Summary information and primary citation
- PDB-id
- 6iod; SNAP-derived features in text and JSON formats;
DNAproDB
- Class
- DNA binding protein-DNA
- Method
- X-ray (1.66 Å)
- Summary
- The structure of udgx in complex with single-stranded DNA
- Reference
- Tu J, Chen R, Yang Y, Cao W, Xie W (2019): "Suicide inactivation of the uracil DNA glycosylase UdgX by covalent complex formation." Nat.Chem.Biol., 15, 615-622. doi: 10.1038/s41589-019-0290-x.
- Abstract
- A uracil DNA glycosylase (UDG) from Mycobacterium smegmatis (MsmUdgX) shares sequence similarity with family 4 UDGs and forms exceedingly stable complexes with single-stranded uracil-containing DNAs (ssDNA-Us) that are resistant to denaturants. However, MsmUdgX has been reported to be inactive in excising uracil from ssDNA-Us and the underlying structural basis is unclear. Here, we report high-resolution crystal structures of MsmUdgX in the free, uracil- and DNA-bound forms, respectively. The structural information, supported by mutational and biochemical analyses, indicates that the conserved residue His109 located on a characteristic loop forms an irreversible covalent linkage with the deoxyribose at the apyrimidinic site of ssDNA-U, thus rendering the enzyme unable to regenerate. By proposing the catalytic pathway and molecular mechanism for MsmUdgX, our studies provide an insight into family 4 UDGs and UDGs in general.
