6MU5

Bst DNA polymerase I TNA/DNA binary complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.912 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 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. --: --

  • 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
580Geobacillus 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')P10synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
TNA (5'-D(P*(TG)P*(TFT)P*(FA2)P*(TC)P*(TG)P*(TFT)P*(TG)P*(FA2)P*(TFT)P*(TC)P*(TG)P*(TC)P*(FA2))-3')T13synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, P
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
TC
Query on TC
T
RNA linkingC8 H11 N3 O7 PC
FA2
Query on FA2
T
RNA LINKINGC9 H12 N5 O6 PDA
TG
Query on TG
T
RNA linkingC9 H11 N5 O7 PG
TFT
Query on TFT
T
DNA LINKINGC9 H13 N2 O8 PDT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.912 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.390α = 90.00
b = 93.280β = 90.00
c = 103.750γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (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