Crystal Structure of Queuosine Biosynthesis Enzyme QueF Bound to Substrate PreQ0

Abstract

This invention provides for the design of novel nitrile oxidoreductases that can be used as biocatalysts for industrial chemical processes and; and thus, provide attractive alternatives to traditional chemical synthesis. Generally, this technology relates to crystal structures of nitrile oxidoreductases, and of crystal structures of nitrile oxidoreductases complexed with substrates and co-factors. For example, the invention provides for the crystalline structure of the nitrile oxidoreductase, QueF, as well as for a computer-readable medium having QueF crystal structure information stored thereon.

The claimed invention is: 
     
         1 . A computer-based method for the analysis of the interaction of a ligand with QueF, which comprises: providing the QueF structure of  FIG. 2 ; providing the QueF active site structures of  FIG. 3  and  FIG. 4 ; providing the amino acids and three-dimensional coordinates of any or all of Tables 1-4, wherein the coordinates of Tables 14 can be optionally varied by a root mean square distance (rmsd) of less than 1.5 Å, or selected coordinates thereof; providing a ligand structure to be fitted to said QueF structure or selected coordinates thereof; and fitting the ligand structure to the QueF structure, wherein the ligand structure is fitted to at least one atom from the amino acids shown in Tables 14. 
     
     
         2 . The method of  claim 1 , wherein the coordinates of Tables 1-4 can be optionally varied by a rmsd of less than 0.5 Å or selected coordinates thereof. 
     
     
         3 . A method of providing data for designing and/or performing optimization of QueF mutants that catalyze the conversion of a nitrile containing compound to the corresponding amine, the method comprising:
 (i) establishing communication with a remote device containing computer-readable data comprising the structure of any or all of Tables 1-4, optionally varied by a rmsd of less than 1.5 Å or selected coordinates thereof; and   (ii) receiving the computer-readable data from the remote device.   
     
     
         4 . The method of  claim 3 , wherein the structure of any or all of Tables 1-4 can be optionally varied by a rmsd of less than 0.5 Å. 
     
     
         5 . The method of  claim 3 , wherein the designing and/or performing optimization of QueF mutants may involve the substitution, deletion, or addition of at least one amino acid residue. 
     
     
         6 . The method of  claim 5 , wherein the at least one amino acid does not interact with the ligand. 
     
     
         7 . The method of  claim 5 , wherein the at least one amino acid does interact with the ligand. 
     
     
         8 . The method of  claim 2 , wherein the ability of a modified QueF to catalyze the conversion of a nitrile containing compound to the corresponding amine is determined by screening various nitrile containing compounds against the modified QueF.