1TKD

T7 DNA polymerase ternary complex with 8 oxo guanosine and dCMP at the elongation site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.

Brieba, L.G.Eichman, B.F.Kokoska, R.J.Doublie, S.Kunkel, T.A.Ellenberger, T.

(2004) Embo J. 23: 3452-3461

  • DOI: 10.1038/sj.emboj.7600354
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Accurate DNA replication involves polymerases with high nucleotide selectivity and proofreading activity. We show here why both fidelity mechanisms fail when normally accurate T7 DNA polymerase bypasses the common oxidative lesion 8-oxo-7, 8-dihydro- ...

    Accurate DNA replication involves polymerases with high nucleotide selectivity and proofreading activity. We show here why both fidelity mechanisms fail when normally accurate T7 DNA polymerase bypasses the common oxidative lesion 8-oxo-7, 8-dihydro-2'-deoxyguanosine (8oG). The crystal structure of the polymerase with 8oG templating dC insertion shows that the O8 oxygen is tolerated by strong kinking of the DNA template. A model of a corresponding structure with dATP predicts steric and electrostatic clashes that would reduce but not eliminate insertion of dA. The structure of a postinsertional complex shows 8oG(syn).dA (anti) in a Hoogsteen-like base pair at the 3' terminus, and polymerase interactions with the minor groove surface of the mismatch that mimic those with undamaged, matched base pairs. This explains why translesion synthesis is permitted without proofreading of an 8oG.dA mismatch, thus providing insight into the high mutagenic potential of 8oG.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase
A
698Enterobacteria phage T7Mutation(s): 0 
EC: 2.7.7.7, 3.1.11.-
Find proteins for P00581 (Enterobacteria phage T7)
Go to UniProtKB:  P00581
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Thioredoxin 1
B
108Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: trxA (fipA, tsnC)
Find proteins for P0AA25 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA25
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DOC))-3')P22N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*CP*AP*(8OG)P*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3')T26N/A
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
D3T
Query on D3T

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Download CCD File 
A
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O13 P3
URGJWIFLBWJRMF-JGVFFNPUSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-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: 2.49 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.514α = 90.00
b = 215.112β = 90.00
c = 52.035γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance