3U7E | pdb_00003u7e

Crystal structure of mPNKP catalytic fragment (D170A)

• PDB DOI: https://doi.org/10.2210/pdb3U7E/pdb

• Classification: HYDROLASE,TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-10-13 Released: 2011-12-14 
• Deposition Author(s): Coquelle, N., Havali, Z., Bernstein, N., Green, R., Glover, J.N.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.195 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

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 U S A 108: 21022-21027

• PubMed: 22171004 
• DOI: https://doi.org/10.1073/pnas.1112036108
• Primary Citation Related Structures: 
  3U7E, 3U7F, 3U7G, 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 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.

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Organizational Affiliation: 
• Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.96 kDa 
• Atom Count: 3,489 
• Modeled Residue Count: 380 
• Deposited Residue Count: 381 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional polynucleotide phosphatase/kinase	A [auth B]	381	Mus musculus	Mutation(s): 1  Gene Names: Pnkp EC: 3.1.3.32 (PDB Primary Data), 2.7.1.78 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9JLV6 (Mus musculus) Explore Q9JLV6  Go to UniProtKB:  Q9JLV6
IMPC:  MGI:1891698

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth B], E [auth B], F [auth B], G [auth B], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A [auth B]	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
MSE	A [auth B]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.195 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.82	α = 90
b = 63.19	β = 88.23
c = 68.12	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MxDC	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-14 
Deposition Author(s): Coquelle, N., Havali, Z., Bernstein, N., Green, R., Glover, J.N.M.

Revision History  

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2012-08-29
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Database references, Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary