6LY3

PylRS C-terminus domain mutant bound with 3-Benzothienyl-L-alanine and AMPNP

Summary for 6LY3

• Entry DOI: 10.2210/pdb6ly3/pdb
• Descriptor: Pyrrolysine--tRNA ligase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: trna synthetase, ligase
• Biological source: Methanosarcina mazei
• Total number of polymer chains: 1
• Total formula weight: 32775.68

Authors

Weng, J.H.,Tsai, M.D.,Wang, Y.S. (deposition date: 2020-02-13, release date: 2020-07-08, Last modification date: 2023-11-29)

Primary citation

Jiang, H.K.,Wang, Y.H.,Weng, J.H.,Kurkute, P.,Li, C.L.,Lee, M.N.,Chen, P.J.,Tseng, H.W.,Tsai, M.D.,Wang, Y.S.
Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues.
Biochemistry, 59:2205-2209, 2020

PubMed Abstract: pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA have been evolved to generate genetically encoded noncanonical amino acids (ncAAs). Use of tryptophan (Trp) analogues with pyrrole ring modification for their spatial and polarity tuning in enzyme activity and substrate specificity is still limited. Herein, we report the application of an evolved PylRS, FOWRS2, for efficient incorporation of five Trp analogues into the deubiquitinase USP30 to decipher the role of W475 for diubiquitin selectivity. Structures of the five FOWRS-C/Trp analogue complexes at 1.7-2.5 Å resolution showed multiple ncAA binding modes. The W475 near the USP30 active site was replaced with Trp analogues, and the effect on the activity as well as the selectivity toward diubiquitin linkage types was examined. It was found that the Trp analogue with a formyl group attached to the nitrogen atom of the indole ring led to an improved activity of USP30 likely due to enhanced polar interactions and that another Trp analogue, 3-benzothienyl-l-alanine, induced a unique K6-specificity. Collectively, genetically encoded noncanonical Trp analogues by evolved PylRS· pair unravel the spatial role of USP30-W475 in its diubiquitin selectivity.

PubMed: 32484330
DOI: 10.1021/acs.biochem.0c00307

Experimental method

X-RAY DIFFRACTION (1.8959014841 Å)