2BQ3

DNA Adduct Bypass Polymerization by Sulfolobus solfataricus Dpo4. Analysis and Crystal Structures of Multiple Base-Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DNA Adduct Bypass Polymerization by Sulfolobus Solfataricus DNA Polymerase Dpo4: Analysis and Crystal Structures of Multiple Base Pair Substitution and Frameshift Products with the Adduct 1,N2-Ethenoguanine.

Zang, H.Goodenough, A.K.Choi, J.Y.Irimia, A.Loukachevitch, L.V.Kozekov, I.D.Angel, K.C.Rizzo, C.J.Egli, M.Guengerich, F.P.

(2005) J.Biol.Chem. 280: 29750

  • DOI: 10.1074/jbc.M504756200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 1,N(2)-Etheno(epsilon)guanine is a mutagenic DNA lesion derived from lipid oxidation products and also from some chemical carcinogens. Gel electrophoretic analysis of the products of primer extension by Sulfolobus solfataricus P2 DNA polymerase IV (D ...

    1,N(2)-Etheno(epsilon)guanine is a mutagenic DNA lesion derived from lipid oxidation products and also from some chemical carcinogens. Gel electrophoretic analysis of the products of primer extension by Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) indicated preferential incorporation of A opposite 3'-(1,N(2)-epsilon-G)TACT-5', among the four dNTPs tested individually. With the template 3'-(1,N(2)-epsilon-G)CACT-5', both G and A were incorporated. When primer extension was done in the presence of a mixture of all four dNTPs, high pressure liquid chromatography-mass spectrometry analysis of the products indicated that (opposite 3'-(1,N(2)-epsilon-G)CACT-5') the major product was 5'-GTGA-3' and the minor product was 5'-AGTGA-3'. With the template 3'-(1,N(2)-epsilon-G)TACT-5', the following four products were identified by high pressure liquid chromatography-mass spectrometry: 5'-AATGA-3', 5'-ATTGA-3', 5'-ATGA-3', and 5'-TGA-3'. An x-ray crystal structure of Dpo4 was solved (2.1 A) with a primer-template and A placed in the primer to be opposite the 1,N(2)-epsilon-G in the template 3'-(1,N(2)-epsilon-G)TACT 5'. The added A in the primer was paired across the template T with classic Watson-Crick geometry. Similar structures were observed in a ternary Dpo4-DNA-dATP complex and a ternary Dpo4-DNA-ddATP complex, with d(d)ATP opposite the template T. A similar structure was observed with a ddGTP adjacent to the primer and opposite the C next to 1,N(2)-epsilon-G in 3'-(1,N(2)-epsilon-G)CACT-5'. We concluded that Dpo4 uses several mechanisms, including A incorporation opposite 1,N(2)-epsilon-G and also a variation of dNTP-stabilized misalignment, to generate both base pair and frameshift mutations.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE IV
A
358Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: dbh (dpo4)
EC: 2.7.7.7
Find proteins for Q97W02 (Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97W02
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*A)-3'P14N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*CP*AP*TP*GNEP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'T18N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GNE
Query on GNE
T
DNA LINKINGC12 H14 N5 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.239 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.679α = 90.00
b = 102.852β = 90.00
c = 53.178γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data scaling
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance