View source for 5xm9


==Crystal structure of AsfvPolX in complex with DNA enzyme.==
<StructureSection load='5xm9' size='340' side='right'caption='[[5xm9]], [[Resolution|resolution]] 3.05&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5xm9]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/African_swine_fever_virus_BA71V African swine fever virus BA71V] 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=5XM9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XM9 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]] 3.053&#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=5xm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xm9 OCA], [https://pdbe.org/5xm9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xm9 RCSB], [https://www.ebi.ac.uk/pdbsum/5xm9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xm9 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DPOLX_ASFB7 DPOLX_ASFB7] Error-prone polymerase lacking a proofreading 3'-5' exonuclease which plays a role in viral DNA repair. Specifically binds intermediates in the single-nucleotide base-excision repair process. Also catalyzes DNA polymerization with low nucleotide-insertion fidelity. Together with the viral DNA ligase, fills the single nucleotide gaps generated by the AP endonuclease.<ref>PMID:12595253</ref> <ref>PMID:11685239</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In addition to storage of genetic information, DNA can also catalyze various reactions. RNA-cleaving DNAzymes are the catalytic DNAs discovered the earliest, and they can cleave RNAs in a sequence-specific manner. Owing to their great potential in medical therapeutics, virus control, and gene silencing for disease treatments, RNA-cleaving DNAzymes have been extensively studied; however, the mechanistic understandings of their substrate recognition and catalysis remain elusive. Here, we report three catalytic form 8-17 DNAzyme crystal structures. 8-17 DNAzyme adopts a V-shape fold, and the Pb(2+) cofactor is bound at the pre-organized pocket. The structures with Pb(2+) and the modification at the cleavage site captured the pre-catalytic state of the RNA cleavage reaction, illustrating the unexpected Pb(2+)-accelerated catalysis, intrinsic tertiary interactions, and molecular kink at the active site. Our studies reveal that DNA is capable of forming a compacted structure and that the functionality-limited bio-polymer can have a novel solution for a functional need in catalysis.

Crystal structure of an RNA-cleaving DNAzyme.,Liu H, Yu X, Chen Y, Zhang J, Wu B, Zheng L, Haruehanroengra P, Wang R, Li S, Lin J, Li J, Sheng J, Huang Z, Ma J, Gan J Nat Commun. 2017 Dec 8;8(1):2006. doi: 10.1038/s41467-017-02203-x. PMID:29222499<ref>PMID:29222499</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5xm9" style="background-color:#fffaf0;"></div>

==See Also==
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: African swine fever virus BA71V]]
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Gan JH]]
[[Category: Liu HH]]