1VBN

Escherichia coli tyrosyl-tRNA synthetase mutant complexed with Tyr-AMS

Summary for 1VBN

• Entry DOI: 10.2210/pdb1vbn/pdb
• Related: 1UDF 1UDJ 1VBM
• Descriptor: Tyrosyl-tRNA synthetase, 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE (3 entities in total)
• Functional Keywords: ligase, structural genomics, riken structural genomics/proteomics initiative, rsgi
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 72235.63

Authors

Kobayashi, T.,Sakamoto, K.,Takimura, T.,Kamata, K.,Sekine, R.,Nishimura, S.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2004-02-27, release date: 2005-01-25, Last modification date: 2023-10-25)

Primary citation

Kobayashi, T.,Sakamoto, K.,Takimura, T.,Sekine, R.,Vincent, K.,Kamata, K.,Nishimura, S.,Yokoyama, S.
Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion
Proc.Natl.Acad.Sci.USA, 102:1366-1371, 2005

PubMed Abstract: The genetic code in a eukaryotic system has been expanded by the engineering of Escherichia coli tyrosyl-tRNA synthetase (TyrRS) with the Y37V and Q195C mutations (37V195C), which specifically recognize 3-iodo-L-tyrosine rather than L-tyrosine. In the present study, we determined the 3-iodo-L-tyrosine- and L-tyrosine-bound structures of the 37V195C mutant of the E. coli TyrRS catalytic domain at 2.0-A resolution. The gamma-methyl group of Val-37 and the sulfur atom of Cys-195 make van der Waals contacts with the iodine atom of 3-iodo-L-tyrosine. The Val-37 and Cys-195 side chains are rigidly fixed by the neighboring residues forming the hydrophobic core of the TyrRS. The major roles of the two mutations are different for the 3-iodo-L-tyrosine-selective recognition in the first step of the aminoacylation reaction (the amino acid activation step): the Y37V mutation eliminates the fatal steric repulsion with the iodine atom, and the Q195C mutation reduces the L-tyrosine misrecognition. The structure of the 37V195C mutant TyrRS complexed with an L-tyrosyladenylate analogue was also solved, indicating that the 3-iodo-L-tyrosine and L-tyrosine side chains are similarly discriminated in the second step (the aminoacyl transfer step). These results demonstrate that the amino acid-binding pocket on the 37V195C mutant is optimized for specific 3-iodo-L-tyrosine recognition.

PubMed: 15671170
DOI: 10.1073/pnas.0407039102

Experimental method

X-RAY DIFFRACTION (2.7 Å)