engleski

Macromolecular complexes of amino acid:[carrier protein] ligases and carrier proteins

Aminoacyl-tRNA synthetases have well established and fundamental role in protein biosynthesis. They catalyze attachment of amino acids to cognate tRNAs, which are subsequently used as substrates for the ribosomal translation of mRNA. We have recently discovered and characterized bacterial homologs of atypical archaeal seryl-tRNA synthetases (aSerRS). These novel aSerRS homologs lack N-terminal tRNA-binding domain and, curiously, they transfer activated amino acids to phosphopantetheine prosthetic group of small carrier proteins (CPs) instead to tRNA. Therefore, they were named amino acid:[carrier protein] ligases (aa:CP ligases). In order to gain insight how these aSerRS homologs recognize substantially different macromolecular substrate, the crystal structure of aa:CP ligase 1 from Bradyrhizobium japonicum in complex with cognate carrier protein was solved. One CP molecule binds to each subunit of homodimeric aa:CP ligase. The phosphopantetheine group of carrier protein enters deep into the active site of the same subunit, from the opposite side than tRNA to aSerRS active site. The structure of the complex revealed that interaction with cognate CP relies on the α-helix idiosyncratic to aa:CP ligases, while kinetic and pull-down experiments showed that recognition of cognate CP is specific. Therefore, a hybrid protein of Bradyrhizobium japonicum aa:CP ligase was constructed, in which the helix involved in CP interaction was replaced with equivalent one from Agrobacterium tumefaciens aa:CP ligase. The hybrid protein displayed altered CP specificity, preferentially recognizing heterologous A. tumefaciens CP. Deletion of the helix resulted in loss of aa:CP ligase interaction with CP. The properties of hybrid protein and deletion variant confirmed that interaction of aa:CP ligases and CP is solely dependent on the identified region. The crystal structure of the hybrid protein in the complex with A. tumefaciens CP was also solved, and revealed unanticipated, slightly different CP orientation compared to B. japonicum complex. The crystal structures of aa:CP ligase complexes with CPs, combined with biochemical experiments, unravel fundamentally different recognition of macromolecular partners by these close aminoacyl- tRNA synthetase relatives.

seryl-tRNA synthetase; amino acid:[carrier protein] ligase; carrier protein; crystallography

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