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2es2

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(New page: 200px<br /><applet load="2es2" size="450" color="white" frame="true" align="right" spinBox="true" caption="2es2, resolution 1.780&Aring;" /> '''Crystal Structure A...)
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[[Image:2es2.gif|left|200px]]<br /><applet load="2es2" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2es2, resolution 1.780&Aring;" />
 
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'''Crystal Structure Analysis of the Bacillus Subtilis Cold Shock Protein Bs-CspB in Complex with Hexathymidine'''<br />
 
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==Overview==
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==Crystal Structure Analysis of the Bacillus Subtilis Cold Shock Protein Bs-CspB in Complex with Hexathymidine==
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Bacterial cold shock proteins (CSPs) are involved in cellular adaptation, to cold stress. They bind to single-stranded nucleic acids with a KD value, in the micro- to nanomolar range. Here we present the structure of the, Bacillus subtilis CspB (Bs-CspB) in complex with hexathymidine (dT6) at a, resolution of 1.78 A. Bs-CspB binds to dT6 with nanomolar affinity via an, amphipathic interface on the protein surface. Individual binding subsites, interact with single nucleobases through stacking interactions and, hydrogen bonding. The sugar-phosphate backbone and the methyl groups of, the thymine nucleobases remain solvent exposed and are not contacted by, protein groups. Fluorescence titration experiments monitoring the binding, of oligopyrimidines to Bs-CspB reveal binding preferences at individual, subsites and allow the design of an optimised heptapyrimidine ligand, which is bound with sub-nanomolar affinity. This study reveals the, stoichiometry and sequence determinants of the binding of single-stranded, nucleic acids to a preformed site on Bs-CspB and thus provides the, structural basis of the RNA chaperone and transcription antitermination, activities of the CSP.
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<StructureSection load='2es2' size='340' side='right'caption='[[2es2]], [[Resolution|resolution]] 1.78&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2es2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ES2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ES2 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.78&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=2es2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2es2 OCA], [https://pdbe.org/2es2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2es2 RCSB], [https://www.ebi.ac.uk/pdbsum/2es2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2es2 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/es/2es2_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2es2 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Bacterial cold shock proteins (CSPs) are involved in cellular adaptation to cold stress. They bind to single-stranded nucleic acids with a KD value in the micro- to nanomolar range. Here we present the structure of the Bacillus subtilis CspB (Bs-CspB) in complex with hexathymidine (dT6) at a resolution of 1.78 A. Bs-CspB binds to dT6 with nanomolar affinity via an amphipathic interface on the protein surface. Individual binding subsites interact with single nucleobases through stacking interactions and hydrogen bonding. The sugar-phosphate backbone and the methyl groups of the thymine nucleobases remain solvent exposed and are not contacted by protein groups. Fluorescence titration experiments monitoring the binding of oligopyrimidines to Bs-CspB reveal binding preferences at individual subsites and allow the design of an optimised heptapyrimidine ligand, which is bound with sub-nanomolar affinity. This study reveals the stoichiometry and sequence determinants of the binding of single-stranded nucleic acids to a preformed site on Bs-CspB and thus provides the structural basis of the RNA chaperone and transcription antitermination activities of the CSP.
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==About this Structure==
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T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB.,Max KE, Zeeb M, Bienert R, Balbach J, Heinemann U J Mol Biol. 2006 Jul 14;360(3):702-14. Epub 2006 Jun 2. PMID:16780871<ref>PMID:16780871</ref>
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2ES2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2ES2 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB., Max KE, Zeeb M, Bienert R, Balbach J, Heinemann U, J Mol Biol. 2006 Jul 14;360(3):702-14. Epub 2006 Jun 2. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16780871 16780871]
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</div>
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<div class="pdbe-citations 2es2" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Bienert, M.]]
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[[Category: Bienert M]]
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[[Category: Heinemann, U.]]
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[[Category: Heinemann U]]
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[[Category: Max, K.E.A.]]
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[[Category: Max KEA]]
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[[Category: CA]]
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[[Category: beta barrel]]
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[[Category: protein-dna complex]]
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[[Category: single-stranded dna]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:06:45 2007''
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Current revision

Crystal Structure Analysis of the Bacillus Subtilis Cold Shock Protein Bs-CspB in Complex with Hexathymidine

PDB ID 2es2

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