1QUM

CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV IN COMPLEX WITH DAMAGED DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis.

Hosfield, D.J.Guan, Y.Haas, B.J.Cunningham, R.P.Tainer, J.A.

(1999) Cell 98: 397-408

  • Primary Citation of Related Structures:  1QTW

  • PubMed Abstract: 
  • Endonuclease IV is the archetype for a conserved apurinic/apyrimidinic (AP) endonuclease family that primes DNA repair synthesis by cleaving the DNA backbone 5' of AP sites. The crystal structures of Endonuclease IV and its AP-DNA complex at 1.02 and ...

    Endonuclease IV is the archetype for a conserved apurinic/apyrimidinic (AP) endonuclease family that primes DNA repair synthesis by cleaving the DNA backbone 5' of AP sites. The crystal structures of Endonuclease IV and its AP-DNA complex at 1.02 and 1.55 A resolution reveal how an alpha8beta8 TIM barrel fold can bind dsDNA. Enzyme loops intercalate side chains at the abasic site, compress the DNA backbone, bend the DNA approximately 90 degrees, and promote double-nucleotide flipping to sequester the extrahelical AP site in an enzyme pocket that excludes undamaged nucleotides. These structures suggest three Zn2+ ions directly participate in phosphodiester bond cleavage and prompt hypotheses that double-nucleotide flipping and sharp bending by AP endonucleases provide exquisite damage specificity while aiding subsequent base excision repair pathway progression.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ENDONUCLEASE IV
A
285Escherichia coli (strain K12)Gene Names: nfo
EC: 3.1.21.2
Find proteins for P0A6C1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6C1
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*TP*CP*C)-3'B6N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*(3DR)P*CP*GP*AP*CP*GP*A)-3'C7N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*G)-3'D13N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
3DR
Query on 3DR
C
DNA LINKINGC5 H11 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 133.120α = 90.00
b = 58.727β = 94.97
c = 51.146γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description