1S9F

DPO with AT matched


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dpo4 is hindered in extending a G.T mismatch by a reverse wobble

Trincao, J.Johnson, R.E.Wolfle, W.T.Escalante, C.R.Prakash, S.Prakash, L.Aggarwal, A.K.

(2004) Nat.Struct.Mol.Biol. 11: 457-462

  • DOI: 10.1038/nsmb755
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ability or inability of a DNA polymerase to extend a mispair directly affects the establishment of genomic mutations. We report here kinetic analyses of the ability of Dpo4, a Y-family polymerase from Sulfolobus solfataricus, to extend from all m ...

    The ability or inability of a DNA polymerase to extend a mispair directly affects the establishment of genomic mutations. We report here kinetic analyses of the ability of Dpo4, a Y-family polymerase from Sulfolobus solfataricus, to extend from all mispairs opposite a template G or T. Dpo4 is equally inefficient at extending these mispairs, which include, surprisingly, a G.T mispair expected to conform closely to Watson-Crick geometry. To elucidate the basis of this, we solved the structure of Dpo4 bound to G.T-mispaired primer template in the presence of an incoming nucleotide. As a control, we also determined the structure of Dpo4 bound to a matched A-T base pair at the primer terminus. The structures offer a basis for the low efficiency of Dpo4 in extending a G.T mispair: a reverse wobble that deflects the primer 3'-OH away from the incoming nucleotide.


    Organizational Affiliation

    Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, New York 10029, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase IV
A, B, C, D
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: 1
MoleculeChainsLengthOrganism
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3'E,F,G,H13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*T*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'I,J,K,L18N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DDY
Query on DDY

Download SDF File 
Download CCD File 
A, B, C, D
2',3'-DIDEOXYCYTOSINE-5'-DIPHOSPHATE
DDCDP
C9 H15 N3 O9 P2
FVSQWXITYSICAK-POYBYMJQSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 104.800α = 90.00
b = 100.300β = 95.20
c = 110.800γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance