2ZNJ

Crystal structure of Pyrrolysyl-tRNA synthetase from Desulfitobacterium hafniense

DOI: 10.2210/pdb2ZNJ/pdb

Classification: LIGASE
Organism(s): Desulfitobacterium hafniense
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-04-25 Released: 2008-12-30
Deposition Author(s): Nozawa, K., Araiso, Y., Soll, D., Ishitani, R., Nureki, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.275
R-Value Work: 0.214
R-Value Observed: 0.214

wwPDB Validation3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality

Nozawa, K., O'Donoghue, P., Gundllapalli, S., Araiso, Y., Ishitani, R., Umehara, T., Soll, D., Nureki, O.

(2009) Nature 457: 1163-1167

PubMed: 19118381 Search on PubMedSearch on PubMed Central
DOI: 10.1038/nature07611
Primary Citation of Related Structures:
2ZNI, 2ZNJ

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.

Organizational Affiliation:

Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B34 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B, C	308	Desulfitobacterium hafniense	Mutation(s): 0 Gene Names: pylS EC: 6.1.1.26
Find proteins for B0S4P3 (Desulfitobacterium hafniense) Explore B0S4P3 Go to UniProtKB: B0S4P3
Protein Feature View Expand
( Mouse scroll to zoom / Hold left click to move ) Reference Sequence