1S59

Structure of nucleoside diphosphate kinase 2 with bound dGTP from Arabidopsis

1S59 の概要

• エントリーDOI: 10.2210/pdb1s59/pdb
• 関連するPDBエントリー: 1S57
• 分子名称: Nucleoside diphosphate kinase II, 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE, 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, ... (4 entities in total)
• 機能のキーワード: transferase, kinase
• 由来する生物種: Arabidopsis thaliana (thale cress)
• 細胞内の位置: Plastid, chloroplast: O64903
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 103424.18

構造登録者

Im, Y.J.,Kim, J.-I.,Shen, Y.,Na, Y.,Han, Y.-J.,Kim, S.-H.,Song, P.-S.,Eom, S.H. (登録日: 2004-01-20, 公開日: 2004-11-30, 最終更新日: 2023-10-25)

主引用文献

Im, Y.J.,Kim, J.-I.,Shen, Y.,Na, Y.,Han, Y.-J.,Kim, S.-H.,Song, P.-S.,Eom, S.H.
Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling
J.Mol.Biol., 343:659-670, 2004

PubMed 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.

PubMed: 15465053
DOI: 10.1016/j.jmb.2004.08.054

実験手法

X-RAY DIFFRACTION (2.6 Å)