3SZQ

Structure of an S. pombe APTX/DNA/AMP/Zn complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.353 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of an aprataxin-DNA complex with insights into AOA1 neurodegenerative disease.

Tumbale, P.Appel, C.D.Kraehenbuehl, R.Robertson, P.D.Williams, J.S.Krahn, J.Ahel, I.Williams, R.S.

(2011) Nat.Struct.Mol.Biol. 18: 1189-1195

  • DOI: 10.1038/nsmb.2146

  • PubMed Abstract: 
  • DNA ligases finalize DNA replication and repair through DNA nick-sealing reactions that can abort to generate cytotoxic 5'-adenylation DNA damage. Aprataxin (Aptx) catalyzes direct reversal of 5'-adenylate adducts to protect genome integrity. Here th ...

    DNA ligases finalize DNA replication and repair through DNA nick-sealing reactions that can abort to generate cytotoxic 5'-adenylation DNA damage. Aprataxin (Aptx) catalyzes direct reversal of 5'-adenylate adducts to protect genome integrity. Here the structure of a Schizosaccharomyces pombe Aptx-DNA-AMP-Zn(2+) complex reveals active site and DNA interaction clefts formed by fusing a histidine triad (HIT) nucleotide hydrolase with a DNA minor groove-binding C(2)HE zinc finger (Znf). An Aptx helical 'wedge' interrogates the base stack for sensing DNA ends or DNA nicks. The HIT-Znf, the wedge and an '[F/Y]PK' pivot motif cooperate to distort terminal DNA base-pairing and direct 5'-adenylate into the active site pocket. Structural and mutational data support a wedge-pivot-cut HIT-Znf catalytic mechanism for 5'-adenylate adduct recognition and removal and suggest that mutations affecting protein folding, the active site pocket and the pivot motif underlie Aptx dysfunction in the neurodegenerative disorder ataxia with oculomotor apraxia 1 (AOA1).


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, North Carolina, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aprataxin-like protein
A
206Schizosaccharomyces pombe (strain 972 / ATCC 24843)Gene Names: hnt3
EC: 3.-.-.-
Find proteins for O74859 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O74859
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*CP*CP*TP*G)-3'B5N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*AP*TP*CP*GP*GP*AP*AP*TP*CP*AP*GP*GP*G)-3'C14N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.353 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 
  • Space Group: I 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 157.050α = 90.00
b = 157.050β = 90.00
c = 157.050γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2011-11-23
    Type: Database references