7CKH

Crystal structure of TMSiPheRS

Summary for 7CKH

• Entry DOI: 10.2210/pdb7ckh/pdb
• Descriptor: Tyrosine--tRNA ligase (2 entities in total)
• Functional Keywords: aminoacyl-trna synthetase, p-trimethysilyl phenylalanine, ligase
• Biological source: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
• Total number of polymer chains: 2
• Total formula weight: 71825.11

Authors

Sun, J.P.,Wang, J.Y.,Zhu, Z.L.,He, Q.T.,Xiao, P. (deposition date: 2020-07-17, release date: 2021-03-31, Last modification date: 2023-11-29)

Primary citation

Liu, Q.,He, Q.T.,Lyu, X.,Yang, F.,Zhu, Z.L.,Xiao, P.,Yang, Z.,Zhang, F.,Yang, Z.Y.,Wang, X.Y.,Sun, P.,Wang, Q.W.,Qu, C.X.,Gong, Z.,Lin, J.Y.,Xu, Z.,Song, S.L.,Huang, S.M.,Guo, S.C.,Han, M.J.,Zhu, K.K.,Chen, X.,Kahsai, A.W.,Xiao, K.H.,Kong, W.,Li, F.H.,Ruan, K.,Li, Z.J.,Yu, X.,Niu, X.G.,Jin, C.W.,Wang, J.,Sun, J.P.
DeSiphering receptor core-induced and ligand-dependent conformational changes in arrestin via genetic encoded trimethylsilyl 1 H-NMR probe.
Nat Commun, 11:4857-4857, 2020

PubMed Abstract: Characterization of the dynamic conformational changes in membrane protein signaling complexes by nuclear magnetic resonance (NMR) spectroscopy remains challenging. Here we report the site-specific incorporation of 4-trimethylsilyl phenylalanine (TMSiPhe) into proteins, through genetic code expansion. Crystallographic analysis revealed structural changes that reshaped the TMSiPhe-specific amino-acyl tRNA synthetase active site to selectively accommodate the trimethylsilyl (TMSi) group. The unique up-field H-NMR chemical shift and the highly efficient incorporation of TMSiPhe enabled the characterization of multiple conformational states of a phospho-β2 adrenergic receptor/β-arrestin-1(β-arr1) membrane protein signaling complex, using only 5 μM protein and 20 min of spectrum accumulation time. We further showed that extracellular ligands induced conformational changes located in the polar core or ERK interaction site of β-arr1 via direct receptor transmembrane core interactions. These observations provided direct delineation and key mechanism insights that multiple receptor ligands were able to induce distinct functionally relevant conformational changes of arrestin.

PubMed: 32978402
DOI: 10.1038/s41467-020-18433-5

Experimental method

X-RAY DIFFRACTION (1.79492679758 Å)