1ph6: Difference between revisions
New page: left|200px<br /><applet load="1ph6" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ph6, resolution 2.10Å" /> '''Crystal Structure of... |
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[[Image:1ph6.gif|left|200px]]<br /><applet load="1ph6" size=" | [[Image:1ph6.gif|left|200px]]<br /><applet load="1ph6" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1ph6, resolution 2.10Å" /> | caption="1ph6, resolution 2.10Å" /> | ||
'''Crystal Structure of THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGTGG'''<br /> | '''Crystal Structure of THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGTGG'''<br /> | ||
==Overview== | ==Overview== | ||
Sequence-specific protein recognition of single-stranded nucleic acids is | 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. | ||
==About this Structure== | ==About this Structure== | ||
1PH6 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 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | 1PH6 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 <scene name='pdbligand=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PH6 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Sterkiella nova]] | [[Category: Sterkiella nova]] | ||
[[Category: Schultz, S | [[Category: Schultz, S C.]] | ||
[[Category: Theobald, D | [[Category: Theobald, D L.]] | ||
[[Category: NA]] | [[Category: NA]] | ||
[[Category: noncognate]] | [[Category: noncognate]] | ||
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[[Category: telomeres]] | [[Category: telomeres]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:28:43 2008'' | ||
Revision as of 15:28, 21 February 2008
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Crystal Structure of THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGTGG
OverviewOverview
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.
About this StructureAbout this Structure
1PH6 is a Protein complex structure of sequences from Sterkiella nova with as ligand. Full crystallographic information is available from OCA.
ReferenceReference
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:12912928
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