Restrictive endonucleases and ligases are critical tool enzymes for DNA manipulation and genetic engineering. If you have similar tool enzymes for protein manipulation and engineering, it will be much easier than current approaches to design and reconstruct new proteins with desired performance. Restrictive proteinase can recognize and cleave off polypeptide at only a certain amino acid or a certain amino acid order, while polypeptide ligase link different polypeptide chains together to reconstruct a new protein. Do those enzymes exist in nature? Or is it possible for us to design and synthesize these kind of enzymes?
Protein ligase activity is not too common, outside of ubiquitin ligases. However, engineered protein ligase activity can be found in the case of split intein sequences that can be used to reconsitute two protein fragments into a single polypeptide.
Selective proteases, in constrast, are much easier to come by. You can find many examples of naturally occuring proteases that are fairly sequence-specific in the application of affinity tag removal (e.g. thrombin, Factor Xa, enterokinase). Sequence specificity varies a lot by protease class, with some being fairly promiscuous, while others are exceedingly sequence specific. Probably one of the best examples of the highly sequence specific protease activity is TEV protease.
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