5III

Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating 8-oxo-dG and an incoming dATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A fidelity mechanism in DNA polymerase lambda promotes error-free bypass of 8-oxo-dG.

Burak, M.J.Guja, K.E.Hambardjieva, E.Derkunt, B.Garcia-Diaz, M.

(2016) Embo J. 35: 2045-2059

  • DOI: 10.15252/embj.201694332
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 8-oxo-7,8-dihydroxy-2'-deoxyguanosine (8-oxo-dG) has high mutagenic potential as it is prone to mispair with deoxyadenine (dA). In order to maintain genomic integrity, post-replicative 8-oxo-dG:dA mispairs are removed through DNA polymerase lambda (P ...

    8-oxo-7,8-dihydroxy-2'-deoxyguanosine (8-oxo-dG) has high mutagenic potential as it is prone to mispair with deoxyadenine (dA). In order to maintain genomic integrity, post-replicative 8-oxo-dG:dA mispairs are removed through DNA polymerase lambda (Pol λ)-dependent MUTYH-initiated base excision repair (BER). Here, we describe seven novel crystal structures and kinetic data that fully characterize 8-oxo-dG bypass by Pol λ. We demonstrate that Pol λ has a flexible active site that can tolerate 8-oxo-dG in either the anti- or syn-conformation. Importantly, we show that discrimination against the pro-mutagenic syn-conformation occurs at the extension step and identify the residue responsible for this selectivity. This residue acts as a kinetic switch, shunting repair toward long-patch BER upon correct dCMP incorporation, thus enhancing repair efficiency. Moreover, this switch also provides a potential mechanism to increase repair fidelity of MUTYH-initiated BER.


    Organizational Affiliation

    Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase lambda
A
334Homo sapiensMutation(s): 0 
Gene Names: POLL
EC: 2.7.7.7, 4.2.99.-
Find proteins for Q9UGP5 (Homo sapiens)
Go to Gene View: POLL
Go to UniProtKB:  Q9UGP5
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*CP*G)-3')D4synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*GP*TP*AP*(DOC))-3')P6synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')T11synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

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Download CCD File 
A
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
8OG
Query on 8OG
T
DNA LINKINGC10 H14 N5 O8 PDG
DOC
Query on DOC
P
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.848α = 90.00
b = 62.681β = 90.00
c = 140.024γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
AutoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references, Derived calculations, Refinement description