6P94

Human APE1 C65A AP-endonuclease product complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance.

McNeill, D.R.Whitaker, A.M.Stark, W.J.Illuzzi, J.L.McKinnon, P.J.Freudenthal, B.D.Wilson, D.M.

(2019) Mutagenesis --: --

  • DOI: 10.1093/mutage/gez046
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA is susceptible to a range of chemical modifications, with one of the most frequent lesions being apurinic/apyrimidinic (AP) sites. AP sites arise due to damage-induced (e.g. alkylation) or spontaneous hydrolysis of the N-glycosidic bond that link ...

    DNA is susceptible to a range of chemical modifications, with one of the most frequent lesions being apurinic/apyrimidinic (AP) sites. AP sites arise due to damage-induced (e.g. alkylation) or spontaneous hydrolysis of the N-glycosidic bond that links the base to the sugar moiety of the phosphodiester backbone, or through the enzymatic activity of DNA glycosylases, which release inappropriate bases as part of the base excision repair (BER) response. Unrepaired AP sites, which lack instructional information, have the potential to cause mutagenesis or to arrest progressing DNA or RNA polymerases, potentially causing outcomes such as cellular transformation, senescence or death. The predominant enzyme in humans responsible for repairing AP lesions is AP endonuclease 1 (APE1). Besides being a powerful AP endonuclease, APE1 possesses additional DNA repair activities, such as 3'-5' exonuclease, 3'-phophodiesterase and nucleotide incision repair. In addition, APE1 has been shown to stimulate the DNA-binding activity of a number of transcription factors through its 'REF1' function, thereby regulating gene expression. In this article, we review the structural and biochemical features of this multifunctional protein, while reporting on new structures of the APE1 variants Cys65Ala and Lys98Ala. Using a functional complementation approach, we also describe the importance of the repair and REF1 activities in promoting cell survival, including the proposed passing-the-baton coordination in BER. Finally, results are presented indicating a critical role for APE1 nuclease activities in resistance to the genotoxins methyl methanesulphonate and bleomycin, supporting biologically important functions as an AP endonuclease and 3'-phosphodiesterase, respectively.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA.,Food and Drug Administration, Silver Spring, MD, USA.,Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.,Department of Genetics and Tumor Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-(apurinic or apyrimidinic site) lyase
A, B
276Homo sapiensMutation(s): 0 
Gene Names: APEX1 (APE, APE1, APEX, APX, HAP1, REF1)
EC: 3.1.-.-, 4.2.99.18
Find proteins for P27695 (Homo sapiens)
Go to Gene View: APEX1
Go to UniProtKB:  P27695
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')D11synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')P10synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')V21synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
D
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.186 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 43.585α = 83.69
b = 60.459β = 79.47
c = 71.924γ = 88.74
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXphasing
PHENIXrefinement
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-01
    Type: Initial release