity of SoxR in response to specific types of oxidative stress. Upon reduction of 2Fe-2S cluster, SoxR reversibly loses its transcriptional activity, but retains its DNA binding affinity.
== 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/zh/2zhg_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2zhg ConSurf].
<div style="clear:both"></div>


'''Crystal structure of SoxR in complex with DNA'''
==See Also==
 
*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
The [2Fe-2S] transcription factor SoxR, a member of the MerR family, functions as a bacterial sensor of oxidative stress such as superoxide and nitric oxide. SoxR is activated by reversible one-electron oxidation of the [2Fe-2S] cluster and then enhances the production of various antioxidant proteins through the soxRS regulon. In the active state, SoxR and other MerR family proteins activate transcription from unique promoters, which have a long 19- or 20-bp spacer between the -35 and -10 operator elements, by untwisting the promoter DNA. Here, we show the crystal structures of SoxR and its complex with the target promoter in the oxidized (active) state. The structures reveal that the [2Fe-2S] cluster of SoxR is completely solvent-exposed and surrounded by an asymmetric environment stabilized by interaction with the other subunit. The asymmetrically charged environment of the [2Fe-2S] cluster probably causes redox-dependent conformational changes of SoxR and the target promoter. Compared with the promoter structures with the 19-bp spacer previously studied, the DNA structure is more sharply bent, by approximately 1 bp, with the two central base pairs holding Watson-Crick base pairs. Comparison of the target promoter sequences of the MerR family indicates that the present DNA structure represents the activated conformation of the target promoter with a 20-bp spacer in the MerR family.
[[Category: Escherichia coli K-12]]
 
[[Category: Large Structures]]
==About this Structure==
[[Category: Kita A]]
2ZHG is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZHG OCA].
[[Category: Kobayashi K]]
 
[[Category: Miki K]]
==Reference==
[[Category: Watanabe S]]
Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA., Watanabe S, Kita A, Kobayashi K, Miki K, Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4121-6. Epub 2008 Mar 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18334645 18334645]
[[Category: Escherichia coli]]
[[Category: Protein complex]]
[[Category: Kita, A.]]
[[Category: Kobayashi, K.]]
[[Category: Miki, K.]]
[[Category: Watanabe, S.]]
[[Category: 2fe-2]]
[[Category: activator]]
[[Category: dna-binding]]
[[Category: iron]]
[[Category: iron-sulfur]]
[[Category: merr family]]
[[Category: metal-binding]]
[[Category: oxidative stress]]
[[Category: transcription]]
[[Category: transcription regulation]]
[[Category: transcription/dna complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 09:55:24 2008''

Latest revision as of 16:57, 13 March 2024

Crystal structure of SoxR in complex with DNACrystal structure of SoxR in complex with DNA

Structural highlights

2zhg is a 2 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 2.8Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SOXR_ECOLI Activates the transcription of the soxS gene which itself controls the superoxide response regulon. SoxR contains a 2Fe-2S iron-sulfur cluster that may act as a redox sensor system that recognizes superoxide. The variable redox state of the Fe-S cluster is employed in vivo to modulate the transcriptional activity of SoxR in response to specific types of oxidative stress. Upon reduction of 2Fe-2S cluster, SoxR reversibly loses its transcriptional activity, but retains its DNA binding affinity.

Evolutionary Conservation

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

See Also

2zhg, resolution 2.80Å

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