8DH1

T7 RNA polymerase elongation complex with unnatural base dDs-PaTP pair


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

Starting Model: experimental
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Literature

Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.

Oh, J.Kimoto, M.Xu, H.Chong, J.Hirao, I.Wang, D.

(2023) Nat Commun 14: 195-195

  • DOI: https://doi.org/10.1038/s41467-022-35755-8
  • Primary Citation of Related Structures:  
    8DH0, 8DH1, 8DH2, 8DH3, 8DH4, 8DH5

  • PubMed Abstract: 

    Bacteriophage T7 RNA polymerase (T7 RNAP) is widely used for synthesizing RNA molecules with synthetic modifications and unnatural base pairs (UBPs) for a variety of biotechnical and therapeutic applications. However, the molecular basis of transcription recognition of UBPs by T7 RNAP remains poorly understood. Here we focused on a representative UBP, 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and pyrrole 2-carbaldehyde (Pa), and investigated how the hydrophobic Ds-Pa pair is recognized by T7 RNAP. Our kinetic assays revealed that T7 RNAP selectively recognizes the Ds or Pa base in the templates and preferentially incorporates their cognate unnatural base nucleotide substrate (PaTP or DsTP) over natural NTPs. Our structural studies reveal that T7 RNAP recognizes the unnatural substrates at the pre-insertion state in a distinct manner compared to natural substrates. These results provide mechanistic insights into transcription recognition of UBP by T7 RNAP and provide valuable information for designing the next generation of UBPs.


  • Organizational Affiliation

    Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T7 RNA polymeraseA [auth B],
E,
I,
L
883Escherichia phage T7Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P00573 (Escherichia phage T7)
Explore P00573 
Go to UniProtKB:  P00573
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00573
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
Template strand DNAB [auth A],
F,
J,
M
18synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA
C, G, K, N
12synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
Non-template strand DNA
D, H, O
9synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S8L (Subject of Investigation/LOI)
Query on S8L

Download Ideal Coordinates CCD File 
Q [auth B]1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-1H-pyrrole-2-carbaldehyde
C10 H16 N O14 P3
CLXMUGOYLDUWBK-PBVVMKELSA-N
GOL
Query on GOL

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P [auth B],
S [auth C],
U [auth I]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
R [auth B],
T [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.866α = 89.85
b = 86.156β = 85.09
c = 201.676γ = 69.56
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM102362

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description