Thymine-DNA glycosylase (TDG)  -  DNA

Biological function
Thymine-DNA glycosylases (TDGs), proteins of the Escherichia coli MUG family, have the ability to detect and repair thymine bases in DNA in the context of G · T mismatches in addition to a G · U repair activity in the base excision repair (BER) pathway. The human TDG and MBD4/MIG proteins thereby display lower G · T than G · U repair activity.

Structural evidence
NMR data show that a region encompassing 60 residues immediately preceding the catalytic domain and specifically required for G · T repair undergoes a dramatic dynamic change in the context of the entire protein. Even though the isolated N-terminus exhibits an overall extended conformation, this same region still adopts a small degree of organization and is able to bind small double-stranded DNA molecules in a sequence-independent manner. In contrast, region 1-50 of the N-terminus adopts a totally disordered structure. This region is neither affected by the absence of the catalytic domain nor interacts with DNA directly.

Biochemical evidence
Deletion of the 1-50 residues of NTD as well as the deletion of the full C-terminus leads to a significant increase of TDG glycosylase activity.

TDG exist in two forms: the ’closed’ form, when the catalytic domain is involved in intra-molecular interactions, and an ’open’ form, which lacks these contacts. The turnover of this enzyme is regulated by the disordered N- and C-terminal domains (NTD and CTD), the removal of which increases the turnover of GT and GU activities by 50% and 100%, respectively. The NTD was proposed to facilitate the transition towards the ’closed’ form of TDG, which is the DNA-binding competent conformation. Owing to alternative recognition modes, this arrangement is more favorable for GT than for GU repair. Hence the disordered NTD regulates these two activities by shifting population between the ’open’ and ’closed’ conformations. In addition, both the N- and C-terminal residues compete for DNA contact sites hampering interactions between TDG and DNA.

Mechanism category
conformational selection

Fuzzy regions shift populations towards the DNA-binding competent conformation. In addition, the fluctuating C-terminal domain provides a steric hindrance in the complex and imparts length-dependent regulation on substrate-binding affinity.