Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33545.35 
• Atom Count: 2083 
• Residue Count: 248 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1P59

Structure of a non-covalent Endonuclease III-DNA Complex

• DOI: 10.2210/pdb1P59/pdb
• NDB: PD0427

• Classification: HYDROLASE/DNA
• Expression System: Escherichia coli


• Deposited: 2003-04-25 Released: 2003-07-15 
• Deposition Author(s): Fromme, J.C., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.269 
• R-Value Work: 0.214 

Literature

Structure of a Trapped Endonuclease III-DNA Covalent Intermediate

Fromme, J.C., Verdine, G.L.

(2003) Embo J. 22: 3461-3471

• PubMed: 12840008 
• DOI: 10.1093/emboj/cdg311
• Primary Citation of Related Structures:  
  1ORP, 1ORN


• PubMed Abstract: 
  

Nearly all cells express proteins that confer resistance to the mutagenic effects of oxidative DNA damage. The primary defense against the toxicity of oxidative nucleobase lesions in DNA is the base-excision repair (BER) pathway. Endonuclease III (EndoIII) is a [4Fe-4S] cluster-containing DNA glycosylase with repair activity specific for oxidized pyrimidine lesions in duplex DNA. We have determined the crystal structure of a trapped intermediate that represents EndoIII frozen in the act of repairing DNA. The structure of the protein-DNA complex provides insight into the ability of EndoIII to recognize and repair a diverse array of oxidatively damaged bases. This structure also suggests a rationale for the frequent occurrence in certain human cancers of a specific mutation in the related DNA repair protein MYH.

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Organizational Affiliation: 

Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Endonuclease III	A	226	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(*AP*AP*GP*AP*CP*GP*(5IU)P*GP*GP*AP*C)-3'	B	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(TP*GP*(5IU)P*CP*CP*AP*(3DR)P*GP*(5IU)P*CP*T)-3'	C	11	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SF4	A	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3DR	C	DNA LINKING	C5 H11 O6 P		--
5IU	B, C	DNA LINKING	C9 H12 I N2 O8 P		DU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.269 
• R-Value Work: 0.214 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 66.321	α = 90.00
b = 105.896	β = 90.00
c = 41.518	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-25 
• Released Date: 2003-07-15 
• Deposition Author(s): Fromme, J.C., Verdine, G.L.

Revision History 

• Version 1.0: 2003-07-15
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description