6P5C

Bacillus Fragment DNA polymerase mutant I716M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The importance of Ile716 toward the mutagenicity of 8-Oxo-2'-deoxyguanosine with Bacillus fragment DNA polymerase.

Hamm, M.L.Garcia, A.A.Gilbert, R.Johri, M.Ricart, M.Sholes, S.L.Murray-Nerger, L.A.Wu, E.Y.

(2020) DNA Repair (Amst.) 89: 102826-102826

  • DOI: 10.1016/j.dnarep.2020.102826

  • PubMed Abstract: 
  • 8-oxo-2'-deoxyguanosine (OdG) is a prominent DNA lesion that can direct the incorporation of dCTP or dATP during replication. As the latter reaction can lead to mutation, the ratio of dCTP/dATP incorporation can significantly affect the mutagenic pot ...

    8-oxo-2'-deoxyguanosine (OdG) is a prominent DNA lesion that can direct the incorporation of dCTP or dATP during replication. As the latter reaction can lead to mutation, the ratio of dCTP/dATP incorporation can significantly affect the mutagenic potential of OdG. Previous work with the A-family polymerase BF and seven analogues of OdG identified a major groove amino acid, Ile716, which likely influences the dCTP/dATP incorporation ratio opposite OdG. To further probe the importance of this amino acid, dCTP and dATP incorporations opposite the same seven analogues were tested with two BF mutants, I716M and I716A. Results from these studies support the presence of clashing interactions between Ile716 and the C8-oxygen and C2-amine during dCTP and dATP incorporations, respectively. Crystallographic analysis suggests that residue 716 alters the conformation of the template base prior to insertion into the active site, thereby affecting enzymatic efficiency. These results are also consistent with previous work with A-family polymerases, which indicate they have tight, rigid active sites that are sensitive to template perturbations.


    Organizational Affiliation

    Department of Chemistry, University of Richmond, 138 UR Drive, Richmond, VA, 23173, United States.,Department of Biology, University of Richmond, 138 UR Drive, Richmond, VA 23173, United States.,Department of Chemistry, University of Richmond, 138 UR Drive, Richmond, VA, 23173, United States. Electronic address: mhamm@richmond.edu.,Department of Biology, University of Richmond, 138 UR Drive, Richmond, VA 23173, United States. Electronic address: ewu@richmond.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase I
A
581Geobacillus stearothermophilusMutation(s): 1 
Gene Names: DPO1 (polA)
EC: 2.7.7.7
Find proteins for D9N168 (Geobacillus stearothermophilus)
Go to UniProtKB:  D9N168
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*C)-3')B9synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*GP*TP*GP*AP*TP*CP*G)-3')C9synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.217α = 90.00
b = 93.521β = 90.00
c = 105.279γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-05-30 
  • Released Date: 2020-03-25 
  • Deposition Author(s): Wu, E.Y.

Revision History 

  • Version 1.0: 2020-03-25
    Type: Initial release