3HT3

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus V713P mutant bound to G:dCTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism.

Wu, E.Y.Beese, L.S.

(2011) J.Biol.Chem. 286: 19758-19767

  • DOI: 10.1074/jbc.M110.191130
  • Primary Citation of Related Structures:  3HP6, 3HPO

  • PubMed Abstract: 
  • To achieve accurate DNA synthesis, DNA polymerases must rapidly sample and discriminate against incorrect nucleotides. Here we report the crystal structure of a high fidelity DNA polymerase I bound to DNA primer-template caught in the act of binding ...

    To achieve accurate DNA synthesis, DNA polymerases must rapidly sample and discriminate against incorrect nucleotides. Here we report the crystal structure of a high fidelity DNA polymerase I bound to DNA primer-template caught in the act of binding a mismatched (dG:dTTP) nucleoside triphosphate. The polymerase adopts a conformation in between the previously established "open" and "closed" states. In this "ajar" conformation, the template base has moved into the insertion site but misaligns an incorrect nucleotide relative to the primer terminus. The displacement of a conserved active site tyrosine in the insertion site by the template base is accommodated by a distinctive kink in the polymerase O helix, resulting in a partially open ternary complex. We suggest that the ajar conformation allows the template to probe incoming nucleotides for complementarity before closure of the enzyme around the substrate. Based on solution fluorescence, kinetics, and crystallographic analyses of wild-type and mutant polymerases reported here, we present a three-state reaction pathway in which nucleotides either pass through this intermediate conformation to the closed conformation and catalysis or are misaligned within the intermediate, leading to destabilization of the closed conformation.


    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 I, large fragment
A, D
579Geobacillus stearothermophilusGene Names: DPO1
EC: 2.7.7.7
Find proteins for D9N168 (Geobacillus stearothermophilus)
Go to UniProtKB:  D9N168
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3'B,E9N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*CP*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3'C,F12N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

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A, D
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
SO4
Query on SO4

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D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DCP
Query on DCP

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A, D
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O13 P3
RGWHQCVHVJXOKC-SHYZEUOFSA-N
 Ligand Interaction
MG
Query on MG

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A, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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: 1.7 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 93.280α = 90.00
b = 108.790β = 90.00
c = 152.090γ = 90.00
Software Package:
Software NamePurpose
SERGUIdata collection
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
REFMACphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2009-06-11 
  • Released Date: 2010-07-14 
  • Deposition Author(s): Wu, E.Y., Beese, L.S.

Revision History 

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description