title: Crystal structure of the cysteine desulfurase DndA from Streptomyces lividans which is involved in DNA phosphorothioation.
abstract: DNA phosphorothioation is widespread among prokaryotes, and might function to restrict gene transfer among different kinds of bacteria. There has been little investigation into the structural mechanism of the DNA phosphorothioation process. DndA is a cysteine desulfurase which is involved in the first step of DNA phosphorothioation. In this study, we determined the crystal structure of Streptomyces lividans DndA in complex with its covalently bound cofactor PLP, to a resolution of 2.4 Å. Our structure reveals the molecular mechanism that DndA employs to recognize its cofactor PLP, and suggests the potential binding site for the substrate L-cysteine on DndA. In contrast to previously determined structures of cysteine desulfurases, the catalytic cysteine of DndA was found to reside on a β strand. This catalytic cysteine is very far away from the presumable location of the substrate, suggesting that a conformational change of DndA is required during the catalysis process to bring the catalytic cysteine close to the substrate cysteine. Moreover, our in vitro enzymatic assay results suggested that this conformational change is unlikely to be a simple result of random thermal motion, since moving the catalytic cysteine two residues forward or backward in the primary sequence completely disabled the cysteine desulfurase activity of DndA.
authors.affiliation: State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Fukun
authors.initials: F
authors.lastname: Chen
authors.forename: Zhenyi
authors.initials: Z
authors.lastname: Zhang
authors.forename: Kui
authors.initials: K
authors.lastname: Lin
authors.forename: Tianle
authors.initials: T
authors.lastname: Qian
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Delin
authors.initials: D
authors.lastname: You
authors.forename: Xinyi
authors.initials: X
authors.lastname: He
authors.forename: Zhijun
authors.initials: Z
authors.lastname: Wang
authors.forename: Jingdan
authors.initials: J
authors.lastname: Liang
authors.forename: Zixin
authors.initials: Z
authors.lastname: Deng
authors.forename: Geng
authors.initials: G
authors.lastname: Wu
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D013437:Carbon-Sulfur Lyases / Q000737:chemistry* / Q000378:metabolism; D002384:Catalysis; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004789:Enzyme Activation; D044127:Epigenesis, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D011732:Pyridoxal Phosphate / Q000378:metabolism; D016415:Sequence Alignment; D048170:Streptomyces lividans / Q000201:enzymology* / Q000235:genetics
chemical_list: D011732:Pyridoxal Phosphate; D004247:DNA; D013437:Carbon-Sulfur Lyases; C080546:cysteine desulfurase; D003545:Cysteine