4r2d: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4r2d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R2D FirstGlance]. <br> | <table><tr><td colspan='2'>[[4r2d]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R2D FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5FC:5-FORMYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5FC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.088Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5FC:5-FORMYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5FC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4r2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r2d OCA], [https://pdbe.org/4r2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r2d RCSB], [https://www.ebi.ac.uk/pdbsum/4r2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r2d ProSAT]</span></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=4r2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r2d OCA], [https://pdbe.org/4r2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r2d RCSB], [https://www.ebi.ac.uk/pdbsum/4r2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r2d ProSAT]</span></td></tr> | ||
</table> | </table> | ||
Latest revision as of 20:42, 20 September 2023
Egr1/Zif268 zinc fingers in complex with formylated DNAEgr1/Zif268 zinc fingers in complex with formylated DNA
Structural highlights
FunctionEGR1_HUMAN Transcriptional regulator. Recognizes and binds to the DNA sequence 5'-CGCCCCCGC-3'(EGR-site). Activates the transcription of target genes whose products are required for mitogenesis and differentiation. Publication Abstract from PubMedIn mammalian DNA, cytosine occurs in several chemical forms, including unmodified cytosine (C), 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5mC is a major epigenetic signal that acts to regulate gene expression. 5hmC, 5fC, and 5caC are oxidized derivatives that might also act as distinct epigenetic signals. We investigated the response of the zinc finger DNA-binding domains of transcription factors early growth response protein 1 (Egr1) and Wilms tumor protein 1 (WT1) to different forms of modified cytosine within their recognition sequence, 5'-GCG(T/G)GGGCG-3'. Both displayed high affinity for the sequence when C or 5mC was present and much reduced affinity when 5hmC or 5fC was present, indicating that they differentiate primarily oxidized C from unoxidized C, rather than methylated C from unmethylated C. 5caC affected the two proteins differently, abolishing binding by Egr1 but not by WT1. We ascribe this difference to electrostatic interactions in the binding sites. In Egr1, a negatively charged glutamate conflicts with the negatively charged carboxylate of 5caC, whereas the corresponding glutamine of WT1 interacts with this group favorably. Our analyses shows that zinc finger proteins (and their splice variants) can respond in modulated ways to alternative modifications within their binding sequence. Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence.,Hashimoto H, Olanrewaju YO, Zheng Y, Wilson GG, Zhang X, Cheng X Genes Dev. 2014 Sep 25. pii: gad.250746.114. PMID:25258363[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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