4DQQ

Ternary complex of Bacillus DNA Polymerase I Large Fragment E658A, DNA duplex, and rCTP (paired with dG of template) in presence of Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.595 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides.

Wang, W.Wu, E.Y.Hellinga, H.W.Beese, L.S.

(2012) J.Biol.Chem. 287: 28215-28226

  • DOI: 10.1074/jbc.M112.366609
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In addition to discriminating against base pair mismatches, DNA polymerases exhibit a high degree of selectivity for deoxyribonucleotides over ribo- or dideoxynucleotides. It has been proposed that a single active site residue (steric gate) blocks pr ...

    In addition to discriminating against base pair mismatches, DNA polymerases exhibit a high degree of selectivity for deoxyribonucleotides over ribo- or dideoxynucleotides. It has been proposed that a single active site residue (steric gate) blocks productive binding of nucleotides containing 2'-hydroxyls. Although this steric gate plays a role in sugar moiety discrimination, its interactions do not account fully for the observed behavior of mutants. Here we present 10 high resolution crystal structures and enzyme kinetic analyses of Bacillus DNA polymerase I large fragment variants complexed with deoxy-, ribo-, and dideoxynucleotides and a DNA substrate. Taken together, these data present a more nuanced and general mechanism for nucleotide discrimination in which ensembles of intermediate conformations in the active site trap non-cognate substrates. It is known that the active site O-helix transitions from an open state in the absence of nucleotide substrates to a ternary complex closed state in which the reactive groups are aligned for catalysis. Substrate misalignment in the closed state plays a fundamental part in preventing non-cognate nucleotide misincorpation. The structures presented here show that additional O-helix conformations intermediate between the open and closed state extremes create an ensemble of binding sites that trap and misalign non-cognate nucleotides. Water-mediated interactions, absent in the fully closed state, play an important role in formation of these binding sites and can be remodeled to accommodate different non-cognate substrates. This mechanism may extend also to base pair discrimination.


    Related Citations: 
    • Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.
      Wang, W.,Hellinga, H.W.,Beese, L.S.
      (2011) Proc.Natl.Acad.Sci.USA 108: 17644


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase
A, D
592Geobacillus kaustophilus (strain HTA426)Mutation(s): 2 
Gene Names: polA
EC: 2.7.7.7
Find proteins for Q5KWC1 (Geobacillus kaustophilus (strain HTA426))
Go to UniProtKB:  Q5KWC1
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3')B,E9N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3')C,F13N/A
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CTP
Query on CTP

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Download CCD File 
A, D
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A, D
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
B, E
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.595 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 93.540α = 90.00
b = 107.970β = 90.00
c = 149.880γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-02-16 
  • Released Date: 2012-06-06 
  • Deposition Author(s): Wang, W., Beese, L.S.

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2012-06-13
    Type: Database references
  • Version 1.2: 2012-11-21
    Type: Database references