6CVS

Human Aprataxin (Aptx) L248M bound to DNA, AMP and Zn product

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

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This is version 1.3 of the entry. See complete history. 


Literature

Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease.

Tumbale, P., Schellenberg, M.J., Mueller, G.A., Fairweather, E., Watson, M., Little, J.N., Krahn, J., Waddell, I., London, R.E., Williams, R.S.

(2018) EMBO J 37

  • DOI: https://doi.org/10.15252/embj.201798875
  • Primary Citation of Related Structures:  
    6CVO, 6CVP, 6CVQ, 6CVR, 6CVS, 6CVT

  • PubMed Abstract: 

    • The failure of DNA ligases to complete their catalytic reactions generates cytotoxic adenylated DNA strand breaks. The APTX RNA-DNA deadenylase protects genome integrity and corrects abortive DNA ligation arising during ribonucleotide excision repair and base excision DNA repair, and APTX human mutations cause the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1) ...

    The failure of DNA ligases to complete their catalytic reactions generates cytotoxic adenylated DNA strand breaks. The APTX RNA-DNA deadenylase protects genome integrity and corrects abortive DNA ligation arising during ribonucleotide excision repair and base excision DNA repair, and APTX human mutations cause the neurodegenerative disorder ataxia with oculomotor ataxia 1 (AOA1). How APTX senses cognate DNA nicks and is inactivated in AOA1 remains incompletely defined. Here, we report X-ray structures of APTX engaging nicked RNA-DNA substrates that provide direct evidence for a wedge-pivot-cut strategy for 5'-AMP resolution shared with the alternate 5'-AMP processing enzymes POLβ and FEN1. Our results uncover a DNA-induced fit mechanism regulating APTX active site loop conformations and assembly of a catalytically competent active center. Further, based on comprehensive biochemical, X-ray and solution NMR results, we define a complex hierarchy for the differential impacts of the AOA1 mutational spectrum on APTX structure and activity. Sixteen AOA1 variants impact APTX protein stability, one mutation directly alters deadenylation reaction chemistry, and a dominant AOA1 variant unexpectedly allosterically modulates APTX active site conformations.

    Organizational Affiliation: 

    Genome Integrity and Structural Biology Laboratory, Department of Health and Human Services, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, NC, USA williamsrs@niehs.nih.gov.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AprataxinA, B182Homo sapiensMutation(s): 1 
Gene Names: APTX, AXA1
EC: 3.1.11.7 (PDB Primary Data), 3.1.12.2 (PDB Primary Data), 3.6.1.71 (UniProt), 3.6.1.72 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z2E3 (Homo sapiens)
Explore Q7Z2E3 
Go to UniProtKB:  Q7Z2E3
PHAROS:  Q7Z2E3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z2E3
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3')C [auth D],
D [auth E],
E [auth G],
F [auth H]		10Homo sapiens
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP
Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]		ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N		 Ligand Interaction
BME
Query on BME
Download Ideal Coordinates CCD File 
I [auth A],
L [auth B]		BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
H [auth A],
K [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.384α = 90
b = 116.316β = 90
c = 117.559γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1Z01ES102765

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-25
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence