1sgs
From Proteopedia
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Crystal structure of a free kB DNA
Overview
The dimeric NF-kappaB transcription factors regulate gene expression by, recognizing specific DNA sequences located within the promoters of target, genes. The DNA sequences, referred to as kappaB DNA, are divided into two, broad classes. Class I kappaB DNA binds optimally to p50 and p52 NF-kappaB, subunits, while class II kappaB DNAs are recognized specifically by the, NF-kappaB subunits c-Rel and p65. We determined the X-ray crystal, structure of a class II kappaB DNA sequence at 1.60 A resolution. This, structure provides a detailed picture of kappaB DNA hydration, counter ion, binding, and conformation in the absence of NF-kappaB binding partner., X-ray structures of both class I and class II kappaB DNA bound to, NF-kappaB dimers were determined previously. Additionally, the NMR, solution structure of a class I kappaB DNA is known. Comparison of the, protein-bound and unbound kappaB DNA structures reveals that the free form, of both classes approximates ideal B-form DNA more closely. Local, geometries about specific DNA bases differ significantly upon binding to, NF-kappaB. This is particularly evident at the 5'-GG/CC base-pairs; a, signature of NF-kappaB specific DNA binding sequences. Differential, phosphate group conformations, minor groove widths, buckle, twist, and, tilt angles are observed between bound and unbound kappaB DNA. We observe, that the presence of an extra G:C base-pair, 5'- to the GGA sequence in, class I kappaB DNA, alters the geometry of the two internal G:C base-pairs, within the GGGA tetranucleotide, which explains, at least in part, the, structural basis for distinct NF-kappaB dimer recruitment by the two, different classes of kappaB DNA. Together, these observations suggest that, NF-kappaB dimers recognize specific structural features of kappaB DNA in, order to make sequence-specific complexes.
About this Structure
1SGS is a Protein complex structure of sequences from [1] with CA as ligand. Full crystallographic information is available from OCA.
Reference
Crystal structure of a free kappaB DNA: insights into DNA recognition by transcription factor NF-kappaB., Huang DB, Phelps CB, Fusco AJ, Ghosh G, J Mol Biol. 2005 Feb 11;346(1):147-60. Epub 2004 Dec 13. PMID:15663934
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