7pbk | pdb_00007pbk

Vibriophage phiVC8 family A DNA polymerase (DpoZ), two conformations: thumb-exo open and thumb-exo closed

spinqualitylabelsall models 7pbk, resolution 2.80Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7pbk is a 2 chain structure with sequence from Vibrio phage phiVC8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.8Å Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function 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] 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also DNA polymerase 3D structures

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