Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

Based on evolutionary information and heuristics, an Evolutionary Trace Annotation (ETA) pipeline built templates for 98 enzymes, half taken from the PSI, and sought matches in a non-redundant structure database. On average each template matched 2.7 distinct proteins, of which 2.0 share the first three Enzyme Commission digits as the template's enzyme of origin. In many cases (61%) a single most likely function could be predicted as the annotation with the most matches, and in these cases such a plurality vote identified the correct function with 87% accuracy. ETA was also found to be complementary to sequence homology-based annotations. When matches are required to both geometrically match the 3D template and to be sequence homologs found by BLAST or PSI-BLAST, the annotation accuracy is greater than either method alone, especially in the region of lower sequence identity where homology-based annotations are least reliable.These data suggest that knowledge of evolutionarily important residues improves functional annotation among distant enzyme homologs. Since, unlike other 3D template approaches, the ETA method bypasses the need for experimental knowledge of the catalytic mechanism, it should prove a useful, large scale, and general adjunct to combine with other methods to decipher protein function in the structural proteome.Structural genomics projects such as the Protein Structure Initiative ("PSI") aim to provide an experimental structure for all proteins [1-3], but as of May 2007 over one third of the nearly 4,400 protein structures deposited into the protein structure databank (PDB) [4] with the keyword "structural genomics" were either hypothetical proteins or without known function. The annotation of these structures remains an important goal essential to understanding their biological meaning. Ideally, such annotations might be obtained experimentally, through automated generalized screens for some enzymes [5]. However, further efforts are required to devel