What's in a name?

Despite the fact that the term "nitrilase" seems to have quite an obvious origin using the obvious enzyme naming template that a chemist might use (nitrilase = nitrile + ase... so must be something that acts on nitriles), there is a flaw in this. "Nitrilase" has actually been taken by biologists to mean a class of similar enzymes that attack molecules with C-N bonds. In fact, it is only Group 1 nitrilases actually do the "nitrile to carboxylic acid" conversion which we are currently working on, and the other groups which do other types of C-N bond breaking reactions. Table 1 in Charles Brenner's 2002 "Catalysis in the Nitrilase Superfamily" review in Current Opinions in Structural Opinions shows the breadth of other chemistries that appear in the nitrilase superfamily.This broad use of a name explains why there are so many PDB files listed for a search for "nitrilase" which do not actually do the nitrile-acid conversion as well as why there is great confusion between nitrile hydratase and nitrilase activities in many databases.

If you look through the 29 PDB files which are labelled as nitrilase, there is in fact only one enzyme which is a Group 1 nitrilase- and that is the nitrilase from the hyperthermophile Pyrococcus abyssi GE5 (this is an example of a PDB of this enzyme) which was described in a 2011 Journal of Structural Biology paper (doi: 10.1016/j.jsb.2010.11.017) by Rypniewski. As Martinkova has commented in her 2010 Current Opinions in Chemical Biology review (doi: 10.1016/j.cbpa.2009.11.018), this lack of crystal structures made structure–function relationship studies for nitrilases difficult.