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4xid

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Revision as of 17:36, 26 April 2023

AntpHD with 15bp DNA duplex

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.
Ligands:	,
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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Zandarashvili L, Nguyen D, Anderson KM, White MA, Gorenstein DG, Iwahara J. Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate. Biophys J. 2015 Sep 1;109(5):1026-37. doi: 10.1016/j.bpj.2015.07.032. PMID:26331260 doi:http://dx.doi.org/10.1016/j.bpj.2015.07.032

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4xid"

@@ Line 1: / Line 1: @@
 ==AntpHD with 15bp DNA duplex==
-<StructureSection load='4xid' size='340' side='right' caption='[[4xid]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='4xid' size='340' side='right'caption='[[4xid]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xid]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XID OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XID FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xid]] 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=4XID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XID FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4xic|4xic]]</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=4xid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xid OCA], [https://pdbe.org/4xid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xid RCSB], [https://www.ebi.ac.uk/pdbsum/4xid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xid ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Antp, CG1028 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xid OCA], [http://pdbe.org/4xid PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xid RCSB], [http://www.ebi.ac.uk/pdbsum/4xid PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xid ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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.
+[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 ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Drome]]
+[[Category: Drosophila melanogaster]]
-[[Category: Iwahara, J]]
+[[Category: Large Structures]]
-[[Category: White, M A]]
+[[Category: Unidentified]]
-[[Category: Zandarashvili, L]]
+[[Category: Iwahara J]]
-[[Category: Dna-binding protein]]
+[[Category: White MA]]
-[[Category: Homeodomain]]
+[[Category: Zandarashvili L]]
-[[Category: Transcription regulator-dna complex]]
-[[Category: Transcription-dna complex]]

4xid

From Proteopedia

Revision as of 17:36, 26 April 2023

AntpHD with 15bp DNA duplex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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