3UXP

Co-crystal Structure of Rat DNA polymerase beta Mutator I260Q: Enzyme-DNA-ddTTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.723 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Changes in the Hydrophobic Hinge Region Adversely Affect the Activity and Fidelity of the I260Q Mutator DNA Polymerase beta.

Gridley, C.L.Rangarajan, S.Firbank, S.Dalal, S.Sweasy, J.B.Jaeger, J.

(2013) Biochemistry 52: 4422-4432

  • DOI: 10.1021/bi301368f
  • Primary Citation of Related Structures:  3UXN, 3UXO

  • PubMed Abstract: 
  • The I260Q variant of DNA polymerase β is an efficient mutator polymerase with fairly indiscriminate misincorporation activities opposite all template bases. Previous modeling studies have suggested that I260Q harbors structural variations in its hing ...

    The I260Q variant of DNA polymerase β is an efficient mutator polymerase with fairly indiscriminate misincorporation activities opposite all template bases. Previous modeling studies have suggested that I260Q harbors structural variations in its hinge region. Here, we present the crystal structures of wild type and I260Q rat polymerase β in the presence and absence of substrates. Both the I260Q apoenzyme structure and the closed ternary complex with double-stranded DNA and ddTTP show ordered water molecules in the hydrophobic hinge near Gln260, whereas this is not the case in the wild type polymerase. Compared to wild type polymerase β ternary complexes, there are subtle movements around residues 260, 272, 295, and 296 in the mutant. The rearrangements in this region, coupled with side chain movements in the immediate neighborhood of the dNTP-binding pocket, namely, residues 258 and 272, provide an explanation for the altered activity and fidelity profiles observed in the I260Q mutator polymerase.


    Organizational Affiliation

    Division of Genetics, Wadsworth Center, New York State Department of Health, New Scotland Avenue, Albany, New York 12208, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase beta
A, B
335Rattus norvegicusGene Names: Polb
EC: 2.7.7.7, 4.2.99.-
Find proteins for P06766 (Rattus norvegicus)
Go to UniProtKB:  P06766
Entity ID: 2
MoleculeChainsLengthOrganism
DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3'P,D7N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3'T,E9N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
D3T
Query on D3T

Download SDF File 
Download CCD File 
A, B
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O13 P3
URGJWIFLBWJRMF-JGVFFNPUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.723 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 100.321α = 90.00
b = 56.607β = 102.04
c = 93.144γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references