1KLN

DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of DNA polymerase I Klenow fragment bound to duplex DNA.

Beese, L.S.Derbyshire, V.Steitz, T.A.

(1993) Science 260: 352-355


  • PubMed Abstract: 
  • Klenow fragment of Escherichia coli DNA polymerase I, which was cocrystallized with duplex DNA, positioned 11 base pairs of DNA in a groove that lies at right angles to the cleft that contains the polymerase active site and is adjacent to the 3' to 5 ...

    Klenow fragment of Escherichia coli DNA polymerase I, which was cocrystallized with duplex DNA, positioned 11 base pairs of DNA in a groove that lies at right angles to the cleft that contains the polymerase active site and is adjacent to the 3' to 5' exonuclease domain. When the fragment bound DNA, a region previously referred to as the "disordered domain" became more ordered and moved along with two helices toward the 3' to 5' exonuclease domain to form the binding groove. A single-stranded, 3' extension of three nucleotides bound to the 3' to 5' exonuclease active site. Although this cocrystal structure appears to be an editing complex, it suggests that the primer strand approaches the catalytic site of the polymerase from the direction of the 3' to 5' exonuclease domain and that the duplex DNA product may bend to enter the cleft that contains the polymerase catalytic site.


    Related Citations: 
    • Co-Crystal Structure of an Editing Complex of Klenow Fragment with DNA
      Freemont, P.S.,Friedman, J.M.,Beese, L.S.,Steitz, T.A.
      (1988) Proc.Natl.Acad.Sci.USA 85: 8924
    • Structure of Large Fragment of Escherichia Coli DNA Polymerase I Complexed with dTMP
      Ollis, D.L.,Brick, P.,Hamlin, R.,Xuong, N.G.,Steitz, T.A.
      (1985) Nature 313: 762
    • Structural Basis for the 3'-5' Exonuclease Activity of Escherichia Coli DNA Polymerase I: A Two Metal Ion Mechanism
      Beese, L.S.,Steitz, T.A.
      (1991) Embo J. 10: 25


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7))
A
605Escherichia coli (strain K12)Gene Names: polA (resA)
EC: 2.7.7.7
Find proteins for P00582 (Escherichia coli (strain K12))
Go to UniProtKB:  P00582
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*TP*CP*GP*CP*GP*GP*CP*GP*GP*C)-3')B13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*GP*CP*GP*AP*GP*GP*C)-3')C10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Work: 0.230 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 104.300α = 90.00
b = 104.300β = 90.00
c = 86.000γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-11-30
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance