5UD5 image
Entry Detail
PDB ID:
5UD5
Keywords:
Title:
Crystal structure of the tRNA binding domain of Pyrrolysyl-tRNA synthetase bound to tRNA(Pyl)
Biological Source:
PDB Version:
Deposition Date:
2016-12-23
Release Date:
2017-10-11
Method Details:
Experimental Method:
Resolution:
2.35 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 31 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Pyrrolysine--tRNA ligase
Chain IDs:A, B
Chain Length:109
Number of Molecules:2
Biological Source:Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)
Polymer Type:polyribonucleotide
Description:RNA (70-MER)
Chain IDs:C, D
Chain Length:72
Number of Molecules:2
Biological Source:Methanosarcina mazei Go1
Ligand Molecules
Primary Citation
Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase.
Nat. Chem. Biol. 13 1261 1266 (2017)
PMID: 29035363 DOI: 10.1038/nchembio.2497

Abstact

Pyrrolysyl-tRNA synthetase (PylRS) is a major tool in genetic code expansion using noncanonical amino acids, yet its structure and function are not completely understood. Here we describe the crystal structure of the previously uncharacterized essential N-terminal domain of this unique enzyme in complex with tRNAPyl. This structure explains why PylRS remains orthogonal in a broad range of organisms, from bacteria to humans. The structure also illustrates why tRNAPyl recognition by PylRS is anticodon independent: the anticodon does not contact the enzyme. Then, using standard microbiological culture equipment, we established a new method for laboratory evolution-a noncontinuous counterpart of the previously developed phage-assisted continuous evolution. With this method, we evolved novel PylRS variants with enhanced activity and amino acid specificity. Finally, we employed an evolved PylRS variant to determine its N-terminal domain structure and show how its mutations improve PylRS activity in the genetic encoding of a noncanonical amino acid.

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Primary Citation of related structures