title: Prediction and assignment of function for a divergent N-succinyl amino acid racemase.
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.
authors.affiliation: Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
authors.forename: Ling
authors.initials: L
authors.lastname: Song
authors.forename: Chakrapani
authors.initials: C
authors.lastname: Kalyanaraman
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Fedorov
authors.forename: Elena V
authors.initials: EV
authors.lastname: Fedorov
authors.forename: Margaret E
authors.initials: ME
authors.lastname: Glasner
authors.forename: Shoshana
authors.initials: S
authors.lastname: Brown
authors.forename: Heidi J
authors.initials: HJ
authors.lastname: Imker
authors.forename: Patricia C
authors.initials: PC
authors.lastname: Babbitt
authors.forename: Steven C
authors.initials: SC
authors.lastname: Almo
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Jacobson
authors.forename: John A
authors.initials: JA
authors.lastname: Gerlt
mesh_terms: D000591:Amino Acid Isomerases / Q000737:chemistry*; D001407:Bacillus / Q000378:metabolism; D001409:Bacillus cereus / Q000378:metabolism; D001665:Binding Sites; D004926:Escherichia coli / Q000378:metabolism; D013058:Mass Spectrometry; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D019998:Racemases and Epimerases / Q000737:chemistry; D012984:Software; D021241:Spectrometry, Mass, Electrospray Ionization; D013379:Substrate Specificity
chemical_list: D019998:Racemases and Epimerases; D000591:Amino Acid Isomerases; C084211:lysine racemase