5DG0

Human APE1 phosphorothioate substrate complex with Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Capturing snapshots of APE1 processing DNA damage.

Freudenthal, B.D.Beard, W.A.Cuneo, M.J.Dyrkheeva, N.S.Wilson, S.H.

(2015) Nat Struct Mol Biol 22: 924-931

  • DOI: 10.1038/nsmb.3105
  • Primary Citation of Related Structures:  
    5DG0, 5DFH, 5DFJ, 5DFI, 5DFF

  • PubMed Abstract: 
  • DNA apurinic-apyrimidinic (AP) sites are prevalent noncoding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA-repair intermediate that is potentially cytoto ...

    DNA apurinic-apyrimidinic (AP) sites are prevalent noncoding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA-repair intermediate that is potentially cytotoxic. The molecular events of the incision reaction remain elusive, owing in part to limited structural information. We report multiple high-resolution human APE1-DNA structures that divulge new features of the APE1 reaction, including the metal-binding site, the nucleophile and the arginine clamps that mediate product release. We also report APE1-DNA structures with a T-G mismatch 5' to the AP site, representing a clustered lesion occurring in methylated CpG dinucleotides. These structures reveal that APE1 molds the T-G mismatch into a unique Watson-Crick-like geometry that distorts the active site, thus reducing incision. These snapshots provide mechanistic clarity for APE1 while affording a rational framework to manipulate biological responses to DNA damage.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Research Triangle Park, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-(apurinic or apyrimidinic site) lyaseAB276Homo sapiensMutation(s): 0 
Gene Names: APEX1APEAPE1APEXAPXHAP1REF1
EC: 3.1 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
Find proteins for P27695 (Homo sapiens)
Explore P27695 
Go to UniProtKB:  P27695
NIH Common Fund Data Resources
PHAROS  P27695
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(OMC)P*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')P21synthetic construct
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

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

Download CCD File 
A, B, P
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.365α = 83.12
b = 60.601β = 80.68
c = 73.316γ = 89.04
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

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 States--

Revision History 

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-10-28
    Changes: Database references
  • Version 1.2: 2015-12-02
    Changes: Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence, Derived calculations