Prediction and assignment of function for a divergent N-succinyl amino acid racemase

Nat Chem Biol. 2007 Aug;3(8):486-91. doi: 10.1038/nchembio.2007.11. Epub 2007 Jul 1.

Abstract

The protein databases contain many proteins with unknown function. A computational approach for predicting ligand specificity that requires only the sequence of the unknown protein would be valuable for directing experiment-based assignment of function. We focused on a family of unknown proteins in the mechanistically diverse enolase superfamily and used two approaches to assign function: (i) enzymatic assays using libraries of potential substrates, and (ii) in silico docking of the same libraries using a homology model based on the most similar (35% sequence identity) characterized protein. The results matched closely; an experimentally determined structure confirmed the predicted structure of the substrate-liganded complex. We assigned the N-succinyl arginine/lysine racemase function to the family, correcting the annotation (L-Ala-D/L-Glu epimerase) based on the function of the most similar characterized homolog. These studies establish that ligand docking to a homology model can facilitate functional assignment of unknown proteins by restricting the identities of the possible substrates that must be experimentally tested.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Isomerases / chemistry*
  • Bacillus / metabolism
  • Bacillus cereus / metabolism
  • Binding Sites
  • Escherichia coli / metabolism
  • Mass Spectrometry
  • Models, Chemical
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Conformation
  • Racemases and Epimerases / chemistry
  • Software
  • Spectrometry, Mass, Electrospray Ionization
  • Substrate Specificity

Substances

  • Racemases and Epimerases
  • Amino Acid Isomerases
  • lysine racemase

Associated data

  • PDB/1TKK
  • PDB/2P88
  • PDB/2P8B
  • PDB/2P8C
  • PIR/24769846
  • PubChem-Substance/24769847
  • PubChem-Substance/24769848
  • PubChem-Substance/24769849
  • PubChem-Substance/24769850
  • PubChem-Substance/24769851
  • PubChem-Substance/24769852
  • PubChem-Substance/24769853
  • PubChem-Substance/24769854
  • PubChem-Substance/24769855
  • PubChem-Substance/24769856
  • PubChem-Substance/24769857
  • PubChem-Substance/24769858
  • PubChem-Substance/24769859
  • PubChem-Substance/24769860
  • PubChem-Substance/24769861
  • PubChem-Substance/24769862
  • PubChem-Substance/24769863
  • PubChem-Substance/24769864
  • PubChem-Substance/24769865
  • PubChem-Substance/24769866
  • PubChem-Substance/24769867
  • PubChem-Substance/24769868
  • PubChem-Substance/24769869
  • PubChem-Substance/24769870
  • PubChem-Substance/24769871
  • PubChem-Substance/24769872
  • PubChem-Substance/24769873
  • PubChem-Substance/24769874
  • PubChem-Substance/24769875
  • PubChem-Substance/24769876
  • PubChem-Substance/24769877
  • PubChem-Substance/24769878