6IOA
The structure of UdgX in complex with uracil
Summary for 6IOA
| Entry DOI | 10.2210/pdb6ioa/pdb |
| Descriptor | Phage SPO1 DNA polymerase-related protein, IRON/SULFUR CLUSTER, URACIL, ... (5 entities in total) |
| Functional Keywords | uracil dna glycosylase, dna repair, iron-sulfur, hydrolase |
| Biological source | Mycobacterium smegmatis MC2 155 |
| Total number of polymer chains | 1 |
| Total formula weight | 24932.44 |
| Authors | |
| Primary citation | Tu, J.,Chen, R.,Yang, Y.,Cao, W.,Xie, W. Suicide inactivation of the uracil DNA glycosylase UdgX by covalent complex formation. Nat.Chem.Biol., 15:615-622, 2019 Cited by PubMed 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. PubMed: 31101915DOI: 10.1038/s41589-019-0290-x PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.15 Å) |
Structure validation
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