3U7G

Crystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA (TCCTAp)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates.

Coquelle, N.Havali-Shahriari, Z.Bernstein, N.Green, R.Glover, J.N.

(2011) Proc.Natl.Acad.Sci.USA 108: 21022-21027

  • DOI: 10.1073/pnas.1112036108
  • Primary Citation of Related Structures:  3U7E, 3U7F, 3U7H

  • PubMed Abstract: 
  • Polynucleotide kinase/phosphatase (PNKP) is a critical mammalian DNA repair enzyme that generates 5'-phosphate and 3'-hydroxyl groups at damaged DNA termini that are required for subsequent processing by DNA ligases and polymerases. The PNKP phosphat ...

    Polynucleotide kinase/phosphatase (PNKP) is a critical mammalian DNA repair enzyme that generates 5'-phosphate and 3'-hydroxyl groups at damaged DNA termini that are required for subsequent processing by DNA ligases and polymerases. The PNKP phosphatase domain recognizes 3'-phosphate termini within DNA nicks, gaps, or at double- or single-strand breaks. Here we present a mechanistic rationale for the recognition of damaged DNA termini by the PNKP phosphatase domain. The crystal structures of PNKP bound to single-stranded DNA substrates reveals a narrow active site cleft that accommodates a single-stranded substrate in a sequence-independent manner. Biochemical studies suggest that the terminal base pairs of double-stranded substrates near the 3'-phosphate are destabilized by PNKP to allow substrate access to the active site. A positively charged surface distinct from the active site specifically facilitates interactions with double-stranded substrates, providing a complex DNA binding surface that enables the recognition of diverse substrates.


    Related Citations: 
    • The molecular architecture of the mammalian DNA repair enzyme, polynucleotide kinase.
      Bernstein, N.K.,Williams, R.S.,Rakovszky, M.L.,Cui, D.,Green, R.,Karimi-Busheri, F.,Mani, R.S.,Galicia, S.,Koch, C.A.,Cass, C.E.,Durocher, D.,Weinfeld, M.,Glover, J.N.
      (2005) Mol.Cell 17: 657


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional polynucleotide phosphatase/kinase
A
379Mus musculusGene Names: Pnkp
EC: 3.1.3.32, 2.7.1.78
Find proteins for Q9JLV6 (Mus musculus)
Go to UniProtKB:  Q9JLV6
Entity ID: 2
MoleculeChainsLengthOrganism
DNAX5N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, X
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.160α = 90.00
b = 43.030β = 107.12
c = 127.270γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
Blu-Icedata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-08-29
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description