3LDS

Crystal structure of RB69 gp43 with DNA and dATP opposite 8-oxoG

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

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This is version 1.4 of the entry. See complete history. 


Literature

Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69.

Hogg, M., Rudnicki, J., Midkiff, J., Reha-Krantz, L., Doublie, S., Wallace, S.S.

(2010) Biochemistry 49: 2317-2325

  • DOI: https://doi.org/10.1021/bi901488d
  • Primary Citation of Related Structures:  
    3LDS

  • PubMed Abstract: 

    • The fidelity of DNA replication is under constant threat from the formation of lesions within the genome. Oxidation of DNA bases leads to the formation of altered DNA bases such as 8-oxo-7,8-dihydroguanine, commonly called 8-oxoG, and 2-hydroxyadenine, or 2-OHA ...

    The fidelity of DNA replication is under constant threat from the formation of lesions within the genome. Oxidation of DNA bases leads to the formation of altered DNA bases such as 8-oxo-7,8-dihydroguanine, commonly called 8-oxoG, and 2-hydroxyadenine, or 2-OHA. In this work we have examined the incorporation kinetics opposite these two oxidatively derived lesions as well as an abasic site analogue by the replicative DNA polymerase from bacteriophage RB69. We compared the kinetic parameters for both wild type and the low fidelity L561A variant. While nucleotide incorporation rates (k(pol)) were generally higher for the variant, the presence of a lesion in the templating position reduced the ability of both the wild-type and variant DNA polymerases to form ternary enzyme-DNA-dNTP complexes. Thus, the L561A substitution does not significantly affect the ability of the RB69 DNA polymerase to recognize damaged DNA; instead, the mutation increases the probability that nucleotide incorporation will occur. We have also solved the crystal structure of the L561A variant forming an 8-oxoG.dATP mispair and show that the propensity for forming this mispair depends on an enlarged polymerase active site.

    Organizational Affiliation: 

    Department of Microbiology and Molecular Genetics, 95 Carrigan Drive, University of Vermont, Burlington, Vermont 05405, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed DNA polymerase903Escherichia phage RB69Mutation(s): 3 
Gene Names: 43
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
UniProt
Find proteins for Q38087 (Escherichia phage RB69)
Explore Q38087 
Go to UniProtKB:  Q38087
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38087
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*AP*AP*(DDG))-3')B [auth P]14N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*AP*(8OG)P*CP*TP*TP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')C [auth T]18N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP
Download Ideal Coordinates CCD File 
D [auth A]2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
H [auth P],
I [auth T]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
MN
Query on MN
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.011α = 90
b = 121.002β = 90
c = 128.668γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Advisory, Structure summary
  • Version 1.3: 2021-10-13
    Changes: Advisory, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description