8-oxoguanine DNA-glycosylase (type-1 OGG1 family)

 

N-glycosylase/DNA lyase; Belongs to the type-1 OGG1 family. This is a DNA repair enzyme that incises DNA at 8-oxoG residues to excise 7,8-dihydro-8-oxoguanine and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine (FAPY) from damaged DNA. Has a beta-lyase activity that nicks DNA 3' to the lesion.

 

Reference Protein and Structure

Sequence
O15527 UniProt (3.2.2.-, 4.2.99.18) IPR004577 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1lwy - hOgg1 Borohydride-Trapped Intermediate without 8-oxoguanine (2.01 Å) PDBe PDBsum 1lwy
Catalytic CATH Domains
1.10.1670.10 CATHdb 1.10.340.30 CATHdb (see all for 1lwy)
Click To Show Structure

Enzyme Reaction (EC:4.2.99.18)

water
CHEBI:15377ChEBI
+
DNA 8-oxoguanine
CHEBI:137052ChEBI
→
7,8-dihydro-8-oxoguanine
CHEBI:52617ChEBI
+
hydron
CHEBI:15378ChEBI
+
DNA with 3-terminal trans-a,b-unsaturated sugar
CHEBI:137051ChEBI
+
DNA 5'-phosphate
CHEBI:4294ChEBI
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

Lys249 attacks the DNA 8-oxoguanine substrate in a nucleophilic substitution reaction that yields enzyme bound DNA and the conjugate base of 8-oxoguanine. Lys249 initiates an intramolecular elimination, cleaving the C-O bond in the DNA ribose ring and resulting in the deprotonation of 8-oxoguanine. The conjugate base of 8-oxoguanine deprotonates the C2 of the open-form ribose. Lys249 initiates an elimination resulting in the loss of the 3' phosphate-end of the DNA from the ribose ring. Water attacks the ribose at the carbon where Lys249 is bound in a nucleophilic addition reaction. The released phosphate deprotonates the hydroxyl group, initiating an elimination of the covalently bound Lys249. Cyclisation of the final DNA with 3-terminal trans-a,b-unsaturated sugar product occurs outside the enzyme active site.

Catalytic Residues Roles

UniProt PDB* (1lwy)
Lys249 Lys249(246)A(C) Acts as a catalytic nucleophile. covalently attached, hydrogen bond donor, nucleofuge, proton acceptor, proton donor, nucleophile, electron pair acceptor, electron pair donor
Asp268 Asp268(265)A(C) Helps stabilise the reactive intermediates and transition states formed during the course of the reaction. hydrogen bond acceptor, electrostatic stabiliser
*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

bimolecular nucleophilic substitution, overall reactant used, enzyme-substrate complex formation, intermediate formation, proton transfer, intramolecular elimination, decyclisation, schiff base formed, overall product formed, unimolecular elimination by the conjugate base, bimolecular electrophilic addition, bimolecular elimination, enzyme-substrate complex cleavage, intermediate terminated, intermediate collapse, native state of enzyme regenerated, reaction occurs outside the enzyme, cyclisation

References

  1. Chung SJ et al. (2004), Chem Biol, 11, 1643-1649. Structures of End Products Resulting from Lesion Processing by a DNA Glycosylase/Lyase. DOI:10.1016/j.chembiol.2004.09.014. PMID:15610848.
  2. Sowlati-Hashjin S et al. (2015), Phys Chem Chem Phys, 17, 24696-24706. Quantum mechanical study of the β- and δ-lyase reactions during the base excision repair process: application to FPG. DOI:10.1039/c5cp04250j. PMID:26352486.
  3. Kellie JL et al. (2012), J Phys Chem B, 116, 10786-10797. Mechanistic and conformational flexibility of the covalent linkage formed during β-lyase activity on an AP-site: application to hOgg1. DOI:10.1021/jp306344g. PMID:22877319.
  4. Norman DP et al. (2003), Biochemistry, 42, 1564-1572. Structural and Biochemical Exploration of a Critical Amino Acid in Human 8-Oxoguanine Glycosylase†,‡. DOI:10.1021/bi026823d. PMID:12578369.
  5. Fromme JC et al. (2003), Nat Struct Biol, 10, 204-211. Product-assisted catalysis in base-excision DNA repair. DOI:10.1038/nsb902. PMID:12592398.

