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Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling.

Im YJ, Kim JI, Shen Y, Na Y, Han YJ, Kim SH, Song PS, Eom SH
J Mol Biol 343 659-70 (2004)
Related entries: 1s59, 1u8w

Cited: 15 times
EuropePMC logo PMID: 15465053

Abstract

In plants, nucleoside diphosphate kinases (NDPKs) play a key role in the signaling of both stress and light. However, little is known about the structural elements involved in their function. Of the three NDPKs (NDPK1-NDPK3) expressed in Arabidopsis thaliana, NDPK2 is involved in phytochrome-mediated signal transduction. In this study, we found that the binding of dNDP or NTP to NDPK2 strengthens the interaction significantly between activated phytochrome and NDPK2. To better understand the structural basis of the phytochrome-NDPK2 interaction, we determined the X-ray structures of NDPK1, NDPK2, and dGTP-bound NDPK2 from A.thaliana at 1.8A, 2.6A, and 2.4A, respectively. The structures showed that nucleotide binding caused a slight conformational change in NDPK2 that was confined to helices alphaA and alpha2. This suggests that the presence of nucleotide in the active site and/or the evoked conformational change contributes to the recognition of NDPK2 by activated phytochrome. In vitro binding assays showed that only NDPK2 interacted specifically with the phytochrome and the C-terminal regulatory domain of phytochrome is involved in the interaction. A domain swap experiment between NDPK1 and NDPK2 showed that the variable C-terminal region of NDPK2 is important for the activation by phytochrome. The structure of Arabidopsis NDPK1 and NDPK2 showed that the isoforms share common electrostatic surfaces at the nucleotide-binding site, but the variable C-terminal regions have distinct electrostatic charge distributions. These findings suggest that the binding of nucleotide to NDPK2 plays a regulatory role in phytochrome signaling and that the C-terminal extension of NDPK2 provides a potential binding surface for the specific interaction with phytochromes.

Reviews citing this publication (2)

  1. Histidine kinases and the missing phosphoproteome from prokaryotes to eukaryotes. Adam K, Hunter T. Lab Invest 98 233-247 (2018)
  2. Phytochrome phosphorylation in plant light signaling. Kim JI, Park JE, Zarate X, Song PS. Photochem Photobiol Sci 4 681-687 (2005)

Articles citing this publication (13)

  1. Interaction of SOS2 with nucleoside diphosphate kinase 2 and catalases reveals a point of connection between salt stress and H2O2 signaling in Arabidopsis thaliana. Verslues PE, Batelli G, Grillo S, Agius F, Kim YS, Zhu J, Agarwal M, Katiyar-Agarwal S, Zhu JK. Mol Cell Biol 27 7771-7780 (2007)
  2. Proteomic analysis and extensive protein identification from dry, germinating Arabidopsis seeds and young seedlings. Fu Q, Wang BC, Jin X, Li HB, Han P, Wei KH, Zhang XM, Zhu YX. J Biochem Mol Biol 38 650-660 (2005)
  3. Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum. Besir H, Zeth K, Bracher A, Heider U, Ishibashi M, Tokunaga M, Oesterhelt D. FEBS Lett 579 6595-6600 (2005)
  4. NDPK2 as a signal transducer in the phytochrome-mediated light signaling. Shen Y, Kim JI, Song PS. J Biol Chem 280 5740-5749 (2005)
  5. Localisation of Arabidopsis NDPK2--revisited. Bölter B, Sharma R, Soll J. Planta 226 1059-1065 (2007)
  6. 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)
  7. Arabidopsis nucleoside diphosphate kinase-2 as a plant GTPase activating protein. Shen Y, Han YJ, Kim JI, Song PS. BMB Rep 41 645-650 (2008)
  8. Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase. Jeudy S, Lartigue A, Claverie JM, Abergel C. J Virol 83 7142-7150 (2009)
  9. Differential induction of mitochondrial machinery by light intensity correlates with changes in respiratory metabolism and photorespiration in rice leaves. Huang S, Jacoby RP, Shingaki-Wells RN, Li L, Millar AH. New Phytol 198 103-115 (2013)
  10. A Shortest-Path-Based Method for the Analysis and Prediction of Fruit-Related Genes in Arabidopsis thaliana. Zhu L, Zhang YH, Su F, Chen L, Huang T, Cai YD. PLoS One 11 e0159519 (2016)
  11. Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilum. Pédelacq JD, Waldo GS, Cabantous S, Liong EC, Terwilliger TC. Protein Sci 14 2562-2573 (2005)
  12. Crystal structure of nucleoside diphosphate kinase required for coleoptile elongation in rice (Oryza sativa L.). Huang JY, Chang T, Chang CY, Chen CJ. J Struct Biol 150 309-318 (2005)
  13. Retraction of Publication Retraction. Identification, subcellular localization and purification of the nucleoside diphosphate kinase regulated by phytochrome A from etiolated oat seedlings. Hurry V. Physiol Plant 133 458 (2008)


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