2C2R

Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4

Zang, H.Irimia, A.Choi, J.-Y.Angel, K.C.Loukachevitch, L.V.Egli, M.Guengerich, F.P.

(2006) J Biol Chem 281: 2358

  • DOI: 10.1074/jbc.M510889200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • DNA polymerases insert dATP opposite the oxidative damage product 7,8-dihydro-8-oxodeoxyguanosine (8-oxoG) instead of dCTP, to the extent of >90% with some polymerases. Steady-state kinetics with the Y-family Sulfolobus solfataricus DNA polymerase IV ...

    DNA polymerases insert dATP opposite the oxidative damage product 7,8-dihydro-8-oxodeoxyguanosine (8-oxoG) instead of dCTP, to the extent of >90% with some polymerases. Steady-state kinetics with the Y-family Sulfolobus solfataricus DNA polymerase IV (Dpo4) showed 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) was similar for G and 8-oxoG templates. Mass spectral analysis of extended DNA primers showed >/=95% incorporation of dCTP > dATP opposite 8-oxoG. Pre-steady-state kinetics showed faster rates of dCTP incorporation opposite 8-oxoG than G. The measured K(d)(,dCTP) was 15-fold lower for an oligonucleotide containing 8-oxoG than with G. Extension beyond an 8-oxoG:C pair was similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. The E(a) for dCTP insertion opposite 8-oxoG was lower than for opposite G. Crystal structures of Dpo4 complexes with oligonucleotides were solved with C, A, and G nucleoside triphosphates placed opposite 8-oxoG. With ddCTP, dCTP, and dATP the phosphodiester bonds were formed even in the presence of Ca(2+). The 8-oxoG:C pair showed classic Watson-Crick geometry; the 8-oxoG:A pair was in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5' C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshift event observed in the catalytic assays.


    Organizational Affiliation

    Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, 638 Robinson Research Building, 23rd and Pierce Avenues, Nashville, TN 37232-0146, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE IV
A
358Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: dbhdpo4SSO2448
EC: 2.7.7.7
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97W02
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*C)-3'P14N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*CP*AP*C 8OGP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'T18N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCT
Query on DCT

Download CCD File 
A
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
C9 H16 N3 O12 P3
ARLKCWCREKRROD-POYBYMJQSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.2α = 90
b = 100.15β = 90
c = 52γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-29
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance