4X0Q

Ternary complex of human DNA polymerase theta C-terminal domain binding ddGTP opposite dCMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 

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This is version 1.4 of the entry. See complete history


Literature

Human DNA polymerase theta grasps the primer terminus to mediate DNA repair.

Zahn, K.E.Averill, A.M.Aller, P.Wood, R.D.Doublie, S.

(2015) Nat Struct Mol Biol 22: 304-311

  • DOI: 10.1038/nsmb.2993
  • Primary Citation of Related Structures:  
    4X0P, 4X0Q

  • PubMed Abstract: 
  • DNA polymerase θ protects against genomic instability via an alternative end-joining repair pathway for DNA double-strand breaks. Polymerase θ is overexpressed in breast, lung and oral cancers, and reduction of its activity in mammalian cells increases sensitivity to double-strand break-inducing agents, including ionizing radiation ...

    DNA polymerase θ protects against genomic instability via an alternative end-joining repair pathway for DNA double-strand breaks. Polymerase θ is overexpressed in breast, lung and oral cancers, and reduction of its activity in mammalian cells increases sensitivity to double-strand break-inducing agents, including ionizing radiation. Reported here are crystal structures of the C-terminal polymerase domain from human polymerase θ, illustrating two potential modes of dimerization. One structure depicts insertion of ddATP opposite an abasic-site analog during translesion DNA synthesis. The second structure describes a cognate ddGTP complex. Polymerase θ uses a specialized thumb subdomain to establish unique upstream contacts to the primer DNA strand, including an interaction with the 3'-terminal phosphate from one of five distinctive insertion loops. These observations demonstrate how polymerase θ grasps the primer to bypass DNA lesions or extend poorly annealed DNA termini to mediate end-joining.


    Organizational Affiliation

    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase thetaA, B772Homo sapiensMutation(s): 0 
Gene Names: POLQPOLH
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for O75417 (Homo sapiens)
Explore O75417 
Go to UniProtKB:  O75417
PHAROS:  O75417
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75417
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')C [auth E],
E [auth G]
17synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')D [auth F],
F [auth H]
13synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.704α = 90
b = 135.392β = 90
c = 159.819γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA052040

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 1.2: 2015-04-15
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence