2P5G

Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.240 

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


Literature

Caught bending the a-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide.

Zahn, K.E., Belrhali, H., Wallace, S.S., Doublie, S.

(2007) Biochemistry 46: 10551-10561

  • DOI: https://doi.org/10.1021/bi7008807
  • Primary Citation of Related Structures:  
    2OYQ, 2OZM, 2OZS, 2P5G

  • PubMed Abstract: 

    • Damage to DNA involving excision of the nucleobase at the N-glycosidic bond forms abasic sites. If a nucleotide becomes incorporated opposite an unrepaired abasic site during DNA synthesis, most B family polymerases obey the A-rule and preferentially incorporate dAMP without instruction from the template ...

    Damage to DNA involving excision of the nucleobase at the N-glycosidic bond forms abasic sites. If a nucleotide becomes incorporated opposite an unrepaired abasic site during DNA synthesis, most B family polymerases obey the A-rule and preferentially incorporate dAMP without instruction from the template. In addition to being potentially mutagenic, abasic sites provide strong blocks to DNA synthesis. A previous crystal structure of an exonuclease deficient variant of the replicative B family DNA polymerase from bacteriophage RB69 (RB69 gp43 exo-) illustrated these properties, showing that the polymerase failed to translocate the DNA following insertion of dAMP opposite an abasic site. We examine four new structures depicting several steps of translesion DNA synthesis by RB69 gp43 exo-, employing a non-natural purine triphosphate analogue, 5-nitro-1-indolyl-2'-deoxyriboside-5'-triphosphate (5-NITP), that is incorporated more efficiently than dAMP opposite abasic sites. Our structures indicate that a dipole-induced dipole stacking interaction between the 5-nitro group and base 3' to the templating lesion explains the enhanced kinetics of 5-NITP. As with dAMP, the DNA fails to translocate following insertion of 5-NIMP, although distortions at the nascent primer terminus contribute less than previously thought in inducing the stall, given that 5-NIMP preserves relatively undistorted geometry at the insertion site following phosphoryl transfer. An open ternary configuration, novel in B family polymerases, reveals an initial template independent binding of 5-NITP adjacent to the active site of the open polymerase, suggesting that closure of the fingers domain shuttles the nucleotide to the active site while testing the substrate against the template.

    Organizational Affiliation: 

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



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseI [auth A],
J [auth B],
K [auth C],
L [auth D]		903Escherichia phage RB69Mutation(s): 2 
Gene Names: 43
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
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: 1
MoleculeChainsLengthOrganismImage
Template DNAA [auth E],
C [auth G],
E [auth I],
G [auth K]		21N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
Primer DNAB [auth F],
D [auth H],
F [auth J],
H [auth L]		15N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		I [auth A],
J [auth B],
K [auth C],
L [auth D]		L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.628α = 90
b = 122.272β = 96.45
c = 163.871γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description