3Q8Q

Human DNA polymerase iota incorporating dATP opposite 8-oxo-guanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

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Ligand Structure Quality Assessment 


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Literature

Unique active site promotes error-free replication opposite an 8-oxo-guanine lesion by human DNA polymerase iota.

Kirouac, K.N.Ling, H.

(2011) Proc Natl Acad Sci U S A 108: 3210-3215

  • DOI: 10.1073/pnas.1013909108
  • Primary Citation of Related Structures:  
    3Q8P, 3Q8Q, 3Q8R

  • PubMed Abstract: 
  • The 8-oxo-guanine (8-oxo-G) lesion is the most abundant and mutagenic oxidative DNA damage existing in the genome. Due to its dual coding nature, 8-oxo-G causes most DNA polymerases to misincorporate adenine. Human Y-family DNA polymerase iota (polι) preferentially incorporates the correct cytosine nucleotide opposite 8-oxo-G ...

    The 8-oxo-guanine (8-oxo-G) lesion is the most abundant and mutagenic oxidative DNA damage existing in the genome. Due to its dual coding nature, 8-oxo-G causes most DNA polymerases to misincorporate adenine. Human Y-family DNA polymerase iota (polι) preferentially incorporates the correct cytosine nucleotide opposite 8-oxo-G. This unique specificity may contribute to polι's biological role in cellular protection against oxidative stress. However, the structural basis of this preferential cytosine incorporation is currently unknown. Here we present four crystal structures of polι in complex with DNA containing an 8-oxo-G lesion, paired with correct dCTP or incorrect dATP, dGTP, and dTTP nucleotides. An exceptionally narrow polι active site restricts the purine bases in a syn conformation, which prevents the dual coding properties of 8-oxo-G by inhibiting syn/anti conformational equilibrium. More importantly, the 8-oxo-G base in a syn conformation is not mutagenic in polι because its Hoogsteen edge does not form a stable base pair with dATP in the narrow active site. Instead, the syn 8-oxo-G template base forms the most stable replicating base pair with correct dCTP due to its small pyrimidine base size and enhanced hydrogen bonding with the Hoogsteen edge of 8-oxo-G. In combination with site directed mutagenesis, we show that Gln59 in the finger domain specifically interacts with the additional O(8) atom of the lesion base, which influences nucleotide selection, enzymatic efficiency, and replication stalling at the lesion site. Our work provides the structural mechanism of high-fidelity 8-oxo-G replication by a human DNA polymerase.


    Organizational Affiliation

    Department of Biochemistry, University of Western Ontario, London, ON, Canada N6A 5C1.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase iotaA [auth B]420Homo sapiensMutation(s): 0 
Gene Names: POLIRAD30B
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNA4 (Homo sapiens)
Explore Q9UNA4 
Go to UniProtKB:  Q9UNA4
PHAROS:  Q9UNA4
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*CP*AP*(8OG)P*GP*GP*GP*TP*CP*CP*T)-3')B [auth T]11synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3')C [auth P]7synthetic construct
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DTP (Subject of Investigation/LOI)
      Query on DTP

      Download Ideal Coordinates CCD File 
      F [auth T]2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
      C10 H16 N5 O12 P3
      SUYVUBYJARFZHO-RRKCRQDMSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      D [auth B], E [auth B]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.03 Å
      • R-Value Free: 0.253 
      • R-Value Work: 0.227 
      • R-Value Observed: 0.228 
      • Space Group: P 65 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 98.731α = 90
      b = 98.731β = 90
      c = 202.271γ = 120
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      PHASERphasing
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

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      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2011-02-23
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance