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

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 

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Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage phi VC8.

Czernecki, D.Hu, H.Romoli, F.Delarue, M.

(2021) Nucleic Acids Res 49: 11974-11985

  • DOI: https://doi.org/10.1093/nar/gkab955
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    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 ϕVC8, 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 ϕVC8 DpoZ and its close homologues. Through mutagenesis and functional assays we suggest that the preference of ϕVC8 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.

  • Organizational Affiliation

    Unit of Architecture and Dynamics of Biological Macromolecules, CNRS UMR 3528, 25-28 rue du Docteur Roux, Institut Pasteur, 75015 Paris, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase I
A, B
646Vibrio phage phiVC8Mutation(s): 0 
Gene Names: phiVC8_p29
Find proteins for G3FFN8 (Vibrio phage phiVC8)
Explore G3FFN8 
Go to UniProtKB:  G3FFN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3FFN8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.16α = 90
b = 158.44β = 90
c = 79.95γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references, Refinement description
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description