6m3l
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 6m3l is ON HOLD Authors: Miyazono, K., Wang, D., Ito, T., Tanokura, M. Description: Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) ...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex== | |
| + | <StructureSection load='6m3l' size='340' side='right'caption='[[6m3l]], [[Resolution|resolution]] 2.75Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6m3l]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5] 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=6M3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M3L 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]] 2.75Å</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=6m3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m3l OCA], [https://pdbe.org/6m3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m3l RCSB], [https://www.ebi.ac.uk/pdbsum/6m3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m3l ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/G8ZFZ3_PYRAB G8ZFZ3_PYRAB] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | R.PabI is a restriction DNA glycosylase that recognizes the sequence 5'-GTAC-3' and hydrolyses the N-glycosidic bond of adenine in the recognition sequence. R.PabI drastically bends and unwinds the recognition sequence of double-stranded DNA (dsDNA) and flips the adenine and guanine bases in the recognition sequence into the catalytic and recognition sites on the protein surface. In this study, we determined the crystal structure of the R.PabI-dsDNA complex in which the dsDNA is drastically bent by the binding of R.PabI but the base pairs are not unwound. This structure is predicted to be important for the indirect readout of the recognition sequence by R.PabI. In the complex structure, wedge loops of the R.PabI dimer are inserted into the minor groove of dsDNA to stabilize the deformed dsDNA structure. A base stacking is distorted between the two wedge-inserted regions. R.PabI is predicted to utilize the distorted base stacking for the detection of the recognition sequence. | ||
| - | + | Distortion of double-stranded DNA structure by the binding of the restriction DNA glycosylase R.PabI.,Miyazono KI, Wang D, Ito T, Tanokura M Nucleic Acids Res. 2020 Mar 31. pii: 5814050. doi: 10.1093/nar/gkaa184. PMID:32232412<ref>PMID:32232412</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 6m3l" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: Tanokura | + | <references/> |
| - | [[Category: | + | __TOC__ |
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Pyrococcus abyssi GE5]] | ||
| + | [[Category: Synthetic construct]] | ||
| + | [[Category: Ito T]] | ||
| + | [[Category: Miyazono K]] | ||
| + | [[Category: Tanokura M]] | ||
| + | [[Category: Wang D]] | ||
Current revision
Crystal structure of the R.PabI(Y68F-K154A)-dsDNA(nonspecific) complex
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