7Y9I

Complex structure of AtYchF1 with ppGpp

Summary for 7Y9I

• Entry DOI: 10.2210/pdb7y9i/pdb
• Descriptor: Obg-like ATPase 1, GUANOSINE-5',3'-TETRAPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: atychf1, gtp-binding protein, ppgpp, ychf-type, p-loop ntpase, hydrolase
• Biological source: Arabidopsis thaliana (thale cress)
• Total number of polymer chains: 1
• Total formula weight: 45163.49

Authors

Li, X.,Chen, Z. (deposition date: 2022-06-24, release date: 2023-07-12, Last modification date: 2023-11-29)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.07 Å)