4xid | pdb_00004xid

AntpHD with 15bp DNA duplex

spinqualitylabelsall models 4xid, resolution 2.70Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4xid is a 6 chain structure with sequence from Drosophila melanogaster and Unidentified. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.701Å Ligands: MPD, NI Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function ANTP_DROME Sequence-specific transcription factor which is part of a developmental regulatory system that regulates segmental identity in the mesothorax. Provides cells with specific positional identities on the anterior-posterior axis. Publication Abstract from PubMed Dithioation of DNA phosphate is known to enhance binding affinities, at least for some proteins. We mechanistically characterized this phenomenon for the Antennapedia homeodomain-DNA complex by integrated use of fluorescence, isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography. By fluorescence and isothermal titration calorimetry, we found that this affinity enhancement is entropy driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH3(+) groups involved in ion pairs with DNA. By x-ray crystallography, we compared the structures of the complexes with and without dithioation of the phosphate. Our NMR and x-ray data show that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively suggest that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface. Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate.,Zandarashvili L, Nguyen D, Anderson KM, White MA, Gorenstein DG, Iwahara J Biophys J. 2015 Sep 1;109(5):1026-37. doi: 10.1016/j.bpj.2015.07.032. PMID:26331260 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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