4xic: Difference between revisions
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==ANTPHD WITH 15BP di-thioate modified DNA DUPLEX== | |||
<StructureSection load='4xic' size='340' side='right'caption='[[4xic]], [[Resolution|resolution]] 2.69Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4xic]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Unidentified Unidentified]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XIC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XIC FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.69Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2S:CYTIDINE-5-DITHIOPHOSPHORATE'>C2S</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4xic FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xic OCA], [https://pdbe.org/4xic PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xic RCSB], [https://www.ebi.ac.uk/pdbsum/4xic PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xic ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/ANTP_DROME 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. | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:26331260</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 4xic" style="background-color:#fffaf0;"></div> | ||
[[Category: White | == References == | ||
[[Category: | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Drosophila melanogaster]] | |||
[[Category: Large Structures]] | |||
[[Category: Unidentified]] | |||
[[Category: Iwahara J]] | |||
[[Category: White MA]] | |||
[[Category: Zandarashvili L]] | |||
Latest revision as of 10:46, 27 September 2023
ANTPHD WITH 15BP di-thioate modified DNA DUPLEXANTPHD WITH 15BP di-thioate modified DNA DUPLEX
Structural highlights
FunctionANTP_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 PubMedDithioation 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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