4RZR

Bypass of a bulky adduct dG1,8 by DPO4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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This is version 1.1 of the entry. See complete history


Literature

Mechanistic Basis for the Bypass of a Bulky DNA Adduct Catalyzed by a Y-Family DNA Polymerase.

Vyas, R.Efthimiopoulos, G.Tokarsky, E.J.Malik, C.K.Basu, A.K.Suo, Z.

(2015) J Am Chem Soc 137: 12131-12142

  • DOI: 10.1021/jacs.5b08027
  • Primary Citation of Related Structures:  
    4RZR

  • PubMed Abstract: 
  • 1-Nitropyrene (1-NP), an environmental pollutant, induces DNA damage in vivo and is considered to be carcinogenic. The DNA adducts formed by the 1-NP metabolites stall replicative DNA polymerases but are presumably bypassed by error-prone Y-family DNA polymerases at the expense of replication fidelity and efficiency in vivo ...

    1-Nitropyrene (1-NP), an environmental pollutant, induces DNA damage in vivo and is considered to be carcinogenic. The DNA adducts formed by the 1-NP metabolites stall replicative DNA polymerases but are presumably bypassed by error-prone Y-family DNA polymerases at the expense of replication fidelity and efficiency in vivo. Our running start assays confirmed that a site-specifically placed 8-(deoxyguanosin-N(2)-yl)-1-aminopyrene (dG(1,8)), one of the DNA adducts derived from 1-NP, can be bypassed by Sulfolobus solfataricus DNA polymerase IV (Dpo4), although this representative Y-family enzyme was paused strongly by the lesion. Pre-steady-state kinetic assays were employed to determine the low nucleotide incorporation fidelity and establish a minimal kinetic mechanism for the dG(1,8) bypass by Dpo4. To reveal a structural basis for dCTP incorporation opposite dG(1,8), we solved the crystal structures of the complexes of Dpo4 and DNA containing a templating dG(1,8) lesion in the absence or presence of dCTP. The Dpo4·DNA-dG(1,8) binary structure shows that the aminopyrene moiety of the lesion stacks against the primer/template junction pair, while its dG moiety projected into the cleft between the Finger and Little Finger domains of Dpo4. In the Dpo4·DNA-dG(1,8)·dCTP ternary structure, the aminopyrene moiety of the dG(1,8) lesion, is sandwiched between the nascent and junction base pairs, while its base is present in the major groove. Moreover, dCTP forms a Watson-Crick base pair with dG, two nucleotides upstream from the dG(1,8) site, creating a complex for "-2" frameshift mutation. Mechanistically, these crystal structures provide additional insight into the aforementioned minimal kinetic mechanism.


    Organizational Affiliation

    Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVA, D352Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: dbhdpo4SSO2448
EC: 2.7.7.7
UniProt
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97W02 
Go to UniProtKB:  Q97W02
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*TP*GP*C*(2JV)P*GP*AP*CP*TP*GP*GP*TP*AP*TP*TP*GP*GP*G)-3')B, E18synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*CP*CP*CP*AP*AP*TP*AP*CP*CP*AP*GP*TP*C)-3')C, F13synthetic construct
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 5 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DCP (Subject of Investigation/LOI)
      Query on DCP

      Download Ideal Coordinates CCD File 
      K [auth D]2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
      C9 H16 N3 O13 P3
      RGWHQCVHVJXOKC-SHYZEUOFSA-N
       Ligand Interaction
      TRS
      Query on TRS

      Download Ideal Coordinates CCD File 
      J [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
      C4 H12 N O3
      LENZDBCJOHFCAS-UHFFFAOYSA-O
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      O [auth D], P [auth D]GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      CA
      Query on CA

      Download Ideal Coordinates CCD File 
      G [auth A], H [auth A], L [auth D], M [auth D]CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      NA
      Query on NA

      Download Ideal Coordinates CCD File 
      I [auth A], N [auth D]SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.20 Å
      • R-Value Free: 0.250 
      • R-Value Work: 0.199 
      • R-Value Observed: 0.201 
      • Space Group: P 31
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 56.397α = 90
      b = 56.397β = 90
      c = 288.776γ = 120
      Software Package:
      Software NamePurpose
      PHASERphasing
      REFMACrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

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      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      • Deposited Date: 2014-12-23 
      • Released Date: 2015-09-16 
      • Deposition Author(s): Vyas, R., Suo, Z.

      Revision History  (Full details and data files)

      • Version 1.0: 2015-09-16
        Type: Initial release
      • Version 1.1: 2015-10-07
        Changes: Database references