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Gene Review

def  -  peptide deformylase

Escherichia coli O157:H7 str. Sakai

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Disease relevance of def


High impact information on def

  • Peptide deformylase (PDF) catalyzes the hydrolytic removal of the N-terminal formyl group from nascent proteins [1].
  • A novel class of PDF inhibitors (PDF-I), the N-alkyl urea hydroxamic acids, were synthesized and evaluated for their activities against the M. tuberculosis PDF enzyme as well as their antimycobacterial effects [1].
  • PDF from M. tuberculosis strain H37Rv was cloned, expressed, and purified as an N-terminal histidine-tagged recombinant protein in Escherichia coli [1].
  • Mechanism of time-dependent inhibition of polypeptide deformylase by actinonin [3].
  • Polypeptide deformylase (PDF) is an essential bacterial metalloenzyme responsible for the removal of the N-formyl group from the N-terminal methionine of nascent polypeptides [3].

Chemical compound and disease context of def

  • The most potent inhibitor was calpeptin, N-CBZ-Leu-norleucinal, which was a competitive inhibitor of the zinc-containing metalloenzymes, E. coli and B. subtilis PDF with Ki values of 26.0 and 55.6 microM, respectively [6].

Biological context of def

  • Macrolactin N inhibited Staphylococcus aureus peptide deformylase with an IC50 value of 7.5 microM and also showed antibacterial activity against Escherichia coli and S. aureus [5].
  • The comparison of the QSARs between the cell free and whole cell system indicate that the active binding sites in PDF isolated from E. coli and in M. catarrhalis RA21 are similar and the whole cell antibacterial activity is mainly due to the inhibition of PDF [7].

Associations of def with chemical compounds

  • In addition, we demonstrate that BB-3497 is also a time-dependent inhibitor of PDF with an extremely slow off-rate [3].
  • In sharp contrast, the previously reported small molecule PDF inhibitor, SB-543668, is a competitive, readily reversible inhibitor (t(1/2) for dissociation = 2.8 s) [3].
  • In a randomized cross-over setting eight stable diabetic CAPD patients performed the third and fourth exchange of the day with either G-PDF or with glucose-containing PDF (D-PDF) of comparable osmolality [8].

Analytical, diagnostic and therapeutic context of def


  1. Peptide deformylase inhibitors as potent antimycobacterial agents. Teo, J.W., Thayalan, P., Beer, D., Yap, A.S., Nanjundappa, M., Ngew, X., Duraiswamy, J., Liung, S., Dartois, V., Schreiber, M., Hasan, S., Cynamon, M., Ryder, N.S., Yang, X., Weidmann, B., Bracken, K., Dick, T., Mukherjee, K. Antimicrob. Agents Chemother. (2006) [Pubmed]
  2. Expression of Escherichia coli methionyl-tRNA formyltransferase in Saccharomyces cerevisiae leads to formylation of the cytoplasmic initiator tRNA and possibly to initiation of protein synthesis with formylmethionine. Ramesh, V., Köhrer, C., RajBhandary, U.L. Mol. Cell. Biol. (2002) [Pubmed]
  3. Mechanism of time-dependent inhibition of polypeptide deformylase by actinonin. Van Aller, G.S., Nandigama, R., Petit, C.M., DeWolf, W.E., Quinn, C.J., Aubart, K.M., Zalacain, M., Christensen, S.B., Copeland, R.A., Lai, Z. Biochemistry (2005) [Pubmed]
  4. Synthesis and antibacterial activity of peptide deformylase inhibitors. Huntington, K.M., Yi, T., Wei, Y., Pei, D. Biochemistry (2000) [Pubmed]
  5. Macrolactin N, a new peptide deformylase inhibitor produced by Bacillus subtilis. Yoo, J.S., Zheng, C.J., Lee, S., Kwak, J.H., Kim, W.G. Bioorg. Med. Chem. Lett. (2006) [Pubmed]
  6. Peptide aldehyde inhibitors of bacterial peptide deformylases. Durand, D.J., Gordon Green, B., O'Connell, J.F., Grant, S.K. Arch. Biochem. Biophys. (1999) [Pubmed]
  7. 2D-QSAR in hydroxamic acid derivatives as peptide deformylase inhibitors and antibacterial agents. Gupta, M.K., Mishra, P., Prathipati, P., Saxena, A.K. Bioorg. Med. Chem. (2002) [Pubmed]
  8. The effect of glycerol-containing peritoneal dialysis fluid on peritoneal macrophage function in vivo. de Fijter, C.W., Verbrugh, H.A., Oe, P.L., Peters, E.D., van der Meulen, J., Donker, A.J., Verhoef, J., Lameire, N. Advances in peritoneal dialysis. Conference on Peritoneal Dialysis. (1991) [Pubmed]
  9. The evolution of peptide deformylase as a target: contribution of biochemistry, genetics and genomics. Yuan, Z., White, R.J. Biochem. Pharmacol. (2006) [Pubmed]
  10. Cloning, high-level expression, purification and crystallization of peptide deformylase from Leptospira interrogans. Li, Y., Ren, S., Gong, W. Acta Crystallogr. D Biol. Crystallogr. (2002) [Pubmed]
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