8-oxoguanine DNA-glycosylase (Nth/MutY family)

 

The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases. Among these modified bases, 7,8-dihydro-8-oxoguanine (8-oxoG) is an important mutagenic lesion. Base excision repair is a critical mechanism for preventing mutations by removing the oxidative lesion from the DNA. Escherichia coli Nth protein (endonuclease III) has an 8-oxoG DNA glycosylase/AP lyase activity which removes 8-oxoG preferentially from 8-oxoG/G mispairs. Homo sapiens hNTH1 protein, a homologue of Escherichia coli Nth protein, has similar DNA glycosylase/AP lyase activity that removes 8-oxoG from 8-oxoG/G mispairs [PMID:11328882].

 

Reference Protein and Structure

Sequence
P0AB83 UniProt (4.2.99.18) IPR005759 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
2abk - REFINEMENT OF THE NATIVE STRUCTURE OF ENDONUCLEASE III TO A RESOLUTION OF 1.85 ANGSTROM (1.85 Å) PDBe PDBsum 2abk
Catalytic CATH Domains
1.10.1670.10 CATHdb 1.10.340.30 CATHdb (see all for 2abk)
Cofactors
Tetra-mu3-sulfido-tetrairon (1)
Click To Show Structure

Enzyme Reaction (EC:4.2.99.18)

water
CHEBI:15377ChEBI
+
DNA 8-oxoguanine
CHEBI:137052ChEBI
→
DNA with 3-terminal trans-a,b-unsaturated sugar
CHEBI:137051ChEBI
+
DNA 5'-phosphate
CHEBI:4294ChEBI
+
hydron
CHEBI:15378ChEBI
+
7,8-dihydro-8-oxoguanine
CHEBI:52617ChEBI
Alternative enzyme names: E. coli endonuclease III, Micrococcus luteus UV endonuclease, AP endonuclease class I, AP lyase, AP site-DNA 5'-phosphomonoester-lyase, X-ray endonuclease III, Deoxyribonuclease (apurinic or apyrimidinic), Endodeoxyribonuclease (apurinic or apyrimidinic), Phage-T(4) UV endonuclease, Phage-T4 UV endonuclease, E.coli endonuclease III,

Enzyme Mechanism

Introduction

Lys120 forms a Schiff base with the DNA substrate, eliminating the oxoguanine product. The enzyme-substrate intermediate is then broken down by water (activated by Asp138).

Catalytic Residues Roles

UniProt PDB* (2abk)
Lys120 Lys120A Acts as a catalytic nucleophile, forming a Schiff base with the substrate DNA. covalent catalysis
Asp138 Asp138A Thought to act as a general acid/base. proton shuttle (general acid/base)
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Fromme JC et al. (2003), EMBO J, 22, 3461-3471. Structure of a trapped endonuclease III-DNA covalent intermediate. DOI:10.1093/emboj/cdg311. PMID:12840008.
  2. Liu X et al. (2001), Biochemistry, 40, 13617-13622. Mutation at Active Site Lysine 212 to Arginine Uncouples the Glycosylase Activity from the Lyase Activity of Human Endonuclease III†. DOI:10.1021/bi011053b. PMID:11695910.
  3. Matsumoto Y et al. (2001), Nucleic Acids Res, 29, 1975-1981. Escherichia coli Nth and human hNTH1 DNA glycosylases are involved in removal of 8-oxoguanine from 8-oxoguanine/guanine mispairs in DNA. PMID:11328882.
  4. Shekhtman A et al. (1999), Structure, 7, 919-930. Identification of the Archaeoglobus fulgidus endonuclease III DNA interaction surface using heteronuclear NMR methods. DOI:10.1016/s0969-2126(99)80119-1. PMID:10467137.
  5. Thayer MM et al. (1995), EMBO J, 14, 4108-4120. Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. PMID:7664751.
  6. Dodson ML et al. (1994), J Biol Chem, 269, 32709-32712. Unified catalytic mechanism for DNA glycosylases. PMID:7806489.
  7. Kuo CF et al. (1992), Science, 258, 434-440. Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III. DOI:10.2210/pdb1abk/pdb. PMID:1411536.

Step 1.

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Catalytic Residues Roles

Residue Roles
Lys120A covalent catalysis
Asp138A proton shuttle (general acid/base)

Chemical Components

Step 1.

Contributors

Craig Porter, Gemma L. Holliday