View source for 6zpb


==Cyanophage S-2L HD phosphohydrolase (DatZ) bound to dA and two catalytic Co2+ ions==
<StructureSection load='6zpb' size='340' side='right'caption='[[6zpb]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6zpb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cyanobacteria_phage_s-2l Cyanobacteria phage s-2l]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZPB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZPB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3D1:(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL'>3D1</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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=6zpb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zpb OCA], [https://pdbe.org/6zpb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zpb RCSB], [https://www.ebi.ac.uk/pdbsum/6zpb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zpb ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
Bacteriophages have long been known to use modified bases in their DNA to prevent cleavage by the host's restriction endonucleases. Among them, cyanophage S-2L is unique because its genome has all its adenines (A) systematically replaced by 2-aminoadenines (Z). Here, we identify a member of the PrimPol family as the sole possible polymerase of S-2L and we find it can incorporate both A and Z in front of a T. Its crystal structure at 1.5 A resolution confirms that there is no structural element in the active site that could lead to the rejection of A in front of T. To resolve this contradiction, we show that a nearby gene is a triphosphohydolase specific of dATP (DatZ), that leaves intact all other dNTPs, including dZTP. This explains the absence of A in S-2L genome. Crystal structures of DatZ with various ligands, including one at sub-angstrom resolution, allow to describe its mechanism as a typical two-metal-ion mechanism and to set the stage for its engineering.

How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA.,Czernecki D, Legrand P, Tekpinar M, Rosario S, Kaminski PA, Delarue M Nat Commun. 2021 Apr 23;12(1):2420. doi: 10.1038/s41467-021-22626-x. PMID:33893297<ref>PMID:33893297</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 6zpb" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Cyanobacteria phage s-2l]]
[[Category: Large Structures]]
[[Category: Czernecki, D]]
[[Category: Delarue, M]]
[[Category: Legrand, P]]
[[Category: Datz]]
[[Category: Hd phosphohydrolase]]
[[Category: S-2l]]
[[Category: Viral protein]]