7D8Q

The structure of nucleotide phosphatase Sa1684 complex with GDP analogue from Staphylococcus aureus

Summary for 7D8Q

• Entry DOI: 10.2210/pdb7d8q/pdb
• Descriptor: UPF0374 protein SAB1800c, [(2R,3R,4S,5S)-5-(2-azanyl-6-oxidanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl bis(oxidanyl)phosphinothioyl hydrogen phosphate, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: cytosolic protein, nucleitide phosphatase
• Biological source: Staphylococcus aureus RF122
• Total number of polymer chains: 1
• Total formula weight: 22242.47

Authors

Wang, Z.,Li, X. (deposition date: 2020-10-09, release date: 2021-03-17, Last modification date: 2024-05-29)

Primary citation

Wang, Z.,Shen, H.,He, B.,Teng, M.,Guo, Q.,Li, X.
The structural mechanism for the nucleoside tri- and diphosphate hydrolysis activity of Ntdp from Staphylococcus aureus.
Febs J., 288:6019-6034, 2021

PubMed Abstract: Staphylococcus aureus is a well-known clinical pathogenic bacterium. In recent years, due to the emergence of multiple drug-resistant strains of S. aureus in clinical practice, S. aureus infections have become an increasingly severe clinical problem. Ntdp (nucleoside tri- and diphosphatase, also known as Sa1684) is a nucleotide phosphatase that has a significant effect on the proliferation of S. aureus colonies and the killing ability of the host. Here, we identified the nucleoside tri- and diphosphate hydrolysis activity of Ntdp and obtained the three-dimensional structures of apo-Ntdp and three substrate analog (ATP S, GDP S, and GTP S) complexes of Ntdp. Through structural analysis and biochemical verification, we illustrated the structural basis for the divalent cation selectivity, substrate recognition model, and catalytic mechanism of Ntdp. We also revealed a possible basal functional pattern of the DUF402 domain and hypothesized the potential pathways by which the protein regulates the expression of the two-component regulatory factor agr and the downstream virulence factors. Overall, the above findings provide crucial insights into our understanding of the Ntdp functional mechanism in the infection process.

PubMed: 33955674
DOI: 10.1111/febs.15911

Experimental method

X-RAY DIFFRACTION (1.5 Å)