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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1093/nar/gkz513
  • Primary Citation of Related Structures:  

  • 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 bacteria ...

    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

    Department of Molecular Biology and Biochemistry, University of California, CA 92697-3958, USA.,Departments of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA.,Department of Chemistry, University of California, Irvine, CA 92697-3958, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase I
A
577Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA
EC: 2.7.7.7
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Go to UniProtKB:  E1C9K5
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3')P11synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
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')T13synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
UF2
Query on UF2
T
DNA LINKINGC9 H12 F N2 O8 PDU
GFL
Query on GFL
T
DNA LINKINGC10 H13 F N5 O7 PDG
CFL
Query on CFL
T
DNA LINKINGC9 H13 F N3 O7 PDC
A5L
Query on A5L
T
DNA LINKINGC10 H13 F N5 O6 PDA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.835α = 90.00
b = 93.898β = 90.00
c = 105.809γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
autoXDSdata reduction
autoXDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-06-19
    Type: Data collection, Database references
  • Version 1.2: 2019-08-07
    Type: Data collection, Database references
  • Version 1.3: 2019-11-27
    Type: Author supporting evidence