Nucleic Acids in Chemistry and Biology

Escherichia colihas two methyltransferases, an inducible Ada protein that demethylates mainly O^6 -
MeG while the constitutive Ogt protein is more efficient for O^4 -MeT and larger alkyl lesions.^94 Ada also
demethylates DNA phosphate triesters (but only of the (S)-configuration) at a second cysteine site, Cys38.
Methyl phosphate triesters are relatively innocuous lesions, not repaired in eukaryotes. Their repair in bac-
teria functions solely to upregulate the adaptive Ada response(involving the genes ada-alkB, alkA and
aidB), which appears to have evolved to give protection against exogenous SN1 alkylating agents.
AlkB is a bacterial repair enzyme that uses an active iron-oxo intermediate to hydroxylate 1-MeA and
3-MeC, both being products of SN2 methylation of ssDNA. This Fe^2 -dependent dioxygenase gives
hydroxymethylated derivatives that decompose to formaldehyde and the parent nucleotide (Figure 8.40b).
Two human proteins, ABH2 and ABH3, also demethylate 1-MeA and 3-MeC but have only weak activity
on 1-ethyladenine.^84

Covalent Interactions of Nucleic Acids with Small Molecules and Their Repair 327

N

N

N

N

O

dR

N

H

Me

H

Pro

Cys

His

S

H

N

N

N

N

O

dR

N

H

Me

H

Pro

Cys

His

S

H

a b

N

N

dR

NH

O

Me

N

N

dR

NH

O

CH 2 OH

N

N

dR

NH 2

O

O 2 ,

ketoglutarate

AlkB

(Fe2+)

CO 2 ,

succinate

HCHO

Figure 8.40 Repair of methylated DNA. (a) Ada protein demethylates O^6 -methylguanosine through use of a
Pro-Cys-His sequence. (b) Oxidative demethylation of 3-MeC by AlkB

Table 8.1 Human repair enzymes

Gene name Enzyme; major altered base released Chromosome location

Direct reversal of damage
MGMT O^6 -MeG alkyltransferase 10q26
Base excision repair (BER)
UNG U 12q23-q24.1
SMUG1 U 12q13.11-q13.3
MBD4 U or T opposite G at CpG sequences 3q21-q22
TDG U, T or ethenoC opposite G 12q24.1
OGG1 8-oxoG opposite C 3p26.2
MYH A opposite 8-oxoG 1p34.3-p32.1
NTHL1 (NTH1) Ring-saturated or fragmented pyrimidines 16p13.3
MPG 3-meA, A, hypoxanthine 16p13.3
NEIL1 Removes thymine glycol 15q22-q24
NEIL2 Removes oxidative products of C, U 8p23
NEIL2 Removes oxidative products of C, U 8p23
NEIL3 Removes fragmented/oxidized pyrimidines 4q34.2
Nucleotide excision (NER) (XPxeroderma pigmentosum)
XPC, RAD23B, CETN2 Binds damaged DNA as complex 3p25, 3p25.1, Xq28
Mismatch excision repair (MMR)
MSH2 Mismatch and loop recognition 2p22-p21
MSH2, MSH3, MSH6