2f52: Difference between revisions

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{{Seed}}
[[Image:2f52.png|left|200px]]


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==Solution structure of cold shock protein CspB from Bacillus subtilis in complex with heptathymidine==
The line below this paragraph, containing "STRUCTURE_2f52", creates the "Structure Box" on the page.
<StructureSection load='2f52' size='340' side='right'caption='[[2f52]]' 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'>[[2f52]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F52 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F52 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">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f52 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f52 OCA], [https://pdbe.org/2f52 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f52 RCSB], [https://www.ebi.ac.uk/pdbsum/2f52 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f52 ProSAT]</span></td></tr>
{{STRUCTURE_2f52|  PDB=2f52  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/CSPB_BACSU CSPB_BACSU] Binds to the pentamer sequences ATTGG and CCAAT with highest affinity in single-stranded DNA, and also to other sequences. Has greater affinity for ATTGG than CCAAT. Can act as transcriptional activator of cold shock genes by recognizing putative ATTGG-box elements present in promoter regions of genes induced under cold shock conditions.
== 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/f5/2f52_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=2f52 ConSurf].
<div style="clear:both"></div>
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== Publication Abstract from PubMed ==
Cold shock proteins (CSP) belong to the family of single-stranded nucleic acid binding proteins with OB-fold. CSP are believed to function as 'RNA chaperones' and during anti-termination. We determined the solution structure of Bs-CspB bound to the single-stranded DNA (ssDNA) fragment heptathymidine (dT7) by NMR spectroscopy. Bs-CspB reveals an almost invariant conformation when bound to dT7 with only minor reorientations in loop beta1-beta2 and beta3-beta4 and of few aromatic side chains involved in base stacking. Binding studies of protein variants and mutated ssDNA demonstrated that Bs-CspB associates with ssDNA at almost diffusion controlled rates and low sequence specificity consistent with its biological function. A variation of the ssDNA affinity is accomplished solely by changes of the dissociation rate. 15N NMR relaxation and H/D exchange experiments revealed that binding of dT7 increases the stability of Bs-CspB and reduces the sub-nanosecond dynamics of the entire protein and especially of loop beta3-beta4.


===Solution structure of cold shock protein CspB from Bacillus subtilis in complex with heptathymidine===
Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution.,Zeeb M, Max KE, Weininger U, Low C, Sticht H, Balbach J Nucleic Acids Res. 2006;34(16):4561-71. Epub 2006 Sep 6. PMID:16956971<ref>PMID:16956971</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_16956971}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2f52" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 16956971 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_16956971}}
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</StructureSection>
==About this Structure==
2F52 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F52 OCA].
 
==Reference==
Recognition of T-rich single-stranded DNA by the cold shock protein Bs-CspB in solution., Zeeb M, Max KE, Weininger U, Low C, Sticht H, Balbach J, Nucleic Acids Res. 2006;34(16):4561-71. Epub 2006 Sep 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16956971 16956971]
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Balbach, J.]]
[[Category: Balbach J]]
[[Category: Sticht, H.]]
[[Category: Sticht H]]
[[Category: Zeeb, M.]]
[[Category: Zeeb M]]
[[Category: Beta barrel]]
[[Category: Ob-fold]]
 
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