3VGV

E134A mutant nucleoside diphosphate kinase derived from Halomonas sp. 593

Summary for 3VGV

• Entry DOI: 10.2210/pdb3vgv/pdb
• Related: 3VGS 3VGT 3VGU
• Descriptor: Nucleoside diphosphate kinase (2 entities in total)
• Functional Keywords: halophilic, kinase, ferredoxin fold, atp-binding, nucleotide-binding, transferase
• Biological source: Halomonas
• Cellular location: Cytoplasm (By similarity): Q83WH5
• Total number of polymer chains: 16
• Total formula weight: 243616.86

Authors

Okazaki, N.,Yonezawa, Y.,Arai, S.,Matsumoto, F.,Tamada, T.,Tokunaga, H.,Ishibashi, M.,Tokunaga, M.,Kuroki, R. (deposition date: 2011-08-21, release date: 2012-07-11, Last modification date: 2023-11-08)

Primary citation

Arai, S.,Yonezawa, Y.,Okazaki, N.,Matsumoto, F.,Tamada, T.,Tokunaga, H.,Ishibashi, M.,Blaber, M.,Tokunaga, M.,Kuroki, R.
A structural mechanism for dimeric to tetrameric oligomer conversion in Halomonas sp. nucleoside diphosphate kinase
Protein Sci., 21:498-510, 2012

PubMed Abstract: Nucleoside diphosphate kinase (NDK) is known to form homotetramers or homohexamers. To clarify the oligomer state of NDK from moderately halophilic Halomonas sp. 593 (HaNDK), the oligomeric state of HaNDK was characterized by light scattering followed by X-ray crystallography. The molecular weight of HaNDK is 33,660, and the X-ray crystal structure determination to 2.3 and 2.7 Å resolution showed a dimer form which was confirmed in the different space groups of R3 and C2 with an independent packing arrangement. This is the first structural evidence that HaNDK forms a dimeric assembly. Moreover, the inferred molecular mass of a mutant HaNDK (E134A) indicated 62.1-65.3 kDa, and the oligomerization state was investigated by X-ray crystallography to 2.3 and 2.5 Å resolution with space groups of P2(1) and C2. The assembly form of the E134A mutant HaNDK was identified as a Type I tetramer as found in Myxococcus NDK. The structural comparison between the wild-type and E134A mutant HaNDKs suggests that the change from dimer to tetramer is due to the removal of negative charge repulsion caused by the E134 in the wild-type HaNDK. The higher ordered association of proteins usually contributes to an increase in thermal stability and substrate affinity. The change in the assembly form by a minimum mutation may be an effective way for NDK to acquire molecular characteristics suited to various circumstances.

PubMed: 22275000
DOI: 10.1002/pro.2032

Experimental method

X-RAY DIFFRACTION (2.5 Å)