View source for 4kyw


==Restriction endonuclease DPNI in complex with two DNA molecules==
<StructureSection load='4kyw' size='340' side='right'caption='[[4kyw]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4kyw]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_TIGR4 Streptococcus pneumoniae TIGR4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KYW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KYW 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]] 2.35&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MA:N6-METHYL-DEOXY-ADENOSINE-5-MONOPHOSPHATE'>6MA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=4kyw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kyw OCA], [https://pdbe.org/4kyw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kyw RCSB], [https://www.ebi.ac.uk/pdbsum/4kyw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kyw ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/T2D1_STRPN T2D1_STRPN] Recognizes the double-stranded and methylated sequence G(Me)ATC and cleaves after A-2.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
R.DpnI consists of N-terminal catalytic and C-terminal winged helix domains that are separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we present a crystal structure of R.DpnI with oligoduplexes bound to the catalytic and winged helix domains and identify the catalytic domain residues that are involved in interactions with the substrate methyl groups. We show that these methyl groups in the Gm6ATC target sequence are positioned very close to each other. We further show that the presence of the two methyl groups requires a deviation from B-DNA conformation to avoid steric conflict. The methylation compatible DNA conformation is complementary with binding sites of both R.DpnI domains. This indirect readout of methylation adds to the specificity mediated by direct favorable interactions with the methyl groups and solvation/desolvation effects. We also present hydrogen/deuterium exchange data that support 'crosstalk' between the two domains in the identification of methylated DNA, which should further enhance R.DpnI methylation specificity.

Structural basis of the methylation specificity of R.DpnI.,Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M Nucleic Acids Res. 2014 Jun 25. pii: gku546. PMID:24966351<ref>PMID:24966351</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4kyw" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Streptococcus pneumoniae TIGR4]]
[[Category: Bochtler M]]
[[Category: Bujnicki JM]]
[[Category: Czapinska H]]
[[Category: Mierzejewska K]]
[[Category: Siwek W]]
[[Category: Skowronek K]]