6K21

Pyrophosphatase from Acinetobacter baumannii

Summary for 6K21

• Entry DOI: 10.2210/pdb6k21/pdb
• Descriptor: Inorganic pyrophosphatase, MAGNESIUM ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: pyrophosphatase from acinetobacter baumannii, hydrolase
• Biological source: Acinetobacter baumannii
• Total number of polymer chains: 1
• Total formula weight: 19550.44

Authors

Su, J. (deposition date: 2019-05-13, release date: 2019-10-02, Last modification date: 2024-03-27)

Primary citation

Si, Y.,Wang, X.,Yang, G.,Yang, T.,Li, Y.,Ayala, G.J.,Li, X.,Wang, H.,Su, J.
Crystal Structures of Pyrophosphatase from Acinetobacter baumannii: Snapshots of Pyrophosphate Binding and Identification of a Phosphorylated Enzyme Intermediate.
Int J Mol Sci, 20:-, 2019

PubMed Abstract: All living things have pyrophosphatases that hydrolyze pyrophosphate and release energy. This energetically favorable reaction drives many energetically unfavorable reactions. An accepted catalytic model of pyrophosphatase shows that a water molecule activated by two divalent cations (M1 and M2) within the catalytic center can attack pyrophosphate in an S2 mechanism and thus hydrolyze the molecule. However, our co-crystal structure of pyrophosphatase with pyrophosphate shows that a water molecule from the solvent may, in fact, be the actual catalytic water. In the co-crystal structure of the wild-type pyrophosphatase with pyrophosphate, the electron density of the catalytic centers of each monomer are different from one another. This indicates that pyrophosphates in the catalytic center are dynamic. Our mass spectroscopy results have identified a highly conserved lysine residue (Lys30) in the catalytic center that is phosphorylated, indicating that the enzyme could form a phosphoryl enzyme intermediate during hydrolysis. Mutation of Lys30 to Arg abolished the activity of the enzyme. In the structure of the apo wild type enzyme, we observed that a Na ion is coordinated by residues within a loop proximal to the catalytic center. Therefore, we mutated three key residues within the loop (K143R, P147G, and K149R) and determined Na and K-induced inhibition on their activities. Compared to the wild type enzyme, P147G is most sensitive to these cations, whereas K143R was inactive and K149R showed no change in activity. These data indicate that monovalent cations could play a role in down-regulating pyrophosphatase activity in vivo. Overall, our results reveal new aspects of pyrophosphatase catalysis and could assist in the design of specific inhibitors of growth.

PubMed: 31500178
DOI: 10.3390/ijms20184394

Experimental method

X-RAY DIFFRACTION (2 Å)