1DE9

HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination

Mol, C.D.Izumi, T.Mitra, S.Tainer, J.A.

(2000) Nature 403: 451-456

  • DOI: 10.1038/35000249
  • Primary Citation of Related Structures:  1DE8, 1DEW

  • PubMed Abstract: 
  • Non-coding apurinic/apyrimidinic (AP) sites in DNA are continually created in cells both spontaneously and by damage-specific DNA glycosylases. The biologically critical human base excision repair enzyme APE1 cleaves the DNA sugar-phosphate backbone ...

    Non-coding apurinic/apyrimidinic (AP) sites in DNA are continually created in cells both spontaneously and by damage-specific DNA glycosylases. The biologically critical human base excision repair enzyme APE1 cleaves the DNA sugar-phosphate backbone at a position 5' of AP sites to prime DNA repair synthesis. Here we report three co-crystal structures of human APE1 bound to abasic DNA which show that APE1 uses a rigid, pre-formed, positively charged surface to kink the DNA helix and engulf the AP-DNA strand. APE1 inserts loops into both the DNA major and minor grooves and binds a flipped-out AP site in a pocket that excludes DNA bases and racemized beta-anomer AP sites. Both the APE1 active-site geometry and a complex with cleaved AP-DNA and Mn2+ support a testable structure-based catalytic mechanism. Alanine substitutions of the residues that penetrate the DNA helix unexpectedly show that human APE1 is structurally optimized to retain the cleaved DNA product. These structural and mutational results show how APE1 probably displaces bound glycosylases and retains the nicked DNA product, suggesting that APE1 acts in vivo to coordinate the orderly transfer of unstable DNA damage intermediates between the excision and synthesis steps of DNA repair.


    Organizational Affiliation

    Skaggs Institute for Chemical Biology, and the Department of Molecular Biology, La Jolla, California 92037-1027, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE
A, B
276Homo sapiensGene 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: 1
MoleculeChainsLengthOrganism
5'-d(*CP*TP*AP*C)-3'X,U4N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-d(P*(3DR)P*GP*AP*TP*C)-3'Y,V5N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3'Z,W9N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
V, Y
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 90.060α = 90.00
b = 98.350β = 90.00
c = 101.050γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance