2O3C

Crystal structure of zebrafish Ape


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease

Georgiadis, M.M.Luo, M.Gaur, R.K.Delaplane, S.Li, X.Kelley, M.R.

(2008) Mutat.Res. 643: 54-63

  • DOI: 10.1016/j.mrfmmm.2008.04.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human apurinic/apyrimidinic endonuclease (hApe1) encodes two important functional activities: an essential base excision repair (BER) activity and a redox activity that regulates expression of a number of genes through reduction of their transcriptio ...

    Human apurinic/apyrimidinic endonuclease (hApe1) encodes two important functional activities: an essential base excision repair (BER) activity and a redox activity that regulates expression of a number of genes through reduction of their transcription factors, AP-1, NFkappaB, HIF-1alpha, CREB, p53 and others. The BER function is highly conserved from prokaryotes (E. coli exonuclease III) to humans (hApe1). Here, we provide evidence supporting a redox function unique to mammalian Apes. An evolutionary analysis of Ape sequences reveals that, of the 7 Cys residues, Cys 93, 99, 208, 296, and 310 are conserved in both mammalian and non-mammalian vertebrate Apes, while Cys 65 is unique to mammalian Apes. In the zebrafish Ape (zApe), selected as the vertebrate sequence most distant from human, the residue equivalent to Cys 65 is Thr 58. The wild-type zApe enzyme was tested for redox activity in both in vitro EMSA and transactivation assays and found to be inactive, similar to C65A hApe1. Substitution of Thr 58 with Cys in zApe, however, resulted in a redox active enzyme, suggesting that a Cys residue in this position is indeed critical for redox function. In order to further probe differences between redox active and inactive enzymes, we have determined the crystal structures of vertebrate redox inactive enzymes, the C65A human Ape1 enzyme and the zApe enzyme at 1.9 and 2.3A, respectively. Our results provide new insights on the redox function and highlight a dramatic gain-of-function activity for Ape1 in mammals not found in non-mammalian vertebrates or lower organisms.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202-5122, United States. mgeorgia@iupui.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APEX nuclease 1
A, B, C
282Danio rerioMutation(s): 0 
Gene Names: apex1 (apex1a, apex1b)
EC: 3.1.-.-, 4.2.99.18
Find proteins for A0MTA1 (Danio rerio)
Go to UniProtKB:  A0MTA1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PB
Query on PB

Download SDF File 
Download CCD File 
A, B, C
LEAD (II) ION
Pb
RVPVRDXYQKGNMQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.660α = 90.00
b = 117.780β = 98.34
c = 85.840γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
MOLREPphasing
CNSrefinement
JBluIce-EPICSdata collection
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description