2ABK

REFINEMENT OF THE NATIVE STRUCTURE OF ENDONUCLEASE III TO A RESOLUTION OF 1.85 ANGSTROM

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure.

Thayer, M.M., Ahern, H., Xing, D., Cunningham, R.P., Tainer, J.A.

(1995) EMBO J 14: 4108-4120

  • Primary Citation of Related Structures:  
    2ABK

  • PubMed Abstract: 

    • The 1.85 A crystal structure of endonuclease III, combined with mutational analysis, suggests the structural basis for the DNA binding and catalytic activity of the enzyme. Helix-hairpin-helix (HhH) and [4Fe-4S] cluster loop (FCL) motifs, which we ha ...

    The 1.85 A crystal structure of endonuclease III, combined with mutational analysis, suggests the structural basis for the DNA binding and catalytic activity of the enzyme. Helix-hairpin-helix (HhH) and [4Fe-4S] cluster loop (FCL) motifs, which we have named for their secondary structure, bracket the cleft separating the two alpha-helical domains of the enzyme. These two novel DNA binding motifs and the solvent-filled pocket in the cleft between them all lie within a positively charged and sequence-conserved surface region. Lys120 and Asp138, both shown by mutagenesis to be catalytically important, lie at the mouth of this pocket, suggesting that this pocket is part of the active site. The positions of the HhH motif and protruding FCL motif, which contains the DNA binding residue Lys191, can accommodate B-form DNA, with a flipped-out base bound within the active site pocket. The identification of HhH and FCL sequence patterns in other DNA binding proteins suggests that these motifs may be a recurrent structural theme for DNA binding proteins.

    Related Citations: 
    • Crystallization and Crystallographic Characterization of the Iron-Sulfur Containing DNA-Repair Enzyme Endonuclease III from Escherichia Coli Enzyme Endonuclease III
      Kuo, C.-F., Mcree, D.E., Cunningham, R.P., Tainer, J.A.
      (1992) J Mol Biol 227: 347
    • Atomic Structure of the DNA Repair [4Fe-4S] Enzyme Endonuclease III
      Kuo, C.-F., Mcree, D.E., Fisher, C.L., Handley, S., Cunningham, R.P., Tainer, J.A.
      (1992) Science 258: 434
    Organizational Affiliation: 

    Scripps Research Institute, Department of Molecular Biology-MB4, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDONUCLEASE IIIA211Escherichia coliMutation(s): 0 
EC: 4.2.99.18
Find proteins for P0AB83 (Escherichia coli (strain K12))
Explore P0AB83 
Go to UniProtKB:  P0AB83
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.5α = 90
b = 65.8β = 90
c = 86.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other