1P59 | pdb_00001p59

Structure of a non-covalent Endonuclease III-DNA Complex

• PDB DOI: https://doi.org/10.2210/pdb1P59/pdb
• NAKB: 1P59

• Classification: HYDROLASE/DNA
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.50 Å
• R-Value Free: 
  0.269 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1093/emboj/cdg311
• Primary Citation Related Structures: 
  1ORN, 1ORP, 1P59


• 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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.55 kDa 
• Atom Count: 2,114 
• Modeled Residue Count: 235 
• Deposited Residue Count: 248 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease III	C [auth A]	226	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: NTH

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

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.269 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.321	α = 90
b = 105.896	β = 90
c = 41.518	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description