8GTY

Crystal structure of exopolyphosphatase (PPX) from Zymomonas mobilis in complex with magnesium ions

Summary for 8GTY

• Entry DOI: 10.2210/pdb8gty/pdb
• Descriptor: Ppx/GppA phosphatase, MAGNESIUM ION (3 entities in total)
• Functional Keywords: polyphosphate, ppx/gppa, metal binding protein
• Biological source: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
• Total number of polymer chains: 1
• Total formula weight: 53524.21

Authors

Lu, Z.,Wang, J.,Zhang, B. (deposition date: 2022-09-09, release date: 2023-09-13, Last modification date: 2026-03-04)

Primary citation

Lu, Z.,Hu, Y.,Wang, J.,Zhang, B.,Zhang, Y.,Cui, Z.,Zhang, L.,Zhang, A.
Structure of the exopolyphosphatase (PPX) from Zymomonas mobilis reveals a two-magnesium-ions PPX.
Int.J.Biol.Macromol., 262:129796-129796, 2024

PubMed Abstract: Rapid adaptation of metabolic capabilities is crucial for bacterial survival in habitats with fluctuating nutrient availability. In such conditions, the bacterial stringent response is a central regulatory mechanism activated by nutrient starvation or other stressors. This response is primarily controlled by exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA) enzymes. To gain further insight into these enzymes, the high-resolution crystal structure of PPX from Zymomonas mobilis (ZmPPX) was determined at 1.8 Å. The phosphatase activity of PPX was strictly dependent on the presence of divalent metal cations. Notably, the structure of ZmPPX revealed the presence of two magnesium ions in the active site center, which is atypical compared to other PPX structures where only one divalent ion is observed. ZmPPX exists as a dimer in solution and belongs to the "long" PPX group consisting of four domains. Remarkably, the dimer configuration exhibits a substantial and deep aqueduct with positive potential along its interface. This aqueduct appears to extend towards the active site region, suggesting that this positively charged aqueduct could potentially serve as a binding site for polyP.

PubMed: 38311144
DOI: 10.1016/j.ijbiomac.2024.129796

Experimental method

X-RAY DIFFRACTION (1.8 Å)