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SJTU Research Team Made Progress in DNA Phosphorothioate (PT) Modification

April 29, 2020      Author: Wu Geng

Recently, a paper titled "Structural Analysis of an L-Cysteine Desulfurase from an Ssp DNA Phosphorothioation System" was published in mBio. It presented the latest findings of the cooperation between a team led by Professor Wu Geng from State Key Laboratory of Microial Metabolism, School of Life Sciences and Biotechnology, SJTU, and a team led by Professor Wang Lianrong and Professor Chen Shi from Wu Han University. Liu Liqiong and others are the first authors; Wu Geng and Wang Lianrong are the corresponding authors; the State Key Laboratory of Microbial Metabolism from SJTU is the first unit.

This research is supported by National Natural Science Foundation of China(31872627、31670106).

Abstract:

DNA phosphorothioate (PT) modification, in which the nonbridging oxygen in the sugar-phosphate backbone is substituted by sulfur, is catalyzed by DndABCDE or SspABCD in a double-stranded or single-stranded manner, respectively. In Dnd and Ssp systems, mobilization of sulfur in PT formation starts with the activation of the sulfur atom of cysteine catalyzed by the DndA and SspA cysteine desulfurases, respectively. Despite playing the same biochemical role, SspA cannot be functionally replaced by DndA, indicating its unique physiological properties. In this study, we solved the crystal structure of Vibrio cyclitrophicus SspA in complex with its natural substrate, cysteine, and cofactor, pyridoxal phosphate (PLP), at a resolution of 1.80 Å. Our solved structure revealed the molecular mechanism that SspA employs to recognize its cysteine substrate and PLP cofactor, suggesting a common binding mode shared by cysteine desulfurases. In addition, although the distance between the catalytic Cys314 and the substrate cysteine is 8.9 Å, which is too far for direct interaction, our structural modeling and biochemical analysis revealed a conformational change in the active site region toward the cysteine substrate to move them close to each other to facilitate the nucleophilic attack. Finally, the pulldown analysis showed that SspA could form a complex with SspD, an ATP pyrophosphatase, suggesting that SspD might potentially accept the activated sulfur atom directly from SspA, providing further insights into the biochemical pathway of Ssp-mediated PT modification.

 

Link: https://mbio.asm.org/content/11/2/e00488-20

Translated  by Fu Jing     Reviewed by Wang Bingyu

 
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