Prediction of the odorant binding site of olfactory receptor proteins by human-mouse comparisons

Protein Sci. 2004 Jan;13(1):240-54. doi: 10.1110/ps.03296404.


Olfactory receptors (ORs) are a large family of proteins involved in the recognition and discrimination of numerous odorants. These receptors belong to the G-protein coupled receptor (GPCR) hyperfamily, for which little structural data are available. In this study we predict the binding site residues of OR proteins by analyzing a set of 1441 OR protein sequences from mouse and human. The central insight utilized is that functional contact residues would be conserved among pairs of orthologous receptors, but considerably less conserved among paralogous pairs. Using judiciously selected subsets of 218 ortholog pairs and 518 paralog pairs, we have identified 22 sequence positions that are both highly conserved among the putative orthologs and variable among paralogs. These residues are disposed on transmembrane helices 2 to 7, and on the second extracellular loop of the receptor. Strikingly, although the prediction makes no assumption about the location of the binding site, these amino acid positions are clustered around a pocket in a structural homology model of ORs, mostly facing the inner lumen. We propose that the identified positions constitute the odorant binding site. This conclusion is supported by the observation that all but one of the predicted binding site residues correspond to ligand-contact positions in other rhodopsin-like GPCRs.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / chemistry
  • Animals
  • Binding Sites
  • Cluster Analysis
  • Consensus Sequence
  • Conserved Sequence
  • Databases, Protein
  • Humans
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Phylogeny
  • Protein Binding
  • Receptors, Odorant / chemistry*
  • Receptors, Odorant / genetics
  • Receptors, Odorant / metabolism*
  • Sequence Homology, Amino Acid
  • Signal Transduction
  • Species Specificity


  • Amino Acids
  • Receptors, Odorant