3M9N

Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4.

Wong, J.H.Brown, J.A.Suo, Z.Blum, P.Nohmi, T.Ling, H.

(2010) Embo J. 29: 2059-2069

  • DOI: 10.1038/emboj.2010.101
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Y-family DNA polymerases bypass Pt-GG, the cisplatin-DNA double-base lesion, contributing to the cisplatin resistance in tumour cells. To reveal the mechanism, we determined three structures of the Y-family DNA polymerase, Dpo4, in complex with Pt-GG ...

    Y-family DNA polymerases bypass Pt-GG, the cisplatin-DNA double-base lesion, contributing to the cisplatin resistance in tumour cells. To reveal the mechanism, we determined three structures of the Y-family DNA polymerase, Dpo4, in complex with Pt-GG DNA. The crystallographic snapshots show three stages of lesion bypass: the nucleotide insertions opposite the 3'G (first insertion) and 5'G (second insertion) of Pt-GG, and the primer extension beyond the lesion site. We observed a dynamic process, in which the lesion was converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4. The DNA translocation-coupled conformational change may account for additional inhibition on the second insertion reaction. The structures illustrate that Pt-GG disturbs the replicating base pair in the active site, which reduces the catalytic efficiency and fidelity. The in vivo relevance of Dpo4-mediated Pt-GG bypass was addressed by a dpo-4 knockout strain of Sulfolobus solfataricus, which exhibits enhanced sensitivity to cisplatin and proteomic alterations consistent with genomic stress.


    Organizational Affiliation

    Department of Biochemistry, University of Western Ontario, London, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase IV
B
352Sulfolobus 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
DNA (5'-D(*GP*GP*GP*GP*AP*AP*GP*GP*AP*AP*AP*GP*C)-3')P13N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')T18N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPT
Query on CPT

Download SDF File 
Download CCD File 
T
Cisplatin
diammine(dichloro)platinum
Cl2 H6 N2 Pt
LXZZYRPGZAFOLE-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CTP
Query on CTP

Download SDF File 
Download CCD File 
B
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 98.227α = 90.00
b = 103.233β = 90.00
c = 52.259γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-03-22 
  • Released Date: 2010-06-16 
  • Deposition Author(s): Wong, J.H.Y., Ling, H.

Revision History 

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description