6LL7

Type II inorganic pyrophosphatase (PPase) from the psychrophilic bacterium Shewanella sp. AS-11, Mn-activated form

Summary for 6LL7

• Entry DOI: 10.2210/pdb6ll7/pdb
• Descriptor: Inorganic pyrophosphatase, MANGANESE (II) ION, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: manganese-dependent inorganic pyrophosphatase, metal binding protein
• Biological source: Shewanella sp. AS-11
• Total number of polymer chains: 4
• Total formula weight: 135518.97

Authors

Horitani, M.,Kusubayashi, K.,Oshima, K.,Yato, A.,Sugimoto, H.,Watanabe, K. (deposition date: 2019-12-21, release date: 2020-03-25, Last modification date: 2023-11-22)

Primary citation

Horitani, M.,Kusubayashi, K.,Oshima, K.,Yato, A.,Sugimoto, H.,Watanabe, K.
X-ray Crystallography and Electron Paramagnetic Resonance Spectroscopy Reveal Active Site Rearrangement of Cold-Adapted Inorganic Pyrophosphatase.
Sci Rep, 10:4368-4368, 2020

PubMed Abstract: Inorganic pyrophosphatase (PPase) catalyses the hydrolysis reaction of inorganic pyrophosphate to phosphates. Our previous studies showed that manganese (Mn) activated PPase from the psychrophilic bacterium Shewanella sp. AS-11 (Mn-Sh-PPase) has a characteristic temperature dependence of the activity with an optimum at 5 °C. Here we report the X-ray crystallography and electron paramagnetic resonance (EPR) spectroscopy structural analyses of Sh-PPase in the absence and presence of substrate analogues. We successfully determined the crystal structure of Mn-Sh-PPase without substrate and Mg-activated Sh-PPase (Mg-Sh-PPase) complexed with substrate analogue (imidodiphosphate; PNP). Crystallographic studies revealed a bridged water placed at a distance from the di-Mn centre in Mn-Sh-PPase without substrate. The water came closer to the metal centre when PNP bound. EPR analysis of Mn-Sh-PPase without substrate revealed considerably weak exchange coupling, whose magnitude was increased by binding of substrate analogues. The data indicate that the bridged molecule has weak bonds with the di-Mn centre, which suggests a 'loose' structure, whereas it comes closer to di-Mn centre by substrate binding, which suggests a 'well-tuned' structure for catalysis. Thus, we propose that Sh-PPase can rearrange the active site and that the 'loose' structure plays an important role in the cold adaptation mechanism.

PubMed: 32152422
DOI: 10.1038/s41598-020-61217-6

Experimental method

X-RAY DIFFRACTION (2.2 Å)