7JK1

Human PrimPol inserting correct dCTP opposite the 8-oxoguanine lesion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase.

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

(2021) Nat Commun 12: 4020-4020

  • DOI: https://doi.org/10.1038/s41467-021-24317-z
  • Primary Citation of Related Structures:  
    7JK1, 7JKL, 7JKP, 7JL8, 7JLG

  • PubMed Abstract: 

    PrimPol is a human DNA polymerase-primase that localizes to mitochondria and nucleus and bypasses the major oxidative lesion 7,8-dihydro-8-oxoguanine (oxoG) via translesion synthesis, in mostly error-free manner. We present structures of PrimPol insertion complexes with a DNA template-primer and correct dCTP or erroneous dATP opposite the lesion, as well as extension complexes with C or A as a 3'-terminal primer base. We show that during the insertion of C and extension from it, the active site is unperturbed, reflecting the readiness of PrimPol to accommodate oxoG(anti). The misinsertion of A opposite oxoG(syn) also does not alter the active site, and is likely less favorable due to lower thermodynamic stability of the oxoG(syn)•A base-pair. During the extension step, oxoG(syn) induces an opening of its base-pair with A or misalignment of the 3'-A primer terminus. Together, the structures show how PrimPol accurately synthesizes DNA opposite oxidatively damaged DNA in human cells.


  • Organizational Affiliation

    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. olga.rechkoblit@mssm.edu.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed primase/polymerase protein
A, B
354Homo sapiensMutation(s): 0 
Gene Names: PRIMPOLCCDC111
EC: 2.7.7 (PDB Primary Data), 2.7.7.102 (UniProt), 2.7.7.7 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LW4 (Homo sapiens)
Explore Q96LW4 
Go to UniProtKB:  Q96LW4
PHAROS:  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*AP*(8OG)P*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')C,
F [auth G]
17synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*TP*GP*TP*GP*GP*TP*AP*GP*CP*G)-3')D,
E [auth F]
12synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DCP
Query on DCP

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
K [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
N [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.242 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.558α = 69.66
b = 65.732β = 82.83
c = 75.179γ = 88.54
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata 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 Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM131780

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description