Co-crystallization of Leptospira interrogans peptide deformylase with a potent inhibitor and molecular-replacement schemes with eight subunits in an asymmetric unit.
Translation initiation in eubacteria involves a formylmethionine at the N-terminus of newly synthesized polypeptides. This N-formyl group is removed by peptide deformylase (PDF) during the post-translation process. Such a formylation/deformylation cycle is essential for the cell survival of eubacteria, but is not utilized in eukaryotic cytosolic protein biosynthesis. In view of the absence of deformylase activity in mammalian cells, this is an attractive target for the design of novel antibiotic drugs. Co-crystallization of peptide deformylase from Leptospira interrogans (LiPDF) with its natural inhibitor actinonin produced diffraction-quality crystals that belong to space group P2(1), with unit-cell parameters a = 87.5, b = 119.1, c = 95.8 A, beta = 111.6 degrees. The 3.1 A resolution data set collected in-house was used to obtain phases by molecular replacement. Three schemes for the correction of the preliminary solutions were proposed and proved successful in determining the structure of LiPDF with eight subunits in the asymmetric unit.
Zhou
Zhaocai
Z
School of Life Sciences, Key Laboratory of Structural Biology, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.
Gong
Weimin
W
D000581:Amidohydrolases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000302:isolation & purification; D000900:Anti-Bacterial Agents / Q000737:chemistry; D003460:Crystallization; D018360:Crystallography, X-Ray; D006877:Hydroxamic Acids / Q000737:chemistry* / Q000302:isolation & purification; D007921:Leptospira interrogans / Q000201:enzymology*; D008958:Models, Molecular
D000900:Anti-Bacterial Agents; D006877:Hydroxamic Acids; D000581:Amidohydrolases; C084507:peptide deformylase; C010531:actinonin