The emergence of multi-drug-resistant strains of Staphylococcus epidermidis emphasizes the need to develop new antibiotics. The unique and essential role of the peptide deformylase (PDF) in catalysing the removal of the N-terminal formyl group from newly synthesized polypeptides in eubacteria makes it an attractive antibacterial drug target. In the present study, both deformylase homologues from S. epidermidis (SePDF-1 and SePDF-2) were cloned and expressed, and their enzymic activities were characterized. Co2+-substituted SePDF-1 exhibited much higher enzymic activity (kcat/Km 6.3×104 M−1 s−1) than those of Ni2+- and Zn2+-substituted SePDF-1, and SePDF-1 showed much weaker binding ability towards Ni2+ than towards Co2+ and Zn2+, which is different from PDF in Staphylococcus aureus (SaPDF), although they share 80 % amino-acid sequence identity. The determined crystal structure of SePDF-1 was similar to that of (SaPDF), except for differences in the metal-binding sites. The other deformylase homologue, SePDF-2, was shown to have no peptide deformylase activity; the function of SePDF-2 needs to be further investigated.
BaldwinE. T.,
HarrisM. S.,
YemA. W.,
WolfeC. L.,
VostersA. F.,
CurryK. A.,
MurrayR. W.,
BockJ. H.,
MarshallV. P.other authors2002; Crystal structure of type II peptide deformylase from Staphylococcus aureus. J Biol Chem 277:31163–31171
BradshawR. A.,
BrickeyW. W.,
WalkerK. W.1998; N-terminal processing: the methionine aminopeptidase and N alpha-acetyl transferase families. Trends Biochem Sci 23:263–267
BrüngerA. T.,
AdamsP. D.,
CloreG. M.,
DeLanoW. L.,
GrosP.,
Grosse-KunstleveR. W.,
JiangJ. S.,
KuszewskiJ.,
NilgesM.other authors1998; Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921
ChanM. K.,
GongW.,
RajagopalanP. T.,
HaoB.,
TsaiC. M.,
PeiD.1997; Crystal structure of the Escherichia coli peptide deformylase. Biochemistry 36:13904–13909
DirkL. M.,
WilliamsM. A.,
HoutzR. L.2001; Eukaryotic peptide deformylases. Nuclear-encoded and chloroplast-targeted enzymes in Arabidopsis. Plant Physiol 127:97–107
DongM.,
LiuH.2008; Origins of the different metal preferences of Escherichia coli peptide deformylase and Bacillus thermoproteolyticus thermolysin: a comparative quantum mechanical/molecular mechanical study. J Phys Chem B 112:10280–10290
Escobar-AlvarezS.,
GoldgurY.,
YangG.,
OuerfelliO.,
LiY.,
ScheinbergD. A.2009; Structure and activity of human mitochondrial peptide deformylase, a novel cancer target. J Mol Biol 387:1211–1228
EvansP. R.1993; Data reduction. In Proceedings of CCP4 Study Weekend on Data Collection and Processing pp 114–122 Warrington, UK: Daresbury Laboratory;
FieulaineS.,
Juillan-BinardC.,
SereroA.,
DardelF.,
GiglioneC.,
MeinnelT.,
FerrerJ. L.2005; The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms. J Biol Chem 280:42315–42324
GiglioneC.,
PierreM.,
MeinnelT.2000a; Peptide deformylase as a target for new generation, broad spectrum antimicrobial agents. Mol Microbiol 36:1197–1205
GrocheD.,
BeckerA.,
SchlichtingI.,
KabschW.,
SchultzS.,
WagnerA. F.1998; Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site. Biochem Biophys Res Commun 246:342–346
GuilloteauJ. P.,
MathieuM.,
GiglioneC.,
BlancV.,
DupuyA.,
ChevrierM.,
GilP.,
FamechonA.,
MeinnelT.other authors2002; The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents. J Mol Biol 320:951–962
