3BDP

DNA POLYMERASE I/DNA COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal.

Kiefer, J.R., Mao, C., Braman, J.C., Beese, L.S.

(1998) Nature 391: 304-307

  • DOI: 10.1038/34693
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • DNA polymerases copy DNA templates with remarkably high fidelity, checking for correct base-pair formation both at nucleotide insertion and at subsequent DNA extension steps. Despite extensive biochemical, genetic and structural studies, the mechanis ...

    DNA polymerases copy DNA templates with remarkably high fidelity, checking for correct base-pair formation both at nucleotide insertion and at subsequent DNA extension steps. Despite extensive biochemical, genetic and structural studies, the mechanism by which nucleotides are correctly incorporated is not known. Here we present high-resolution crystal structures of a thermostable bacterial (Bacillus stearothermophilus) DNA polymerase I large fragments with DNA primer templates bound productively at the polymerase active site. The active site retains catalytic activity, allowing direct observation of the products of several rounds of nucleotide incorporation. The polymerase also retains its ability to discriminate between correct and incorrectly paired nucleotides in the crystal. Comparison of the structures of successively translocated complexes allows the structural features for the sequence-independent molecular recognition of correctly formed base pairs to be deduced unambiguously. These include extensive interactions with the first four to five base pairs in the minor groove, location of the terminal base pair in a pocket of excellent steric complementarity favouring correct base-pair formation, and a conformational switch from B-form to underwound A-form DNA at the polymerase active site.

    Related Citations: 
    • Crystal Structure of a Thermostable Bacillus DNA Polymerase I Large Fragment at 2.1 A Resolution
      Kiefer, J.R.,Mao, C.,Hansen, C.J.,Basehore, S.L.,Hogrefe, H.H.,Braman, J.C.,Beese, L.S.
      (1997) Structure 5: 95

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (DNA POLYMERASE I)
A
580Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA (pol)
EC: 2.7.7.7
Find proteins for P52026 (Geobacillus stearothermophilus)
Go to UniProtKB:  P52026
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*AP*TP*GP*AP*TP*GP*CP*2DT)-3')P10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*CP*AP*TP*CP*AP*TP*GP*C)-3')T10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2DT
Query on 2DT
P
DNA LINKINGC10 H15 N2 O7 PDT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.063α = 90.00
b = 93.547β = 90.00
c = 106.252γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance