6jvz: Difference between revisions
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==RVD HA specifically contacts 5mC through van der Waals interactions== | ==RVD HA specifically contacts 5mC through van der Waals interactions== | ||
<StructureSection load='6jvz' size='340' side='right'caption='[[6jvz]]' scene=''> | <StructureSection load='6jvz' size='340' side='right'caption='[[6jvz]], [[Resolution|resolution]] 2.48Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JVZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JVZ FirstGlance]. <br> | <table><tr><td colspan='2'>[[6jvz]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacterium_campestre_var._armoraciae Bacterium campestre var. armoraciae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JVZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JVZ FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jvz OCA], [http://pdbe.org/6jvz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jvz RCSB], [http://www.ebi.ac.uk/pdbsum/6jvz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jvz ProSAT]</span></td></tr> | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jvz OCA], [http://pdbe.org/6jvz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jvz RCSB], [http://www.ebi.ac.uk/pdbsum/6jvz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jvz ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<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> | |||
</div> | |||
<div class="pdbe-citations 6jvz" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacterium campestre var. armoraciae]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Liu L]] | [[Category: Liu, L]] | ||
[[Category: Yi C]] | [[Category: Yi, C]] | ||
[[Category: Dna binding protein-dna complex]] | |||
[[Category: Methylation tal effector complex]] | |||
Revision as of 10:29, 4 November 2020
RVD HA specifically contacts 5mC through van der Waals interactionsRVD HA specifically contacts 5mC through van der Waals interactions
Structural highlights
Publication 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. References
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