Structure and activity of human mitochondrial peptide deformylase, a novel cancer target.

Abstract	Peptide deformylase proteins (PDFs) participate in the N-terminal methionine excision pathway of newly synthesized peptides. We show that the human PDF (HsPDF) can deformylate its putative substrates derived from mitochondrial DNA-encoded proteins. The first structural model of a mammalian PDF (1.7 A), HsPDF, shows a dimer with conserved topology of the catalytic residues and fold as non-mammalian PDFs. The HsPDF C-terminus topology and the presence of a helical loop (H2 and H3), however, shape a characteristic active site entrance. The structure of HsPDF bound to the peptidomimetic inhibitor actinonin (1.7 A) identified the substrate-binding site. A defined S1' pocket, but no S2' or S3' substrate-binding pockets, exists. A conservation of PDF-actinonin interaction across PDFs was observed. Despite the lack of true S2' and S3' binding pockets, confirmed through peptide binding modeling, enzyme kinetics suggest a combined contribution from P2'and P3' positions of a formylated peptide substrate to turnover.
Authors	Sindy Escobar-Alvarez, Yehuda Goldgur, Guangli Yang, Ouathek Ouerfelli, Yueming Li, David A Scheinberg
Journal	Journal of molecular biology (J Mol Biol) Vol. 387 Issue 5 Pg. 1211-28 (Apr 17 2009) ISSN: 1089-8638 [Electronic] Netherlands
PMID	19236878 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)
Chemical References	DNA Primers DNA, Mitochondrial Oligopeptides Recombinant Proteins Amidohydrolases peptide deformylase
Topics	Amidohydrolases (antagonists & inhibitors, chemistry, genetics, metabolism) Amino Acid Sequence Base Sequence Catalytic Domain Conserved Sequence Crystallography, X-Ray DNA Primers (genetics) DNA, Mitochondrial (genetics) Dimerization Humans In Vitro Techniques Kinetics Mitochondria (enzymology) Models, Molecular Molecular Sequence Data Neoplasms (drug therapy, enzymology) Oligopeptides (chemistry, genetics) Protein Folding Protein Structure, Quaternary Recombinant Proteins (chemistry, genetics, metabolism) Sequence Homology, Amino Acid Static Electricity Substrate Specificity

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