1xjy
From Proteopedia
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The crystal structures of the DNA binding sites of the RUNX1 transcription factor
Overview
Runt-domain (RD) proteins are transcription factors that play fundamental, roles in various developmental pathways. They bind specifically to DNA, sequences of the general form PyGPyGGTPy (Py = pyrimidine), through which, they regulate transcription of target genes. The DNA duplex, TCTGCGGTC/TGACCGCAG, incorporating the binding site for the RD, transcription factors (bold), was crystallized in space group P4(3). X-ray, analysis of two crystals diffracting to 1.7 and 2.0 angstroms resolution, which had slight variations in their unit-cell parameters, revealed two, distinct conformations of the A-DNA helix. The two crystal structures, possessed several structure and hydration features that had previously, been observed in A-DNA duplexes. A comparative analysis of the present, A-DNA structures and those of previously reported B-DNA crystal structures, of RD-binding sites in free and protein-bound states showed the various, duplexes to display several common features. Within this series, the, present A-DNA duplexes adopt two conformations along the pathway from the, canonical A-DNA to the B-DNA forms and the protein-bound helices display, conformational features that are intermediate between those of the current, A-DNA structures and that of the B-DNA-type helix of the free RD target., Based on these data and energy considerations, it is likely that the, propensity of the RD-binding site to adopt the A-DNA or B-DNA conformation, in solution depends on the sequence context and environmental conditions, and that the transition from either DNA form to the protein-bound, conformation involves a small energy barrier.
About this Structure
1XJY is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structures of the DNA-binding site of Runt-domain transcription regulators., Kitayner M, Rozenberg H, Rabinovich D, Shakked Z, Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):236-46. Epub 2005, Feb 24. PMID:15735333
Page seeded by OCA on Sun Nov 25 02:20:34 2007
