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Professor Wei Xie’s group from School of Life Sciences revealed catalytic process by the atypical Uracil DNA glycosylase UdgX

Last updated :2019-07-02

Source: School of Life Sciences
Written by: School of Life Sciences
Edited by: Wang Dongmei

In nature, the vast majority of organisms use DNA as genetic material, the integrity of which is essential for organisms. DNA damage is thought to be the leading cause of cell dysfunction, cell aging, and cancer. In DNA, the deamination of cytosine (dC) forms deoxyuracil (dU), causing the G-to-A conversion (transition). To deal with this type of DNA damage, multiple DNA repair mechanisms including the base-excision repair have been formed in cells. Uracil DNA glycosylase (UDG) is responsible for the excision of deoxyuracil and starts the downstream repair pathway. In recent years, UDG members from each family have been characterized and reported, and their catalytic properties and mechanisms became relatively well understood. However, a novel class of UDG from M. smegmatis (named MsmUdgX) has been found to possess unique biochemical properties. MsmUdgX displays high specificity toward uracil in DNA (especially single-stranded DNA), and forms a robust complex that survives harsh treatments such as detergents. Surprisingly, the enzyme does not appear to remove uracil. However, the catalytic mechanism and the structural basis of MsmUdgX is largely unclear.

Recently, Prof. Wei Xie’s group from the School of Life Sciences at Sun Yat-sen University (SYSU) published the research article titled "Suicide inactivation of the uracil DNA glycosylase UdgX by covalent complex formation” in the renowned journal Nature Chemical Biology on their mechanistic studies of the catalytic process by MsmUdgX. Prof. Wei Xie is the corresponding author, while the PhD student Jie Tu from the School of Life Sciences is the first author and the SYSU School of Life Sciences is the primary affiliation. Prof. Weiguo Cao from Clemson University of the US participated and also provided some suggestions to this work.

By determining a series of crystal structures of apo-MsmUdgX and mutants in various forms (complexed with ligands or DNA) (figures a-d), this study revealed the unique catalytic process by MsmUdgX. Tu et al. discovered that MsmUdgX first removed the target uracil and the conserved residue His109 immediately forms a covalent linkage with the apyrimidinic site of the ribose in single-stranded DNA. However, the enzyme also loses its intrinsic uracil-excision activity due to the fact that it would not regenerate. This study solved five crystal structures of MsmUdgX, each representing a distinct state of the catalytic reaction, and the authors therefore proposed the following pathway with several stages for MsmUdgX catalysis, which involves a so-called oxacarbenium intermediate (figure e). This mechanism not only explained the unique biochemical properties of MsmUdgX, and found that MsmUdgX inhibits its own enzymatic activity in a manner close to “suicide”, which is the first example among the known UDGs. In addition, because UdgXs only exist in bacteria, the structure of the MsmUdgX-DNA covalent complex provides the structural basis for novel antibacterial drug design that may help to trap and stabilize the complex upon its formation, and thus has potential application values.

 
The UdgX structures in various forms and the catalytic model
 
Link: https://www.nature.com/articles/s41589-019-0290-x