Biosynthesis — DNA repair enzymology
DNA glycosylase: base excision repair
How the DNA glycosylase works, in 3 steps. Each step shows the structures and the curved arrows that move the electrons.
In short. A 3-step mechanism. Typical reagents: DNA glycosylase (e.g. uracil-DNA glycosylase), H₂O. Conditions: Physiological pH, 37 °C. Bonds formed: C1′–O (abasic site); free base; bonds broken: N-glycosidic C1′–N bond. Stereochemistry: Inversion or retention at C1′ depending on enzyme. Rate and selectivity: Base flipping and oxocarbenium-like TS control rate.
At a glance
Step 1: Damaged base is flipped out
A DNA glycosylase enzyme flips a damaged base (like a deaminated or alkylated base) out of the double helix into its active site, positioning the N-glycosidic bond connecting that base to the sugar-phosphate backbone for attack.
Step 2: Water displaces the base at C1′
An active-site nucleophile (often a water molecule activated by a nearby acidic residue, or in some glycosylases an active-site amine forming a covalent Schiff-base intermediate) attacks the anomeric carbon, displacing the damaged base — the same oxocarbenium-stabilized substitution chemistry as ordinary glycoside hydrolysis, covered much earlier, just now cleaving a bond instead of forming one.
Step 3: Abasic site, then completion of repair
The result is an abasic site in the DNA strand, later processed by downstream repair enzymes (an AP endonuclease, then polymerase and ligase) to install a correct, undamaged nucleotide — this excision step is the first, chemistry-defining move in one of the cell's primary defenses against DNA damage.
Abbreviations and terms
- R
- R group. Any carbon substituent (alkyl, aryl…) whose identity does not matter for the mechanism.
- H2
- Hydrogen gas. Reductant for catalytic hydrogenation.
- TS
- Transition state. The highest-energy point on the pathway between two minima; it cannot be isolated.
- DNA
- Deoxyribonucleic acid. The genetic polymer.
- Asp
- Aspartate. Acidic amino acid.
How it compares with related reactions
| DNA glycosylase | Cytochrome P450 | Decarboxylative Claisen condensation (fatty acid biosynthesis) | |
|---|---|---|---|
| Reagents | DNA glycosylase (e.g. uracil-DNA glycosylase), H₂O | Cytochrome P450 (heme-thiolate), O₂, NADPH (2 e⁻ via reductase), 2 H⁺, substrate R–H | Malonyl-ACP, acyl-enzyme (KS, e.g. acetyl-KS), β-ketoacyl synthase (KS) |
| Conditions | Physiological pH, 37 °C | Aqueous, pH ~7.4, 37 °C, membrane-bound or soluble enzyme | Aqueous, pH ~7, 37 °C, enzyme active site |
| Stereochemistry | Inversion or retention at C1′ depending on enzyme | Rebound is fast, so configuration is often largely retained | No new stereocentre at this step |
| Rate / selectivity | Base flipping and oxocarbenium-like TS control rate | Compound I formation fast; C–H abstraction is rate-limiting | Irreversible: CO₂ loss pays for the otherwise uphill Claisen condensation |
Test yourself
Try to answer each question before opening it.
Which reagents and conditions are typical for the DNA glycosylase?
DNA glycosylase (e.g. uracil-DNA glycosylase), H₂O. Conditions: Physiological pH, 37 °C.
Which bonds are formed and which are broken?
Formed: C1′–O (abasic site); free base. Broken: N-glycosidic C1′–N bond.
What is the stereochemical outcome?
Inversion or retention at C1′ depending on enzyme
What controls the rate or the selectivity?
Base flipping and oxocarbenium-like TS control rate
Study guides that help with this reaction
- How to learn reaction mechanisms (without memorising everything)
- Curved-arrow notation: rules and the mistakes students make