Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.95 kDa 
• Atom Count: 1798 
• Modelled Residue Count: 211 
• Deposited Residue Count: 211 
• Unique protein chains: 1

2ABK

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

• DOI: 10.2210/pdb2ABK/pdb
• Entry: 2ABK supersedes: 1ABK

• Classification: ENDONUCLEASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1995-05-11 Released: 1995-10-15 
• Deposition Author(s): Thayer, M.M., Tainer, J.A.

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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 

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

• PubMed: 7664751 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDONUCLEASE III	A	211	Escherichia coli	Mutation(s): 0  EC: 4.2.99.18
Find proteins for P0AB83 (Escherichia coli (strain K12)) Explore P0AB83  Go to UniProtKB:  P0AB83

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC

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 = 48.5	α = 90
b = 65.8	β = 90
c = 86.8	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XENGEN	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-05-11 
• Released Date: 1995-10-15 
Deposition Author(s): Thayer, M.M., Tainer, J.A.
• This entry supersedes: 1ABK

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