7pbk: Difference between revisions
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==Vibriophage phiVC8 family A DNA polymerase (DpoZ), two conformations: thumb-exo open and thumb-exo closed== | ==Vibriophage phiVC8 family A DNA polymerase (DpoZ), two conformations: thumb-exo open and thumb-exo closed== | ||
<StructureSection load='7pbk' size='340' side='right'caption='[[7pbk]]' scene=''> | <StructureSection load='7pbk' size='340' side='right'caption='[[7pbk]], [[Resolution|resolution]] 2.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PBK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PBK FirstGlance]. <br> | <table><tr><td colspan='2'>[[7pbk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PBK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PBK FirstGlance]. <br> | ||
</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=7pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pbk OCA], [https://pdbe.org/7pbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pbk RCSB], [https://www.ebi.ac.uk/pdbsum/7pbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pbk ProSAT]</span></td></tr> | </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=7pbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pbk OCA], [https://pdbe.org/7pbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pbk RCSB], [https://www.ebi.ac.uk/pdbsum/7pbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pbk ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[[https://www.uniprot.org/uniprot/DPOZ_BPVC8 DPOZ_BPVC8]] DNA polymerase that preferentially incorporates the non-canonical base aminoadenine/dZTP instead of adenine into the synthesized DNA. More efficient in using dZTP instead of dATP as a substrate. In addition to this preference for dZTP, the phage also encodes a dATP triphosphohydrolase that removes dATP and its precursor dADP from the nucleotide pool of the host.[UniProtKB:A0A2H5BHJ5] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
All genetic information in cellular life is stored in DNA copolymers composed of four basic building blocks (ATGC-DNA). In contrast, a group of bacteriophages belonging to families Siphoviridae and Podoviridae has abandoned the usage of one of them, adenine (A), replacing it with 2-aminoadenine (Z). The resulting ZTGC-DNA is more stable than its ATGC-DNA counterpart, owing to the additional hydrogen bond present in the 2-aminoadenine:thymine (Z:T) base pair, while the additional amino group also confers resistance to the host endonucleases. Recently, two classes of replicative proteins found in ZTGC-DNA-containing phages were characterized and one of them, DpoZ from DNA polymerase A (PolA) family, was shown to possess significant Z-vs-A specificity. Here, we present the crystallographic structure of the apo form of DpoZ of vibriophage varphiVC8, composed of the 3'-5' exonuclease and polymerase domains. We captured the enzyme in two conformations that involve the tip of the thumb subdomain and the exonuclease domain. We highlight insertions and mutations characteristic of varphiVC8 DpoZ and its close homologues. Through mutagenesis and functional assays we suggest that the preference of varphiVC8 DpoZ towards Z relies on a polymerase backtracking process, more efficient when the nascent base pair is A:T than when it is Z:T. | |||
Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage varphiVC8.,Czernecki D, Hu H, Romoli F, Delarue M Nucleic Acids Res. 2021 Nov 18;49(20):11974-11985. doi: 10.1093/nar/gkab955. PMID:34751404<ref>PMID:34751404</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7pbk" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Czernecki D]] | [[Category: Czernecki, D]] | ||
[[Category: Delarue M]] | [[Category: Delarue, M]] | ||
[[Category: Hu H]] | [[Category: Hu, H]] | ||
[[Category: Romoli F]] | [[Category: Romoli, F]] | ||
[[Category: Dpoz]] | |||
[[Category: Phivc8]] | |||
[[Category: Pola]] | |||
[[Category: Thumb-exo closed]] | |||
[[Category: Thumb-exo open]] | |||
[[Category: Viral protein]] | |||