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A structural mechanism for dimeric to tetrameric oligomer conversion in Halomonas sp. nucleoside diphosphate kinase.

Arai S, Yonezawa Y, Okazaki N, Matsumoto F, Tamada T, Tokunaga H, Ishibashi M, Blaber M, Tokunaga M, Kuroki R
Protein Sci 21 498-510 (2012)
Related entries: 3vgs, 3vgt, 3vgu

Cited: 11 times
EuropePMC logo PMID: 22275000

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.

Reviews - 3vgv mentioned but not cited (1)

  1. Structure, Folding and Stability of Nucleoside Diphosphate Kinases. Georgescauld F, Song Y, Dautant A. Int J Mol Sci 21 E6779 (2020)

Articles - 3vgv mentioned but not cited (1)

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


Articles citing this publication (9)

  1. Structure of Nm23-H1 under oxidative conditions. Kim MS, Jeong J, Jeong J, Shin DH, Lee KJ. Acta Crystallogr D Biol Crystallogr 69 669-680 (2013)
  2. Crystal structure of Lamellipodin implicates diverse functions in actin polymerization and Ras signaling. Chang YC, Zhang H, Brennan ML, Wu J. Protein Cell 4 211-219 (2013)
  3. Molecular and structural basis of nucleoside diphosphate kinase-mediated regulation of spore and sclerotia development in the fungus Aspergillus flavus. Wang Y, Wang S, Nie X, Yang K, Xu P, Wang X, Liu M, Yang Y, Chen Z, Wang S. J Biol Chem 294 12415-12431 (2019)
  4. EsxB, a secreted protein from Bacillus anthracis forms two distinct helical bundles. Fan Y, Tan K, Chhor G, Butler EK, Jedrzejczak RP, Missiakas D, Joachimiak A. Protein Sci 24 1389-1400 (2015)
  5. An intersubunit disulfide bridge stabilizes the tetrameric nucleoside diphosphate kinase of Aquifex aeolicus. Boissier F, Georgescauld F, Moynié L, Dupuy JW, Sarger C, Podar M, Lascu I, Giraud MF, Dautant A. Proteins 80 1658-1668 (2012)
  6. Intersubunit ionic interactions stabilize the nucleoside diphosphate kinase of Mycobacterium tuberculosis. Georgescauld F, Moynié L, Habersetzer J, Cervoni L, Mocan I, Borza T, Harris P, Dautant A, Lascu I. PLoS One 8 e57867 (2013)
  7. Cloning, Expression, and Purification of Nucleoside Diphosphate Kinase from Acinetobacter baumannii. Sikarwar J, Kaushik S, Sinha M, Kaur P, Sharma S, Singh TP. Enzyme Res 2013 597028 (2013)
  8. Nucleoside Diphosphate Kinase from Psychrophilic Pseudoalteromonas sp. AS-131 Isolated from Antarctic Ocean. Yonezawa Y, Nagayama A, Tokunaga H, Ishibashi M, Arai S, Kuroki R, Watanabe K, Arakawa T, Tokunaga M. Protein J 34 275-283 (2015)
  9. Cys139Ser mutation in dimeric nucleoside diphosphate kinase generates catalytically competent monomer. Tokunaga H, Arakawa T, Tokunaga M. Int J Biol Macromol 66 66-73 (2014)


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