Prediction and assignment of function for a divergent N-succinyl amino acid racemase.
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.
Song
Ling
L
Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
Kalyanaraman
Chakrapani
C
Fedorov
Alexander A
AA
Fedorov
Elena V
EV
Glasner
Margaret E
ME
Brown
Shoshana
S
Imker
Heidi J
HJ
Babbitt
Patricia C
PC
Almo
Steven C
SC
Jacobson
Matthew P
MP
Gerlt
John A
JA
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
D019998:Racemases and Epimerases; D000591:Amino Acid Isomerases; C084211:lysine racemase