View source for 3waz


==Crystal structure of a restriction enzyme PabI in complex with DNA==
<StructureSection load='3waz' size='340' side='right'caption='[[3waz]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3waz]] is a 4 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=3WAZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WAZ 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]] 3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=ORP:2-DEOXY-5-PHOSPHONO-RIBOSE'>ORP</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=3waz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3waz OCA], [https://pdbe.org/3waz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3waz RCSB], [https://www.ebi.ac.uk/pdbsum/3waz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3waz ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9V2B6_PYRAB Q9V2B6_PYRAB] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Restriction-modification systems consist of genes that encode a restriction enzyme and a cognate methyltransferase. Thus far, it was believed that restriction enzymes are sequence-specific endonucleases that introduce double-strand breaks at specific sites by catalysing the cleavages of phosphodiester bonds. Here we report that based on the crystal structure and enzymatic activity, one of the restriction enzymes, R.PabI, is not an endonuclease but a sequence-specific adenine DNA glycosylase. The structure of the R.PabI-DNA complex shows that R.PabI unwinds DNA at a 5'-GTAC-3' site and flips the guanine and adenine bases out of the DNA helix to recognize the sequence. R.PabI catalyses the hydrolysis of the N-glycosidic bond between the adenine base and the sugar in the DNA and produces two opposing apurinic/apyrimidinic (AP) sites. The opposing AP sites are cleaved by heat-promoted beta elimination and/or by endogenous AP endonucleases of host cells to introduce a double-strand break.

A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi.,Miyazono K, Furuta Y, Watanabe-Matsui M, Miyakawa T, Ito T, Kobayashi I, Tanokura M Nat Commun. 2014;5:3178. doi: 10.1038/ncomms4178. PMID:24458096<ref>PMID:24458096</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3waz" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus abyssi GE5]]
[[Category: Synthetic construct]]
[[Category: Ito T]]
[[Category: Miyakawa T]]
[[Category: Miyazono K]]
[[Category: Tanokura M]]