Zinc protease fold

Table 1. Pairwise comparison of the topology and primary sequence of members of the short spacer family. The alpha carbon atoms defining the zinc protease fold (orange segment. Fig. 3) have been used in the topological superposition [56]. The distances refer to the root mean square deviations of this fold between pairs of structures. The corresponding pairwise primary sequence homology is also shown.

Before our work [39], only one catalytic mechanism for zinc dependent HDACs has been proposed in the literature, which was originated from the crystallographic study of HDLP [47], a histone-deacetylase-like protein that is widely used as a model for class-I HDACs. In the enzyme active site, the catalytic metal zinc is penta-coordinated by two asp residues, one histidine residues as well as the inhibitor [47], Based on their crystal structures, Finnin et al. [47] postulated a catalytic mechanism for HDACs in which the first reaction step is analogous to the hydroxide mechanism for zinc proteases zinc-bound water is a nucleophile and Zn2+ is five-fold coordinated during the reaction process. However, recent experimental studies by Kapustin et al. suggested that the transition state of HDACs may not be analogous to zinc-proteases [48], which cast some doubts on this mechanism. 

Figure 3. The observed fold for astacin. Stereo ribbon [54] drawing of the observed structure of astacin [13], The catalytic zinc atom (cyan sphere) and the zinc binding histidine residues (blue) of the consensus sequence HexxHxxgxxH are identified. The structural elements defining the conserved zinc-endo-protease fold are shown in orange.

Unknown elements of primary sequence and zinc consensus determine the tertiary fold, indicating that the parallel structural and sequence categories classifing the zinc proteases is a result of the fortuitious selection of the proteases used for structural analysis. 

Some zinc-exopeptidases are characterized by the presence of two zinc ions in their active sites. Protein folding of these exopeptidases is extremely different from the one observed in the aforementioned mono-zinc proteases. Despite such a major difference in the overall protein structure, in the GCPII carboxypeptidase (Fig. 7e, PDB code 3BHX) the stmctural elements mentioned above are present [136]. Thus,... 

The growing family of known divalent cation-dependent proteases such as insulinase [51] and dibasic convertase [52], with the variant consensus HxxeH, also present interesting questions as to the possibility of a mirrored active site with or without conservation of the overall topology. Conversely, it is possible that entirely different proteins which have no zinc dependency and completely separate function may adopt the zinc endoprotease topology, simply because this fold provides a stable modular scaffold useful in the construction of multidomain proteins. Results of further structural studies are eagerly awaited. 

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