Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 A resolution

Abstract

The crystal structure of APE2540, the putative trans-editing enzyme ProX from Aeropyrum pernix K1, was determined in a high-throughput manner. The crystal belongs to the monoclinic space group P2(1), with unit-cell parameters a = 47.4, b = 58.9, c = 53.6 A, beta = 106.8 degrees. The structure was solved by the multiwavelength anomalous dispersion method at 1.7 A and refined to an R factor of 16.8% (Rfree = 20.5%). The crystal structure includes two protein molecules in the asymmetric unit. Each monomer consists of eight beta-strands and seven alpha-helices. A structure-homology search revealed similarity between the trans-editing enzyme YbaK (or cysteinyl-tRNAPro deacylase) from Haemophilus influenzae (HI1434; 22% sequence identity) and putative ProX proteins from Caulobacter crescentus (16%) and Agrobacterium tumefaciens (21%).

Figure 1

(a) Quality of the electron-density map. The refined structure is represented by a thin wire. The map is contoured at the 1.0σ level. (b) Stereo diagram of the APE2540 protein. The secondary structures are coloured blue (α-helices) and red (β-strands). (c) Comparison of the structural homologues of the APE2540 protein. The three structures are coloured and oriented in the same direction as in Fig. 1 ▶(b). Figs. 1(b) and 1(c) were produced with Molscript (Kraulis, 1991 ▶) and Raster3D (Merritt & Bacon, 1997 ▶).

Figure 2

Sequence alignment among structural homologues of APE2540. Blue bars and red arrows above the sequences show secondary-structural elements (α-helix and β-sheet). Identical amino acids are highlighted in red. The Lys residues conserved for deacylation activity are highlighted in green.