6jw0: Difference between revisions
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==Universal RVD R* accommodates cytosine via water-mediated interactions== | |||
<StructureSection load='6jw0' size='340' side='right'caption='[[6jw0]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6jw0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas Xanthomonas] 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=6JW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JW0 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]] 2.2Å</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=6jw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jw0 OCA], [https://pdbe.org/6jw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jw0 RCSB], [https://www.ebi.ac.uk/pdbsum/6jw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jw0 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q3ZD72_XANCA Q3ZD72_XANCA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Transcription activator-like effectors (TALEs) recognize DNA through repeat-variable diresidues (RVDs), and TALE-DNA interactions are sensitive to DNA modifications. Our previous study deciphered the recognition of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) by TALEs. Here, we report seven crystal structures of TALE-DNA complexes. The 5mC-specific RVD HA recognizes 5mC through van der Waals interactions and exhibits highly similar loop conformation to natural RVDs. The degenerate RVD RG contacts 5mC and 5hmC via van der Waals interactions as well; however, its loop conformation differs significantly. The loop conformations of universal RVD R* and 5hmC-specific RVD Q* are similar to that of RG, while the interactions of R* with C/5mC/5hmC and Q* with 5hmC are mediated by waters. Together, our findings illustrate the molecular basis for the specific recognition of 5mC and 5hmC by multiple noncanonical TALEs and provide insights into the plasticity of the TALE RVD loops. | |||
Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors.,Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J J Mol Biol. 2020 Feb 14;432(4):1035-1047. doi: 10.1016/j.jmb.2019.11.023. Epub, 2019 Dec 19. PMID:31863750<ref>PMID:31863750</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Liu | <div class="pdbe-citations 6jw0" style="background-color:#fffaf0;"></div> | ||
[[Category: Yi | |||
==See Also== | |||
*[[TAL effector|TAL effector]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Xanthomonas]] | |||
[[Category: Liu L]] | |||
[[Category: Yi C]] | |||
Latest revision as of 13:20, 22 November 2023
Universal RVD R* accommodates cytosine via water-mediated interactionsUniversal RVD R* accommodates cytosine via water-mediated interactions
Structural highlights
FunctionPublication Abstract from PubMedTranscription activator-like effectors (TALEs) recognize DNA through repeat-variable diresidues (RVDs), and TALE-DNA interactions are sensitive to DNA modifications. Our previous study deciphered the recognition of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) by TALEs. Here, we report seven crystal structures of TALE-DNA complexes. The 5mC-specific RVD HA recognizes 5mC through van der Waals interactions and exhibits highly similar loop conformation to natural RVDs. The degenerate RVD RG contacts 5mC and 5hmC via van der Waals interactions as well; however, its loop conformation differs significantly. The loop conformations of universal RVD R* and 5hmC-specific RVD Q* are similar to that of RG, while the interactions of R* with C/5mC/5hmC and Q* with 5hmC are mediated by waters. Together, our findings illustrate the molecular basis for the specific recognition of 5mC and 5hmC by multiple noncanonical TALEs and provide insights into the plasticity of the TALE RVD loops. Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors.,Liu L, Zhang Y, Liu M, Wei W, Yi C, Peng J J Mol Biol. 2020 Feb 14;432(4):1035-1047. doi: 10.1016/j.jmb.2019.11.023. Epub, 2019 Dec 19. PMID:31863750[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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