ISDA: 7CKG

Deposition Date 2020-07-17

Release Date 2021-03-31

Last Version Date 2023-11-29

Entry Detail

PDB ID:

7CKG

Keywords:

LIGASE

Title:

Crystal structure of TMSiPheRS complexed with TMSiPhe

Biological Source:

Source Organism:

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Taxon ID: 243232)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.05 Å

R-Value Free:

0.25

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

P 21 21 21

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Tyrosine--tRNA ligase
Gene (Uniprot):tyrS
Mutagens:Y32H,I63G,L65V,H70Q,D158G,I159G,V164G
Chain IDs:A, B
Chain Length:314
Number of Molecules:2
Biological Source:Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

UniProt ID:Q57834 Pfam ID:PF00579 EC:6.1.1.1

Ligand Molecules

TSQ

Primary Citation

DeSiphering receptor core-induced and ligand-dependent conformational changes in arrestin via genetic encoded trimethylsilyl 1 H-NMR probe.

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.Show

Nat Commun 11 4857 4857 (2020)

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

Abstact

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 1H-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.

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Primary Citation of related structures

Abstact

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