The strand-helix motif is a recurring theme in biological hydrolysis. Does the conformation of the Ramachandran outlier enhance its electrophilicity?
The active site structures of hydrolytic enzymes representing five different protein folds were compared. They contain a strand-helix motif with an active site nucleophile occupying a less favourable region in the Ramachandran plot, as previously described for the alpha/beta-hydrolases. Comparison of the different structures enabled a characterisation of the common denominator and suggests an explanation for the unusual Ramachandran values. According to this, the Ramachandran values reflect the orientation of one of the backbone amino group that stabilises the oxyanion intermediate of catalysis.
Håkansson
Kjell
K
August Krogh Institute, LCMF, Universitetsparken 13, DK-210 0, OE, Copenhagen, Denmark. kohakansson@aki.ku.dk
D000110:Acetylcholinesterase / Q000737:chemistry; D000251:Adenosine Triphosphatases / Q000737:chemistry; D000595:Amino Acid Sequence; D001665:Binding Sites; D002222:Carbamoyl-Phosphate Synthase (Ammonia) / Q000737:chemistry; D002265:Carboxylic Ester Hydrolases / Q000737:chemistry; D016384:Consensus Sequence; D004150:Dipeptidases / Q000737:chemistry; D049071:Endopeptidase Clp; D004798:Enzymes / Q000737:chemistry*; D004950:Esterases / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012697:Serine Endopeptidases / Q000737:chemistry
D004798:Enzymes; D004950:Esterases; D002265:Carboxylic Ester Hydrolases; C041144:chemotactic protein methylesterase; D000110:Acetylcholinesterase; D004150:Dipeptidases; C051396:beta-aspartyl peptidase; D012697:Serine Endopeptidases; D049071:Endopeptidase Clp; D000251:Adenosine Triphosphatases; D002222:Carbamoyl-Phosphate Synthase (Ammonia)