6r64
From Proteopedia
(Difference between revisions)
| Line 3: | Line 3: | ||
<StructureSection load='6r64' size='340' side='right'caption='[[6r64]], [[Resolution|resolution]] 2.64Å' scene=''> | <StructureSection load='6r64' size='340' side='right'caption='[[6r64]], [[Resolution|resolution]] 2.64Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6r64]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R64 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R64 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6r64]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R64 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R64 FirstGlance]. <br> |
</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> | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6ghc|6ghc]], [[6t21|6t21]], [[6t22|6t22]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6ghc|6ghc]], [[6t21|6t21]], [[6t22|6t22]]</td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mcrA, rglA, b1159, JW1145 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6r64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r64 OCA], [http://pdbe.org/6r64 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r64 RCSB], [http://www.ebi.ac.uk/pdbsum/6r64 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r64 ProSAT]</span></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=6r64 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r64 OCA], [http://pdbe.org/6r64 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r64 RCSB], [http://www.ebi.ac.uk/pdbsum/6r64 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r64 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| Line 12: | Line 13: | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| - | Escherichia coli | + | EcoKMcrA from Escherichia coli restricts CpG methylated or hydroxymethylated DNA, and may act as a barrier against host DNA. The enzyme consists of a novel N-terminal specificity domain that we term NEco, and a C-terminal catalytic HNH domain. Here, we report that NEco and full-length EcoKMcrA specificities are consistent. NEco affinity to DNA increases more from hemi- to full-methylation than from non- to hemi-methylation, indicating cooperative binding of the methyl groups. We determined the crystal structures of NEco in complex with fully modified DNA containing three variants of the Y5mCGR EcoKMcrA target sequence: C5mCGG, T5mCGA and T5hmCGA. The structures explain the specificity for the two central base pairs and one of the flanking pairs. As predicted based on earlier biochemical experiments, NEco does not flip any DNA bases. The proximal and distal methyl groups are accommodated in separate pockets. Changes to either pocket reduce DNA binding by NEco and restriction by EcoKMcrA, confirming the relevance of the crystallographically observed binding mode in solution. |
| - | + | Crystal structure of the EcoKMcrA N-terminal domain (NEco): recognition of modified cytosine bases without flipping.,Slyvka A, Zagorskaite E, Czapinska H, Sasnauskas G, Bochtler M Nucleic Acids Res. 2019 Nov 14. pii: 5625526. doi: 10.1093/nar/gkz1017. PMID:31724709<ref>PMID:31724709</ref> | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| Line 23: | Line 24: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Ecoli]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bochtler, M]] | [[Category: Bochtler, M]] | ||
Revision as of 09:24, 27 November 2019
N-terminal domain of modification dependent EcoKMcrA restriction endonuclease (NEco) in complex with C5mCGG target sequence
| |||||||||||
