3U7F | pdb_00003u7f

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

PDB DOI: https://doi.org/10.2210/pdb3U7F/pdb
NAKB: 3U7F

Classification: HYDROLASE,TRANSFERASE/DNA
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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.214 (Depositor), 0.208 (DCC)
R-Value Work:
0.169 (Depositor), 0.166 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 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 U S A 108: 21022-21027

PubMed: 22171004 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 44.39 kDa
Atom Count: 3,429
Modeled Residue Count: 381
Deposited Residue Count: 386
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9JLV6
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA	B [auth X]	5	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth X] MOL2 format, chain H [auth B] MOL2 format, chain I [auth X] mmCIF format, chain H [auth B] mmCIF format, chain I [auth X]	H [auth B], I [auth X]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth B] Focus chain I [auth X] Interactions & Density Focus chain H [auth B] Focus chain I [auth X]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain E [auth B] SDF format, chain D [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B]	D [auth B], E [auth B], F [auth B], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.214 (Depositor), 0.208 (DCC)
R-Value Work: 0.169 (Depositor), 0.166 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.6	α = 90
b = 62.33	β = 91.81
c = 67.97	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

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Entry History

Deposition Data

Released Date: 2011-12-14

Deposition Author(s):

Revision History (Full details and data files)

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: Refinement description
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary