1NZJ

Crystal Structure and Activity Studies of Escherichia Coli Yadb ORF

Summary for 1NZJ

• Entry DOI: 10.2210/pdb1nzj/pdb
• Descriptor: Hypothetical protein yadB, ZINC ION (3 entities in total)
• Functional Keywords: zn cluster, glutamyl t-rna synthetase, structural genomics, unknown function
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 33709.38

Authors

Campanacci, V.,Kern, D.Y.,Becker, H.D.,Spinelli, S.,Valencia, C.,Vincentelli, R.,Pagot, F.,Bignon, C.,Giege, R.,Cambillau, C. (deposition date: 2003-02-18, release date: 2004-04-13, Last modification date: 2023-10-25)

Primary citation

Campanacci, V.,Dubois, D.Y.,Becker, H.D.,Kern, D.,Spinelli, S.,Valencia, C.,Pagot, F.,Salomoni, A.,Grisel, S.,Vincentelli, R.,Bignon, C.,Lapointe, J.,Giege, R.,Cambillau, C.
The Escherichia coli YadB gene product reveals a novel aminoacyl-tRNA synthetase like activity.
J.Mol.Biol., 337:273-283, 2004

PubMed Abstract: 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.

PubMed: 15003446
DOI: 10.1016/j.jmb.2004.01.027

Experimental method

X-RAY DIFFRACTION (1.5 Å)