1KFD

CRYSTAL STRUCTURES OF THE KLENOW FRAGMENT OF DNA POLYMERASE I COMPLEXED WITH DEOXYNUCLEOSIDE TRIPHOSPHATE AND PYROPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate.

Beese, L.S.Friedman, J.M.Steitz, T.A.

(1993) Biochemistry 32: 14095-14101


  • PubMed Abstract: 
  • Crystal structures of the Klenow fragment (KF) of DNA polymerase I from Escherichia coli complexed with deoxynucleoside triphosphate (dNTP) or with pyrophosphate (PPi) determined to 3.9-A resolution by X-ray crystallography show these molecules bindi ...

    Crystal structures of the Klenow fragment (KF) of DNA polymerase I from Escherichia coli complexed with deoxynucleoside triphosphate (dNTP) or with pyrophosphate (PPi) determined to 3.9-A resolution by X-ray crystallography show these molecules binding within the cleft of the polymerase domain and surrounded by residues previously implicated in dNTP binding. The dNTP binds adjacent to the O-helix [Ollis, D. L., Brick, P., Hamlin, R., Xuong, N. G., & Steitz, T. A. (1985a) Nature 313, 762-766] with its triphosphate moiety anchored by three positively charged residues, Arg 754, Arg 682, and Lys 758, plus His 734 and Gln 708. The dNTP binding site observed in the crystal is consistent with the results of chemical modification including cross-linking and is also near many of the amino acid residues whose mutation affects catalysis [Polesky, A. H., Steitz, T. A., Grindley, N. D. F., & Joyce, C. M. (1990) J. Biol. Chem. 265, 14579-14591; Polesky, A. H., Dahlberg, M. E., Benkovic, S. J., Grindley, N. D. F., & Joyce, C. M. (1992) J. Biol. Chem. 267, 8417-8428]. However, we conclude that the position of at least the dNMP moiety of dNTP in the binary complex is not likely to be the same as in its catalytically relevant complex with primer-template DNA.


    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 DNA Polymerase I Klenow Fragment Bound to Duplex DNA
      Beese, L.S.,Derbyshire, V.,Steitz, T.A.
      (1993) Science 260: 352
    • 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 E. Coli DNA Polymerase F: A Two Metal Ion Mechanism
      Beese, L.S.,Steitz, T.A.
      (1991) Embo J. 10: 25


    Organizational Affiliation

    Department of Molecular Biophysics, Yale University, New Haven, Connecticut 06511.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE I KLENOW FRAGMENT
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CTP
Query on CTP

Download SDF File 
Download CCD File 
A
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.9 Å
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 104.300α = 90.00
b = 104.300β = 90.00
c = 86.000γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance