View source for 5iff


==Crystal structure of R.PabI-nonspecific DNA complex==
<StructureSection load='5iff' size='340' side='right'caption='[[5iff]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5iff]] 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=5IFF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IFF 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]] 1.9&#8491;</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=5iff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iff OCA], [https://pdbe.org/5iff PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iff RCSB], [https://www.ebi.ac.uk/pdbsum/5iff PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iff ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9V2B6_PYRAB Q9V2B6_PYRAB] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
R.PabI is a type II restriction enzyme that recognizes the 5'-GTAC-3' sequence and belongs to the HALFPIPE superfamily. Although most restriction enzymes cleave phosphodiester bonds at specific sites by hydrolysis, R.PabI flips the guanine and adenine bases of the recognition sequence out of the DNA helix and hydrolyzes the N-glycosidic bond of the flipped adenine in a similar manner to DNA glycosylases. In this study, we determined the structure of R.PabI in complex with double-stranded DNA without the R.PabI recognition sequence by X-ray crystallography. The 1.9 A resolution structure of the complex showed that R.PabI forms a tetrameric structure to sandwich the double-stranded DNA and the tetrameric structure is stabilized by four salt bridges. DNA binding and DNA glycosylase assays of the R.PabI mutants showed that the residues that form the salt bridges (R70 and D71) are essential for R.PabI to find the recognition sequence from the sea of nonspecific sequences. R.PabI is predicted to utilize the tetrameric structure to bind nonspecific double-stranded DNA weakly and slide along it to find the recognition sequence.

Tetrameric structure of the restriction DNA glycosylase R.PabI in complex with nonspecific double-stranded DNA.,Wang D, Miyazono KI, Tanokura M Sci Rep. 2016 Oct 12;6:35197. doi: 10.1038/srep35197. PMID:27731370<ref>PMID:27731370</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5iff" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus abyssi GE5]]
[[Category: Synthetic construct]]
[[Category: Miyazono K]]
[[Category: Tanokura M]]
[[Category: Wang D]]