1XC9

Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure of a High Fidelity DNA Polymerase Bound to a Benzo[a]pyrene Adduct That Blocks Replication

Hsu, G.W., Huang, X., Luneva, N.P., Geacintov, N.E., Beese, L.S.

(2005) J Biol Chem 280: 3764-3770

  • DOI: 10.1074/jbc.M411276200
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Of the carcinogens to which humans are most frequently exposed, the polycyclic aromatic hydrocarbon benzo[a]pyrene (BP) is one of the most ubiquitous. BP is a byproduct of grilled foods and tobacco and fuel combustion and has long been linked to vari ...

    Of the carcinogens to which humans are most frequently exposed, the polycyclic aromatic hydrocarbon benzo[a]pyrene (BP) is one of the most ubiquitous. BP is a byproduct of grilled foods and tobacco and fuel combustion and has long been linked to various human cancers, particularly lung and skin. BP is metabolized to diol epoxides that covalently modify DNA bases to form bulky adducts that block DNA synthesis by replicative or high fidelity DNA polymerases. Here we present the structure of a high fidelity polymerase from a thermostable strain of Bacillus stearothermophilus (Bacillus fragment) bound to the most common BP-derived N2-guanine adduct base-paired with cytosine. The BP adduct adopts a conformation that places the polycyclic BP moiety in the nascent DNA minor groove and is the first structure of a minor groove adduct bound to a polymerase. Orientation of the BP moiety into the nascent DNA minor groove results in extensive disruption to the interactions between the adducted DNA duplex and the polymerase. The disruptions revealed by the structure of Bacillus fragment bound to a BP adduct provide a molecular basis for rationalizing the potent blocking effect on replication exerted by BP adducts.

    Related Citations: 
    • Observing translation synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase
      Hsu, G.W., Kiefer, J.R., Becherel, O.J., Fuchs, R.P.P., Beese, L.S.
      () To be published --: --
    • Structures of Mismatch Replication Errors Observed in a DNA Polymerase
      Johnson, S.J., Beese, L.S.
      (2004) Cell 116: 803
    Organizational Affiliation: 

    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase I
A
580Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA, pol
EC: 2.7.7.7
Find proteins for P52026 (Geobacillus stearothermophilus)
Go to UniProtKB:  P52026
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA primer strandB10N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA template strand with benzo[a]pyrene adductC15N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC
Download CCD File 
A
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N		 Ligand Interaction
BAP
Query on BAP
Download CCD File 
C
1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE
C20 H16 O3
GFANZDFKCCJYRF-NSISKUIASA-N		 Ligand Interaction
SO4
Query on SO4
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
MG
Query on MG
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.752α = 90
b = 93.733β = 90
c = 104.512γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance