2def
From Proteopedia
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PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 20 STRUCTURES
Overview
In the accompanying paper, we report that zinc is unlikely to be the, co-factor supporting peptide deformylase activity in vivo. In contrast, nickel binding promotes full enzyme activity. The three-dimensional, structure of the resulting nickel-containing peptide deformylase, (catalytic domain, residues 1 to 147) was solved by NMR using a, 13C-15N-doubly labelled protein sample. A set of 2261 restraints could be, collected, with an average of 15.4 per amino acid. The resolution, which, shows a good definition for the position of most side-chains, is greatly, improved compared to that previously reported for the zinc-containing, inactive form. A comparison of the two stuctures indicates however that, both share the same 3D organization. This shows that the nature of the, bound metal is the primary determinant of the hydrolytic activity of this, enzyme. Site-directed mutagenesis enabled us to determine the conserved, residues of PDF involved in the structure of the active site. In, particular, a buried arginine appears to be critical for the positioning, of Cys90, one of the metal ligands. Furthermore, the 3D structure of, peptide deformylase was compared to thermolysin and metzincins. Although, the structural folds are very different, they all display a common, structural motif involving an alpha-helix and a three-stranded beta-sheet., These conserved structural elements build a common scaffold which includes, the active site, suggesting a common hydrolytic mechanism for these, proteases. Finally, an invariant glycine shared by both PDF and metzincins, enables us to extend the conserved motif from HEXXH to HEXXHXXG.
About this Structure
2DEF is a Single protein structure of sequence from Escherichia coli with as ligand. Active as Formylmethionine deformylase, with EC number 3.5.1.31 Known structural/functional Site: . Full crystallographic information is available from OCA.
Reference
Solution structure of nickel-peptide deformylase., Dardel F, Ragusa S, Lazennec C, Blanquet S, Meinnel T, J Mol Biol. 1998 Jul 17;280(3):501-13. PMID:9665852
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