A NEW SUBCLASS OF THE ZINC METALLOPROTEASES SUPERFAMILY REVEALED BY THE SOLUTION STRUCTURE OF PEPTIDE DEFORMYLASE

Escherichia coli peptide deformylase, a member of the zinc metalloprot eases family, is made up of an active core domain composed of 147 resi dues and of an additional and dispensable C-terminal tail of 21 residu es. The three-dimensional structure of the catalytic core could be stu died by NMR. H-1 and N-15 NMR resonances assignments were obtained by two-dimensional and three-dimensional heteronuclear spectroscopy. The structure could be calculated using a set of 1015 restraints for the 1 47 residues of the enzyme. The overall structure is composed of a seri es of antiparallel beta-strands which surround two perpendicular alpha -helices. The C-terminal helix contains the HEXXH motif, which is cruc ial for activity. This helical arrangement and the way the histidines bind the zinc ion clearly are structurally reminiscent of the other me mbers of the metalloprotease family, such as thermolysin or metzincins . Nevertheless, the overall arrangement of secondary and tertiary stru ctures of peptide deformylase and the positioning of its third zinc li gand (a cysteine) are quite different from those of the other members of the family. These discrepancies, together with several biochemical differences, lead us to propose that peptide deformylase is the first example of a new class of the zinc-metalloproteases family. Studies of the interaction of peptide deformylase with either an inhibitor of th e reaction or a product of the catalysed reaction, Met-Ala-Ser, as wel l as comparisons with the structures of other enzymes of the family, h ave enabled us to delineate the area corresponding to their binding si te. The structural basis of the specificity of recognition of the form yl group is discussed in the context of the protease superfamily. (C) 1996 Academic Press Limited