Co-crystallization of Staphylococcus aureus peptide deformylase (PDF) with potent inhibitors.
In bacteria the biosynthesis of all nascent polypeptides begins with N-formylmethionine. The post-translational removal of the N-formyl group is carried out by peptide deformylase (PDF). Processing of the N-formyl group from critical bacterial proteins is required for cell survival. This formylation/deformylation cycle is unique to eubacteria and is not utilized in eucaryotic cytosolic protein biosynthesis. Thus, inhibition of PDF would halt bacterial growth, spare host cell-function, and would be a novel mechanism for a new class of antibiotic. Diffraction-quality Se-met crystals of S. aureus PDF were prepared that belong to space group C222(1) with unit cell parameters of a = 94.1 b = 121.9 c = 47.6 A. Multiple anomalous dispersion data were collected at the Advanced Photon Source 17-ID beamline and used to solve the PDF structure to 1.9 A resolution. Crystals were also prepared with three PDF inhibitors: thiorphan, actinonin and PNU-172550. The thiorphan and actinonin co-crystals belong to space group C222(1) with similar unit-cell dimensions. Repeated attempts to generate a complex structure of PDF with PNU-172550 from the orthorhombic space group were unsuccessful. Crystallization screening identified an alternate C2 crystal form with unit-cell dimensions of a = 93.4 b = 42.5 c = 104.1 A, beta = 93 degrees.
Harris
Melissa S
MS
Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, 301 Henrietta Street, Kalamazoo, MI 49007, USA. melissa.s.harris@pharmacia.com
Bock
Jeffrey H
JH
Choi
Gil
G
Cialdella
Joyce S
JS
Curry
Kimberly A
KA
Deibel
Martin R
MR
Jacobsen
E Jon
EJ
Marshall
Vincent P
VP
Murray
Robert W
RW
Vosters
Anne F
AF
Wolfe
Cindy L
CL
Yem
Anthony W
AW
Baldwin
Eric T
ET
D000581:Amidohydrolases; D000626:Aminopeptidases / Q000037:antagonists & inhibitors / Q000737:chemistry*; D003460:Crystallization; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D011487:Protein Conformation; D013211:Staphylococcus aureus / Q000201:enzymology*
D004791:Enzyme Inhibitors; D000626:Aminopeptidases; D000581:Amidohydrolases; C084507:peptide deformylase