4XA5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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Literature

Nucleotide binding interactions modulate dNTP selectivity and facilitate 8-oxo-dGTP incorporation by DNA polymerase lambda.

Burak, M.J.Guja, K.E.Garcia-Diaz, M.

(2015) Nucleic Acids Res 43: 8089-8099

  • DOI: https://doi.org/10.1093/nar/gkv760
  • Primary Citation of Related Structures:  
    4X5V, 4XA5, 4XUS

  • PubMed Abstract: 

    8-Oxo-7,8,-dihydro-2'-deoxyguanosine triphosphate (8-oxo-dGTP) is a major product of oxidative damage in the nucleotide pool. It is capable of mispairing with adenosine (dA), resulting in futile, mutagenic cycles of base excision repair. Therefore, it is critical that DNA polymerases discriminate against 8-oxo-dGTP at the insertion step. Because of its roles in oxidative DNA damage repair and non-homologous end joining, DNA polymerase lambda (Pol λ) may frequently encounter 8-oxo-dGTP. Here, we have studied the mechanisms of 8-oxo-dGMP incorporation and discrimination by Pol λ. We have solved high resolution crystal structures showing how Pol λ accommodates 8-oxo-dGTP in its active site. The structures indicate that when mispaired with dA, the oxidized nucleotide assumes the mutagenic syn-conformation, and is stabilized by multiple interactions. Steady-state kinetics reveal that two residues lining the dNTP binding pocket, Ala(510) and Asn(513), play differential roles in dNTP selectivity. Specifically, Ala(510) and Asn(513) facilitate incorporation of 8-oxo-dGMP opposite dA and dC, respectively. These residues also modulate the balance between purine and pyrimidine incorporation. Our results shed light on the mechanisms controlling 8-oxo-dGMP incorporation in Pol λ and on the importance of interactions with the incoming dNTP to determine selectivity in family X DNA polymerases.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase lambda325Homo sapiensMutation(s): 0 
Gene Names: POLL
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGP5 (Homo sapiens)
Explore Q9UGP5 
Go to UniProtKB:  Q9UGP5
PHAROS:  Q9UGP5
GTEx:  ENSG00000166169 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UGP5
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DOWNSTREAM PRIMER DNA (5'-D(P*GP*CP*CP*G)-3')B [auth D]4synthetic construct
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
PRIMER DNA (5'-D(*CP*AP*GP*TP*AP*(DOC))-3')C [auth P]6synthetic construct
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Entity ID: 4
MoleculeChains LengthOrganismImage
TEMPLATE DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')D [auth T]11synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8DG
Query on 8DG

Download Ideal Coordinates CCD File 
E [auth A]8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
BUZOGVVQWCXXDP-VPENINKCSA-N
GOL
Query on GOL

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K [auth A],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

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H [auth A],
I [auth A],
J [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG
Query on MG

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F [auth A],
G [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CAS
Query on CAS
A
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.967α = 90
b = 62.34β = 90
c = 141.613γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata 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: 2016-02-10
    Type: Initial release