8JGQ

Crystal structure of Deinococcus radiodurans exopolyphosphatase complexed with P5

Summary for 8JGQ

• Entry DOI: 10.2210/pdb8jgq/pdb
• Descriptor: Exopolyphosphatase, bis[oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate, SULFATE ION, ... (5 entities in total)
• Functional Keywords: polyphosphate, exopolyphosphatase, hydrolase
• Biological source: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Total number of polymer chains: 1
• Total formula weight: 57849.69

Authors

Zhao, Y.,Dai, S. (deposition date: 2023-05-21, release date: 2024-05-15, Last modification date: 2024-07-31)

Primary citation

Dai, S.,Wang, B.,Ye, R.,Zhang, D.,Xie, Z.,Yu, N.,Cai, C.,Huang, C.,Zhao, J.,Zhang, F.,Hua, Y.,Zhao, Y.,Zhou, R.,Tian, B.
Structural Evolution of Bacterial Polyphosphate Degradation Enzyme for Phosphorus Cycling.
Adv Sci, 11:e2309602-e2309602, 2024

PubMed Abstract: Living organisms ranging from bacteria to animals have developed their own ways to accumulate and store phosphate during evolution, in particular as the polyphosphate (polyP) granules in bacteria. Degradation of polyP into phosphate is involved in phosphorus cycling, and exopolyphosphatase (PPX) is the key enzyme for polyP degradation in bacteria. Thus, understanding the structure basis of PPX is crucial to reveal the polyP degradation mechanism. Here, it is found that PPX structure varies in the length of ɑ-helical interdomain linker (ɑ-linker) across various bacteria, which is negatively correlated with their enzymatic activity and thermostability - those with shorter ɑ-linkers demonstrate higher polyP degradation ability. Moreover, the artificial DrPPX mutants with shorter ɑ-linker tend to have more compact pockets for polyP binding and stronger subunit interactions, as well as higher enzymatic efficiency (k/K) than that of DrPPX wild type. In Deinococcus-Thermus, the PPXs from thermophilic species possess a shorter ɑ-linker and retain their catalytic ability at high temperatures (70 °C), which may facilitate the thermophilic species to utilize polyP in high-temperature environments. These findings provide insights into the interdomain linker length-dependent evolution of PPXs, which shed light on enzymatic adaption for phosphorus cycling during natural evolution and rational design of enzyme.

PubMed: 38682481
DOI: 10.1002/advs.202309602

Experimental method

X-RAY DIFFRACTION (2.5 Å)