3PX6

Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (tautomer) in Closed Conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.

Wang, W.Hellinga, H.W.Beese, L.S.

(2011) Proc Natl Acad Sci U S A 108: 17644-17648

  • DOI: https://doi.org/10.1073/pnas.1114496108
  • Primary Citation of Related Structures:  
    3PV8, 3PX0, 3PX4, 3PX6, 3TAN, 3TAP, 3TAQ, 3TAR, 3THV, 3TI0

  • PubMed Abstract: 

    Even though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C • A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly.


  • Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase IA,
B [auth D]
592Geobacillus kaustophilusMutation(s): 2 
Gene Names: polAGK2730
EC: 2.7.7.7
UniProt
Find proteins for Q5KWC1 (Geobacillus kaustophilus (strain HTA426))
Explore Q5KWC1 
Go to UniProtKB:  Q5KWC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5KWC1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')C [auth B],
E
9N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*C*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')D [auth C],
F
13N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DCT
Query on DCT

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
L [auth D]
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
C9 H16 N3 O12 P3
ARLKCWCREKRROD-POYBYMJQSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
N [auth D],
O [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MN
Query on MN

Download Ideal Coordinates CCD File 
I [auth A],
M [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.46α = 90
b = 108.28β = 90
c = 149.76γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2011-11-02
    Changes: Database references
  • Version 1.2: 2011-11-09
    Changes: Database references
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description