6MU4

Bst DNA polymerase I FANA/DNA binary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase.

Jackson, L.N.Chim, N.Shi, C.Chaput, J.C.

(2019) Nucleic Acids Res 47: 6973-6983

  • DOI: https://doi.org/10.1093/nar/gkz513
  • Primary Citation of Related Structures:  
    6MU4, 6MU5

  • PubMed Abstract: 

    Replicative DNA polymerases are highly efficient enzymes that maintain stringent geometric control over shape and orientation of the template and incoming nucleoside triphosphate. In a surprising twist to this paradigm, a naturally occurring bacterial DNA polymerase I member isolated from Geobacillus stearothermophilus (Bst) exhibits an innate ability to reverse transcribe RNA and other synthetic congeners (XNAs) into DNA. This observation raises the interesting question of how a replicative DNA polymerase is able to recognize templates of diverse chemical composition. Here, we present crystal structures of natural Bst DNA polymerase that capture the post-translocated product of DNA synthesis on templates composed entirely of 2'-deoxy-2'-fluoro-β-d-arabino nucleic acid (FANA) and α-l-threofuranosyl nucleic acid (TNA). Analysis of the enzyme active site reveals the importance of structural plasticity as a possible mechanism for XNA-dependent DNA synthesis and provides insights into the construction of variants with improved activity.


  • Organizational Affiliation

    Departments of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase IB [auth A]577Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA
EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Explore E1C9K5 
Go to UniProtKB:  E1C9K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9K5
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3')A [auth P]11synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
FANA (5'-D(P*(UF2)P*(A5L)P*(CFL)P*(GFL)P*(UF2)P*(GFL)P*(A5L)P*(UF2)P*(CFL)P*(GFL)P*(CFL))-3')C [auth T]13synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.835α = 90
b = 93.898β = 90
c = 105.809γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoXDSdata reduction
autoXDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB: 1607111

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description