7Y9I

Complex structure of AtYchF1 with ppGpp

7Y9I の概要

• エントリーDOI: 10.2210/pdb7y9i/pdb
• 分子名称: Obg-like ATPase 1, GUANOSINE-5',3'-TETRAPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: atychf1, gtp-binding protein, ppgpp, ychf-type, p-loop ntpase, hydrolase
• 由来する生物種: Arabidopsis thaliana (thale cress)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 45163.49

構造登録者

Li, X.,Chen, Z. (登録日: 2022-06-24, 公開日: 2023-07-12, 最終更新日: 2023-11-29)

主引用文献

Cheung, M.Y.,Li, X.,Ku, Y.S.,Chen, Z.,Lam, H.M.
Co-crystalization reveals the interaction between AtYchF1 and ppGpp.
Front Mol Biosci, 9:1061350-1061350, 2022

PubMed Abstract: AtYchF1 is an unconventional G-protein in that exhibits relaxed nucleotide-binding specificity. The bindings between AtYchF1 and biomolecules including GTP, ATP, and 26S rRNA have been reported. In this study, we demonstrated the binding of AtYchF1 to ppGpp in addition to the above molecules. AtYchF1 is a cytosolic protein previously reported as a negative regulator of both biotic and abiotic stresses while the accumulation of ppGpp in the cytoplasm induces retarded plant growth and development. By co-crystallization, pull-down experiments, and hydrolytic biochemical assays, we demonstrated the binding and hydrolysis of ppGpp by AtYchF1. ppGpp inhibits the binding of AtYchF1 to ATP, GTP, and 26S rRNA. The ppGpp hydrolyzing activity of AtYchF1 failed to be activated by AtGAP1. The AtYchF1-ppGpp co-crystal structure suggests that ppGpp might prevent His from executing nucleotide hydrolysis. In addition, upon the binding of ppGpp, the conformation between the TGS and helical domains of AtYchF1 changes. Such structural changes probably influence the binding between AtYchF1 and other molecules such as 26S rRNA. Since YchF proteins are conserved among different kingdoms of life, the findings advance the knowledge on the role of AtYchF1 in regulating nucleotide signaling as well as hint at the possible involvement of YchF proteins in regulating ppGpp level in other species.

PubMed: 36533075
DOI: 10.3389/fmolb.2022.1061350

実験手法

X-RAY DIFFRACTION (2.07 Å)