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PDBsum entry 1ph2
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DNA binding protein/DNA
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PDB id
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1ph2
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Nucleotide shuffling and ssdna recognition in oxytricha nova telomere end-Binding protein complexes.
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Authors
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D.L.Theobald,
S.C.Schultz.
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Ref.
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Embo J, 2003,
22,
4314-4324.
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PubMed id
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Abstract
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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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