2ZNI

Crystal structure of Pyrrolysyl-tRNA synthetase-tRNA(Pyl) complex from Desulfitobacterium hafniense

Summary for 2ZNI

• Entry DOI: 10.2210/pdb2zni/pdb
• Descriptor: Pyrrolysyl-tRNA synthetase, bacterial tRNA, CALCIUM ION (3 entities in total)
• Functional Keywords: ligase-rna complex, ligase/rna
• Biological source: Desulfitobacterium hafniense; More
• Total number of polymer chains: 4
• Total formula weight: 117944.04

Authors

Nozawa, K.,Araiso, Y.,Soll, D.,Ishitani, R.,Nureki, O. (deposition date: 2008-04-25, release date: 2008-12-30, Last modification date: 2024-04-03)

Primary citation

Nozawa, K.,O'Donoghue, P.,Gundllapalli, S.,Araiso, Y.,Ishitani, R.,Umehara, T.,Soll, D.,Nureki, O.
Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality
Nature, 457:1163-1167, 2009

PubMed Abstract: Pyrrolysine (Pyl), the 22nd natural amino acid, is genetically encoded by UAG and inserted into proteins by the unique suppressor tRNA(Pyl) (ref. 1). The Methanosarcinaceae produce Pyl and express Pyl-containing methyltransferases that allow growth on methylamines. Homologous methyltransferases and the Pyl biosynthetic and coding machinery are also found in two bacterial species. Pyl coding is maintained by pyrrolysyl-tRNA synthetase (PylRS), which catalyses the formation of Pyl-tRNA(Pyl) (refs 4, 5). Pyl is not a recent addition to the genetic code. PylRS was already present in the last universal common ancestor; it then persisted in organisms that utilize methylamines as energy sources. Recent protein engineering efforts added non-canonical amino acids to the genetic code. This technology relies on the directed evolution of an 'orthogonal' tRNA synthetase-tRNA pair in which an engineered aminoacyl-tRNA synthetase (aaRS) specifically and exclusively acylates the orthogonal tRNA with a non-canonical amino acid. For Pyl the natural evolutionary process developed such a system some 3 billion years ago. When transformed into Escherichia coli, Methanosarcina barkeri PylRS and tRNA(Pyl) function as an orthogonal pair in vivo. Here we show that Desulfitobacterium hafniense PylRS-tRNA(Pyl) is an orthogonal pair in vitro and in vivo, and present the crystal structure of this orthogonal pair. The ancient emergence of PylRS-tRNA(Pyl) allowed the evolution of unique structural features in both the protein and the tRNA. These structural elements manifest an intricate, specialized aaRS-tRNA interaction surface that is highly distinct from those observed in any other known aaRS-tRNA complex; it is this general property that underlies the molecular basis of orthogonality.

PubMed: 19118381
DOI: 10.1038/nature07611

Experimental method

X-RAY DIFFRACTION (3.1 Å)