The Escherichia coli YadB gene product reveals a novel aminoacyl-tRNA synthetase like activity

J Mol Biol. 2004 Mar 19;337(2):273-83. doi: 10.1016/j.jmb.2004.01.027.


In the course of a structural genomics program aiming at solving the structures of Escherichia coli open reading frame products of unknown function, we have determined the structure of YadB at 1.5A using molecular replacement. The YadB protein is 298 amino acid residues long and displays 34% sequence identity with E.coli glutamyl-tRNA synthetase (GluRS). It is much shorter than GluRS, which contains 468 residues, and lacks the complete domain interacting with the tRNA anticodon loop. As E.coli GluRS, YadB possesses a Zn2+ located in the putative tRNA acceptor stem-binding domain. The YadB cluster uses cysteine residues as the first three zinc ligands, but has a weaker tyrosine ligand at the fourth position. It shares with canonical amino acid RNA synthetases a major functional feature, namely activation of the amino acid (here glutamate). It differs, however, from GluRSs by the fact that the activation step is tRNA-independent and that it does not catalyze attachment of the activated glutamate to E.coli tRNAGlu, but to another, as yet unknown tRNA. These results suggest thus a novel function, distinct from that of GluRSs, for the yadB gene family.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Monophosphate / metabolism
  • Adenosine Triphosphate / metabolism
  • Amino Acid Sequence
  • Amino Acyl-tRNA Synthetases / chemistry
  • Amino Acyl-tRNA Synthetases / genetics*
  • Amino Acyl-tRNA Synthetases / metabolism*
  • Carrier Proteins / metabolism
  • Crystallography, X-Ray
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics*
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics*
  • Escherichia coli Proteins / metabolism*
  • Genes, Bacterial
  • Glutamate-tRNA Ligase / chemistry
  • Glutamate-tRNA Ligase / genetics
  • Glutamate-tRNA Ligase / metabolism
  • Glutamic Acid / metabolism
  • Kinetics
  • Ligands
  • Models, Molecular
  • Molecular Sequence Data
  • Neoplasm Proteins / metabolism
  • Nuclear Proteins / metabolism
  • Protein Conformation
  • RNA, Transfer, Glu / metabolism
  • Sequence Homology, Amino Acid
  • Thermus thermophilus / enzymology
  • Thermus thermophilus / genetics
  • Zinc / metabolism


  • Carrier Proteins
  • Escherichia coli Proteins
  • Ligands
  • Neoplasm Proteins
  • Nuclear Proteins
  • RNA, Transfer, Glu
  • TRIM47 protein, human
  • Glutamic Acid
  • Adenosine Monophosphate
  • Adenosine Triphosphate
  • Amino Acyl-tRNA Synthetases
  • Glutamate-tRNA Ligase
  • Zinc

Associated data

  • PDB/1NZJ