HaasM.,
BeyerD.,
GahlmannR.,
FreibergC.2001; YkrB is the main peptide deformylase in Bacillus subtilis, a eubacterium containing two functional peptide deformylases. Microbiology 147:1783–1791
HanC.,
WangQ.,
DongL.,
SunH.,
PengS.,
ChenJ.,
YangY.,
YueJ.,
ShenX.other authors2004; Molecular cloning and characterization of a new peptide deformylase from human pathogenic bacterium Helicobacter pylori. Biochem Biophys Res Commun 319:1292–1298
KabschW.,
SanderC.1983; Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637
LeeM. D.,
SheY.,
SoskisM. J.,
BorellaC. P.,
GardnerJ. R.,
HayesP. A.,
DyB. M.,
HeaneyM. L.,
PhilipsM. R.other authors2004; Human mitochondrial peptide deformylase, a new anticancer target of actinonin-based antibiotics. J Clin Invest 114:1107–1116
LeslieA. G. W.1992; Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4+ESF-EAMCB Newsletter on Protein Crystallography 26:
LiY.,
ChenZ.,
GongW.2002; Enzymatic properties of a new peptide deformylase from pathogenic bacterium Leptospira interrogans. Biochem Biophys Res Commun 295:884–889
MeinnelT.,
BlanquetS.1994; Characterization of the Thermus thermophilus locus encoding peptide deformylase and methionyl-tRNA(fMet) formyltransferase. J Bacteriol 176:7387–7390
MeinnelT.,
MechulamY.,
BlanquetS.1993; Methionine as translation start signal: a review of the enzymes of the pathway in Escherichia coli. Biochimie 75:1061–1075
MeinnelT.,
BlanquetS.,
DardelF.1996; A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase. J Mol Biol 262:375–386
MeinnelT.,
LazennecC.,
VilloingS.,
BlanquetS.1997; Structure-function relationships within the peptide deformylase family. Evidence for a conserved architecture of the active site involving three conserved motifs and a metal ion. J Mol Biol 267:749–761
MurshudovG. N.,
VaginA. A.,
DodsonE. J.1997; Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr53240–255
NguyenK. T.,
HuX.,
ColtonC.,
ChakrabartiR.,
ZshuM. X.,
PeiD.2003; Characterization of a human peptide deformylase: implications for antibacterial drug design. Biochemistry 42:9952–9958
NguyenK. T.,
WuJ. C.,
BoylanJ. A.,
GherardiniF. C.,
PeiD.2007; Zinc is the metal cofactor of Borrelia burgdorferi peptide deformylase. Arch Biochem Biophys 468:217–225
RajagopalanP. T.,
GrimmeS.,
PeiD.2000; Characterization of cobalt(II)-substituted peptide deformylase: function of the metal ion and the catalytic residue Glu-133. Biochemistry 39:779–790
RobienM. A.,
NguyenK. T.,
KumarA.,
HirshI.,
TurleyS.,
PeiD.,
HolW. G.2004; An improved crystal form of Plasmodium falciparum peptide deformylase. Protein Sci 13:1155–1163
SereroA.,
GiglioneC.,
SardiniA.,
Martinez-SanzJ.,
MeinnelT.2003; An unusual peptide deformylase features in the human mitochondrial N-terminal methionine excision pathway. J Biol Chem 278:52953–52963
SharmaA.,
KhullerG. K.,
SharmaS.2009; Peptide deformylase – a promising therapeutic target for tuberculosis and antibacterial drug discovery. Expert Opin Ther Targets 13:753–765
SmithK. J.,
PetitC. M.,
AubartK.,
SmythM.,
McManusE.,
JonesJ.,
FosberryA.,
LewisC.,
LonettoM.other authors2003; Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species. Protein Sci 12:349–360
ZhouZ.,
SongX.,
GongW.2005; Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift. J Biol Chem 280:42391–42396