8JFS

Phosphate bound acylphosphatase from Deinococcus radiodurans at 1 Angstrom resolution

Summary for 8JFS

• Entry DOI: 10.2210/pdb8jfs/pdb
• Descriptor: Acylphosphatase, PHOSPHATE ION, CITRIC ACID, ... (6 entities in total)
• Functional Keywords: phosphate bound acylphosphatase, hydrolase
• Biological source: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Total number of polymer chains: 2
• Total formula weight: 20381.37

Authors

Khakerwala, Z.,Kumar, A.,Makde, R.D. (deposition date: 2023-05-18, release date: 2023-06-14, Last modification date: 2024-05-29)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1 Å)