Pressure adaptation of 3-isopropylmalate dehydrogenase from an extremely piezophilic bacterium is attributed to a single amino acid substitution

Abstract

3-Isopropylmalate dehydrogenase (IPMDH) from the extreme piezophile Shewanella benthica (SbIPMDH) is more pressure-tolerant than that from the atmospheric pressure-adapted Shewanella oneidensis (SoIPMDH). To understand the molecular mechanisms of this pressure tolerance, we analyzed mutated enzymes. The results indicate that only a single mutation at position 266, corresponding to Ala (SbIPMDH) and Ser (SoIPMDH), essentially affects activity under higher-pressure conditions. Structural analyses of SoIPMDH suggests that penetration of three water molecules into the cleft around Ser266 under high-pressure conditions could reduce the activity of the wild-type enzyme; however, no water molecule is observed in the Ala266 mutant.

Enzymes from piezophiles

“…At atmospheric pressures, Mp DHFR is more flexible than EcDHFR as measured by hydrogen-deuterium exchange NMR studies, which may be important in generating the reaction ready conformation but apparently does not influence the chemical step [87]. The piezophile Sb IPMDH is also less stable than its mesophilic homolog SoIPMDH ( T 1/2 are 56.6 °C versus 60.7 °C, respectively) [88]. Analogous to psychrophile enzymes and cold unfolding, stability does not appear to be a very strong evolutionary driving force for piezophile enzymes as long as they are stable at the P g of the parent microbe.…”

High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP+

“…In a high-pressure NMR study of ecDHFR, the structure of the M20 loop was noted to be pressure-sensitive (Kitahara et al, 2000). The maximum pressure in the NMR experiment was 200 MPa, but it is known that the pressure response of protein molecules in crystals shifts to highpressure regions (Katrusiak & Dauter, 1996;Hamajima et al, 2016). Therefore, in our HPPX experiments we pressurized the M20-open and M20-closed crystals up to 750 and 800 MPa, respectively.…”

Pressure-Regulated Gene Expression and Enzymatic Activity of the Two Periplasmic Nitrate Reductases in the Deep-Sea Bacterium Shewanella piezotolerans WP3

“…It is well-known that differences in the amino acid composition and protein structure could result in different tolerances to pressure (Ohmae et al, 2004; Hamajima et al, 2016). The amino acid sequences of NapA1 and NapA2 share 71% identity, and it has been proposed that the two NapA proteins evolved separately (Wang and Chen, 2015).…”