Discovery of a Dipeptide Epimerase Enzymatic Function Guided by Homology Modeling and Virtual Screening

Chakrapani Kalyanaraman, Heidi J. Imker, Alexander A. Fedorov, Elena V. Fedorov, Margaret E. Glasner, Patricia C. