5L2X

Crystal structure of human PrimPol ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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This is version 1.1 of the entry. See complete history


Literature

Structure and mechanism of human PrimPol, a DNA polymerase with primase activity.

Rechkoblit, O.Gupta, Y.K.Malik, R.Rajashankar, K.R.Johnson, R.E.Prakash, L.Prakash, S.Aggarwal, A.K.

(2016) Sci Adv 2: e1601317-e1601317

  • DOI: https://doi.org/10.1126/sciadv.1601317
  • Primary Citation of Related Structures:  
    5L2X

  • PubMed Abstract: 

    PrimPol is a novel human enzyme that contains both DNA primase and DNA polymerase activities. We present the first structure of human PrimPol in ternary complex with a DNA template-primer and an incoming deoxynucleoside triphosphate (dNTP). The ability of PrimPol to function as a DNA primase stems from a simple but remarkable feature-almost complete lack of contacts to the DNA primer strand. This, in turn, allows two dNTPs to bind initiation and elongation sites on the enzyme for the formation of the first dinucleotide. PrimPol shows the ability to synthesize DNA opposite ultraviolet (UV) lesions; however, unexpectedly, the active-site cleft of the enzyme is constrained, which precludes the bypass of UV-induced DNA lesions by conventional translesion synthesis. Together, the structure addresses long-standing questions about how DNA primases actually initiate synthesis and how primase and polymerase activities combine in a single enzyme to carry out DNA synthesis.


  • Organizational Affiliation

    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed primase/polymerase proteinA,
D [auth B]
353Homo sapiensMutation(s): 0 
Gene Names: PRIMPOLCCDC111
EC: 2.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LW4 (Homo sapiens)
Explore Q96LW4 
Go to UniProtKB:  Q96LW4
GTEx:  ENSG00000164306 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LW4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3')B [auth C],
E [auth G]
17Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*GP*TP*AP*GP*CP*(DDG))-3')C [auth D],
F [auth H]
13Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.723α = 67.89
b = 65.212β = 85.22
c = 72.463γ = 86.65
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations