Dimeric structure of nucleoside diphosphate kinase from moderately halophilic bacterium: contrast to the tetramericPseudomonascounterpart

Abstract

Light scattering and chemical cross-linking analyses of nucleoside diphosphate kinase (NDK) from moderate halophile, Halomonas sp. 593 (HaNDK), unambiguously demonstrated that this enzyme formed a dimeric structure, in contrast to the Pseudomonas NDK (PaNDK), a nonhalophilic counterpart, and other NDKs from Gram-negative bacteria, which all formed a tetrameric structure. Comparison of HaNDK and PaNDK showed that the HaNDK was less thermally stable than the PaNDK: the optimum temperature of PaNDK enzyme activity was 20 degrees C higher than that of HaNDK. However, the HaNDK readily refolded and reassembled back to the active dimeric structure, upon heat denaturation at 0.2 M NaCl, as soon as the temperature was lowered. On the contrary, the thermally more stable PaNDK was irreversibly denatured at its melting temperature.

Halophilic characterization of starch-binding domain from Kocuria varians α-amylase

“…We have been studying the distinct characteristics of halophilic proteins, including nucleoside diphosphate kinases [4][5][6][7], ␤-lactamase [8,9] and ␣-amylase secreted from Kocuria varians [10]. The most striking features of halophilic proteins, especially the secretory proteins present in the periplasmic space or the culture medium of moderate halophiles, are their high aqueous solubility in both the native and denatured structures and the high reversibility of refolding from the denatured states without forming aggregation [6,8].…”

Hydrogen/Deuterium Exchange Mass Spectrometry Reveals Mechanistic Details of Activation of Nucleoside Diphosphate Kinases by Oligomerization

“…(42,43) NDPKs contain ferredoxin-like folds (45) which assemble first as dimers and then as tetramers or hexamers. (46)(47)(48) Tetramers are present in gram-negative bacteria and archaea, while hexamers are present in gram-positive bacteria and eukaryotes. Hexamers represent the most abundant type of oligomerization, which specifically relies on the well conserved surface loop that carries the site of the natural "Killer of prune" mutation (Kpn-loop) (Figures 1, S1).…”

Halophilic Properties and their Manipulation and Application

“…To our surprise, the NDK from Halomonas sp. 593 (HaNDK) was a dimer (Yonezawa et al, 2007). It was the first report that a dimeric NDK is the native state.…”