8JFS

Phosphate bound acylphosphatase from Deinococcus radiodurans at 1 Angstrom resolution

8JFS の概要

• エントリーDOI: 10.2210/pdb8jfs/pdb
• 分子名称: Acylphosphatase, PHOSPHATE ION, CITRIC ACID, ... (6 entities in total)
• 機能のキーワード: phosphate bound acylphosphatase, hydrolase
• 由来する生物種: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 20381.37

構造登録者

Khakerwala, Z.,Kumar, A.,Makde, R.D. (登録日: 2023-05-18, 公開日: 2023-06-14, 最終更新日: 2024-05-29)

主引用文献

Khakerwala, Z.,Kumar, A.,Makde, R.D.
Crystal structure of phosphate bound Acyl phosphatase mini-enzyme from Deinococcus radiodurans at 1 angstrom resolution.
Biochem.Biophys.Res.Commun., 671:153-159, 2023

PubMed Abstract: Acylphosphatase (Acp) is a hydrolase which specifically cleaves carboxyl-phosphate bond of intermediates of metabolic pathways. It is a small cytosolic enzyme found in both prokaryotic and eukaryotic organisms. Previous crystal structures of acylphosphatase from different organisms have provided insights into the active site but the complete understanding of substrate binding and catalytic mechanisms in acylphosphatase remain elusive. Here we report the crystal structure of phosphate bound acylphosphatase from a mesothermic bacterium, Deinococcus radiodurans (drAcp) at resolution of 1.0 Å. Our structural analysis shows how the terminal phosphate group of substrates is bound to the active site, highlighting the importance of arginine in substrate recognition, role of asparagine in mode of catalysis and shedding light on the reaction mechanism. Additionally, the protein can refold after thermal melting by gradually lowering the temperature. To further explore the dynamics of drAcp, molecular dynamics simulation of drAcp and homologs from thermophilic organisms were carried out which revealed similar root mean square fluctuation profile but drAcp showed comparatively higher fluctuations.

PubMed: 37302289
DOI: 10.1016/j.bbrc.2023.06.003

実験手法

X-RAY DIFFRACTION (1 Å)