2ZUA

Crystal structure of nucleoside diphosphate kinase from Haloarcula quadrata

Summary for 2ZUA

• Entry DOI: 10.2210/pdb2zua/pdb
• Descriptor: Nucleoside diphosphate kinase (2 entities in total)
• Functional Keywords: ferredoxin fold, kpn loop, transferase, kinase
• Biological source: Haloarcula quadrata
• Cellular location: Cytoplasm (By similarity): Q401C5
• Total number of polymer chains: 4
• Total formula weight: 78946.42

Authors

Ichimura, T.,Yamamura, A.,Ohtsuka, J.,Miyazono, K.,Okai, M.,Nagata, K.,Tanokura, M. (deposition date: 2008-10-15, release date: 2009-08-25, Last modification date: 2023-11-01)

Primary citation

Yamamura, A.,Ichimura, T.,Kamekura, M.,Mizuki, T.,Usami, R.,Makino, T.,Ohtsuka, J.,Miyazono, K.,Okai, M.,Nagata, K.,Tanokura, M.
Molecular mechanism of distinct salt-dependent enzyme activity of two halophilic nucleoside diphosphate kinases
Biophys.J., 96:4692-4700, 2009

PubMed Abstract: Nucleoside diphosphate kinases from haloarchaea Haloarcula quadrata (NDK-q) and H. sinaiiensis (NDK-s) are identical except for one out of 154 residues, i.e., Arg(31) in NDK-q and Cys(31) in NDK-s. However, the salt-dependent activity profiles of NDK-q and NDK-s are quite different: the optimal NaCl concentrations of NDK-q and NDK-s are 1 M and 2 M, respectively. We analyzed the relationships of the secondary, tertiary, and quaternary structures and NDK activity of these NDKs at various salt concentrations, and revealed that 1), NDK-q is present as a hexamer under a wide range of salt concentrations (0.2-4 M NaCl), whereas NDK-s is present as a hexamer at an NaCl concentration above 2 M and as a dimer at NaCl concentrations below 1 M; 2), dimeric NDK-s has lower activity than hexameric NDK-s; and 3), dimeric NDK-s has higher helicity than hexameric NDK-s. We also determined the crystal structure of hexameric NDK-q, and revealed that Arg(31) plays an important role in stabilizing the hexamer. Thus the substitution of Arg (as in NDK-q) to Cys (as in NDK-s) at position 31 destabilizes the hexameric assembly, and causes dissociation to less active dimers at low salt concentrations.

PubMed: 19486691
DOI: 10.1016/j.bpj.2009.03.012

Experimental method

X-RAY DIFFRACTION (2.59 Å)