4PBS: Crystal structure of the M. jannaschii F9 tRNA synthetase variant bound to 4-(2-bromoisobutyramido)-phenylalanine (BibaF)

The site-specific incorporation of non-canonical amino acids (ncAAs) into proteins is an important tool for understanding biological function. Traditionally, each new ncAA targeted for incorporation requires a resource-consuming process of generating new ncAA aminoacyl tRNA synthetase/tRNACUA pairs. However, the discovery that some tRNA synthetases are "permissive", in that they can incorporate multiple ncAAs, means that it is no longer always necessary to develop a new synthetase for each newly desired ncAA. Developing a better understanding of what factors make ncAA synthetases more permissive would increase the utility of this new approach. Here, we characterized two synthetases selected for the same ncAA that have markedly different "permissivity profiles." Remarkably, the more permissive synthetase incorporated an ncAA for which we had not been able to generate a synthetase through de novo selection methods. Crystal structures revealed that the two synthetases recognize their parent ncAA through a conserved core of interactions, with the more permissive synthetase displaying a greater degree of flexibility in its interaction geometries. We also observed that intraprotein interactions not directly involved in ncAA binding can play a crucial role in synthetase permissivity and suggest that optimization of such interactions might provide an avenue to engineering synthetases with enhanced permissivity.
PDB ID: 4PBSDownload
MMDB ID: 121736
PDB Deposition Date: 2014/4/13
Updated in MMDB: 2017/10
Experimental Method:
x-ray diffraction
Resolution: 2.011  Å
Source Organism:
Similar Structures:
Biological Unit for 4PBS: dimeric; determined by author and by software (PISA)
Molecular Components in 4PBS
Label Count Molecule
Proteins (2 molecules)
Tyrosine--trna Ligase(Gene symbol: MJ_RS02045)
Molecule annotation
Chemicals (2 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB