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1ph4

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(New page: 200px<br /><applet load="1ph4" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ph4, resolution 2.30&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:1ph4.gif|left|200px]]<br /><applet load="1ph4" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ph4, resolution 2.30&Aring;" />
 
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'''CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGCG'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGCG==
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Sequence-specific protein recognition of single-stranded nucleic acids is, critical for many fundamental cellular processes, such as DNA replication, DNA repair, transcription, translation, recombination, apoptosis and, telomere maintenance. To explore the mechanisms of sequence-specific ssDNA, recognition, we determined the crystal structures of 10 different, non-cognate ssDNAs complexed with the Oxytricha nova telomere end-binding, protein (OnTEBP) and evaluated their corresponding binding affinities (PDB, ID codes 1PH1-1PH9 and 1PHJ). The thermodynamic and structural effects of, these sequence perturbations could not have been predicted based solely, upon the cognate structure. OnTEBP accommodates non-cognate nucleotides by, both subtle adjustments and surprisingly large structural rearrangements, in the ssDNA. In two complexes containing ssDNA intermediates that occur, during telomere extension by telomerase, entire nucleotides are expelled, from the complex. Concurrently, the sequence register of the ssDNA shifts, to re-establish a more cognate-like pattern. This phenomenon, termed, nucleotide shuffling, may be of general importance in protein recognition, of single-stranded nucleic acids. This set of structural and thermodynamic, data highlights a fundamental difference between protein recognition of, ssDNA versus dsDNA.
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<StructureSection load='1ph4' size='340' side='right'caption='[[1ph4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ph4]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PH4 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]] 2.3&#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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=1ph4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ph4 OCA], [https://pdbe.org/1ph4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ph4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ph4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ph4 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TEBA_STENO TEBA_STENO] May function as protective capping of the single-stranded telomeric overhang. May also participate in telomere length regulation during DNA replication. Binds specifically to the T4G4-containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification.
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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/ph/1ph4_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=1ph4 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1PH4 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova] with NA and CL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PH4 OCA].
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*[[End-binding protein|End-binding protein]]
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__TOC__
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==Reference==
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</StructureSection>
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Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes., Theobald DL, Schultz SC, EMBO J. 2003 Aug 15;22(16):4314-24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12912928 12912928]
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[[Category: Large Structures]]
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[[Category: Protein complex]]
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[[Category: Sterkiella nova]]
[[Category: Sterkiella nova]]
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[[Category: Schultz, S.C.]]
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[[Category: Schultz SC]]
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[[Category: Theobald, D.L.]]
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[[Category: Theobald DL]]
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[[Category: CL]]
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[[Category: NA]]
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[[Category: noncognate]]
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[[Category: ob fold]]
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[[Category: oligonucleotide and oligosaccharide binding fold]]
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[[Category: protein dna interactions]]
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[[Category: protein/dna]]
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[[Category: sequence specificity]]
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[[Category: single strand dna binding protein]]
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[[Category: telomeres]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:48:15 2007''
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Current revision

CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGCG

PDB ID 1ph4

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