1RIQ

The crystal structure of the catalytic fragment of the alanyl-tRNA synthetase

Summary for 1RIQ

• Entry DOI: 10.2210/pdb1riq/pdb
• Descriptor: Alanyl-tRNA synthetase (2 entities in total)
• Functional Keywords: beta sheet and flanking helices, class ii aminoacyl-trna synthetase, helix-loop-helix motif, ligase
• Biological source: Aquifex aeolicus
• Cellular location: Cytoplasm: O67323
• Total number of polymer chains: 1
• Total formula weight: 54147.40

Authors

Swairjo, M.A.,Otero, F.J.,Yang, X.-L.,Lovato, M.A.,Skene, R.J.,McRee, D.E.,Ribas de Pouplana, L.,Schimmel, P. (deposition date: 2003-11-17, release date: 2004-04-06, Last modification date: 2024-10-30)

Primary citation

Swairjo, M.A.,Otero, F.J.,Yang, X.-L.,Lovato, M.A.,Skene, R.J.,McRee, D.E.,Ribas De Pouplana, L.,Schimmel, P.
Alanyl-tRNA Synthetase Crystal Structure and Design for Acceptor-Stem Recognition
Mol.Cell, 13:829-841, 2004

PubMed Abstract: Early work on aminoacylation of alanine-specific tRNA (tRNA(Ala)) by alanyl-tRNA synthetase (AlaRS) gave rise to the concept of an early "second genetic code" imbedded in the acceptor stems of tRNAs. A single conserved and position-specific G:U base pair in the tRNA acceptor stem is the key identity determinant. Further understanding has been limited due to lack of a crystal structure of the enzyme. We determined a 2.14 A crystal structure of the 453 amino acid catalytic fragment of Aquifex aeolicus AlaRS. It contains the catalytic domain characteristic of class II synthetases, a helical domain with a hairpin motif critical for acceptor-stem recognition, and a C-terminal domain of a mixed alpha/beta fold. Docking of tRNA(Ala) on AlaRS shows critical contacts with the three domains, consistent with previous mutagenesis and functional data. It also suggests conformational flexibility within the C domain, which might allow for the positional variation of the key G:U base pair seen in some tRNA(Ala)s.

PubMed: 15053876
DOI: 10.1016/S1097-2765(04)00126-1

Experimental method

X-RAY DIFFRACTION (2.14 Å)