1PH9

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

Summary for 1PH9

• Entry DOI: 10.2210/pdb1ph9/pdb
• Related: 1jb7 1k8g 1kix 1otc 1pa6 1ph1 1ph2 1ph3 1ph4 1ph5 1ph6 1ph7 1ph8 1phj
• Descriptor: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*T)-3', 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*AP*GP*G)-3', Telomere-binding protein alpha subunit, ... (7 entities in total)
• Functional Keywords: single strand dna binding protein, protein dna interactions, sequence specificity, noncognate, oligonucleotide and oligosaccharide binding fold, ob fold, telomeres, protein/dna, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Sterkiella nova; More
• Cellular location: Nucleus: P29549 P16458
• Total number of polymer chains: 5
• Total formula weight: 89083.89

Authors

Theobald, D.L.,Schultz, S.C. (deposition date: 2003-05-29, release date: 2003-06-17, Last modification date: 2024-02-14)

Primary citation

Theobald, D.L.,Schultz, S.C.
Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes
Embo J., 22:4314-4324, 2003

PubMed Abstract: 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.

PubMed: 12912928
DOI: 10.1093/emboj/cdg415

Experimental method

X-RAY DIFFRACTION (2.5 Å)