Step 1. Lys249 attacks the DNA 8-oxoguanine substrate in a nucleophilic substitution reaction that yields enzyme bound DNA and the conjugate base of 8-oxoguanine.

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Catalytic Residues Roles

Residue Roles
Asp268(265)A(C) electrostatic stabiliser
Lys249(246)A(C) nucleophile

Chemical Components

ingold: bimolecular nucleophilic substitution, overall reactant used, enzyme-substrate complex formation, intermediate formation

Step 2. The conjugate base of 8-oxoguanine deprotonates the covalently bound Lys249.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys249(246)A(C) covalently attached, hydrogen bond donor, proton donor

Chemical Components

proton transfer, intermediate formation

Step 3. Lys249 initiates an intramolecular elimination, cleaving the C-O bond in the DNA ribose ring and resulting in the deprotonation of 8-oxoguanine.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys249(246)A(C) covalently attached, electron pair donor

Chemical Components

ingold: intramolecular elimination, proton transfer, intermediate formation, decyclisation, schiff base formed

Step 4. The conjugate base of 8-oxoguanine deprotonates the C2 of the open-form ribose. Evidence suggests both proR and proS deprotonation are possible however proS is thought to be more likely.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys249(246)A(C) covalently attached
Asp268(265)A(C) hydrogen bond acceptor
Lys249(246)A(C) electron pair acceptor

Chemical Components

proton transfer, intermediate formation, overall product formed

Step 5. Lys249 initiates an elimination resulting in the loss of the 3' phosphate-end of the DNA from the ribose ring.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys249(246)A(C) covalently attached
Asp268(265)A(C) hydrogen bond acceptor
Lys249(246)A(C) electron pair donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, intermediate formation

Step 6. Water attacks the ribose at the carbon where Lys249 is bound in a nucleophilic addition reaction.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys249(246)A(C) covalently attached
Asp268(265)A(C) hydrogen bond acceptor
Lys249(246)A(C) proton acceptor, electron pair acceptor

Chemical Components

ingold: bimolecular electrophilic addition, overall reactant used, intermediate formation

Step 7. The released phosphate deprotonates the hydroxyl group, initiating an elimination of the covalently bound Lys249.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp268(265)A(C) hydrogen bond acceptor
Lys249(246)A(C) nucleofuge

Chemical Components

ingold: bimolecular elimination, enzyme-substrate complex cleavage, intermediate terminated, intermediate collapse, overall product formed, native state of enzyme regenerated

Step 8. The a,b-unsaturated aldehyde then undergoes spontaneous ring closure to furnish the DDR end product. The double bond geometry of the Schiff base is not known; if the double bond is configured trans, it would have to isomerise prior to ring closure, because a trans double bond cannot exist in a 5-membered ring, owing to ring strain. Such an isomerisation could foreseeably take place at the stage of either the Schiff base or the a,b-unsaturated aldehyde due to relatively acidic C2' hydrogens in these species.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

reaction occurs outside the enzyme, cyclisation
Download: Image, Marvin File

Step 1. Lys249 attacks the DNA 8-oxoguanine substrate in a nucleophilic substitution reaction that yields enzyme bound DNA and the conjugate base of 8-oxoguanine.

Step 2. The conjugate base of 8-oxoguanine deprotonates the covalently bound Lys249.

Step 3. Lys249 initiates an intramolecular elimination, cleaving the C-O bond in the DNA ribose ring and resulting in the deprotonation of 8-oxoguanine.

Step 4. The conjugate base of 8-oxoguanine deprotonates the C2 of the open-form ribose. Evidence suggests both proR and proS deprotonation are possible however proS is thought to be more likely.

Step 5. Lys249 initiates an elimination resulting in the loss of the 3' phosphate-end of the DNA from the ribose ring.

Step 6. Water attacks the ribose at the carbon where Lys249 is bound in a nucleophilic addition reaction.

Step 7. The released phosphate deprotonates the hydroxyl group, initiating an elimination of the covalently bound Lys249.

Step 8. The a,b-unsaturated aldehyde then undergoes spontaneous ring closure to furnish the DDR end product. The double bond geometry of the Schiff base is not known; if the double bond is configured trans, it would have to isomerise prior to ring closure, because a trans double bond cannot exist in a 5-membered ring, owing to ring strain. Such an isomerisation could foreseeably take place at the stage of either the Schiff base or the a,b-unsaturated aldehyde due to relatively acidic C2' hydrogens in these species.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, James Willey