2DU3

Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase complexed with tRNACys and O-phosphoserine

Summary for 2DU3

• Entry DOI: 10.2210/pdb2du3/pdb
• Related: 2du4 2du5 2du6 2du7
• Descriptor: tRNA, O-phosphoseryl-tRNA synthetase, PHOSPHOSERINE, ... (4 entities in total)
• Functional Keywords: alpha4 tetramer, ligase-rna complex, ligase/rna
• Biological source: Archaeoglobus fulgidus
• Total number of polymer chains: 3
• Total formula weight: 145833.06

Authors

Fukunaga, R. (deposition date: 2006-07-20, release date: 2007-03-13, Last modification date: 2024-03-13)

Primary citation

Fukunaga, R.,Yokoyama, S.
Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.
Nat.Struct.Mol.Biol., 14:272-279, 2007

PubMed Abstract: Cysteine is ligated to tRNA(Cys) by cysteinyl-tRNA synthetase in most organisms. However, in methanogenic archaea lacking cysteinyl-tRNA synthetase, O-phosphoserine is ligated to tRNA(Cys) by O-phosphoseryl-tRNA synthetase (SepRS), and the phosphoseryl-tRNA(Cys) is converted to cysteinyl-tRNA(Cys). In this study, we determined the crystal structure of the SepRS tetramer in complex with tRNA(Cys) and O-phosphoserine at 2.6-A resolution. The catalytic domain of SepRS recognizes the negatively charged side chain of O-phosphoserine at a noncanonical site, using the dipole moment of a conserved alpha-helix. The unique C-terminal domain specifically recognizes the anticodon GCA of tRNA(Cys). On the basis of the structure, we engineered SepRS to recognize tRNA(Cys) mutants with the anticodons UCA and CUA and clarified the anticodon recognition mechanism by crystallography. The mutant SepRS-tRNA pairs may be useful for translational incorporation of O-phosphoserine into proteins in response to the stop codons UGA and UAG.

PubMed: 17351629
DOI: 10.1038/nsmb1219

Experimental method

X-RAY DIFFRACTION (2.6 Å)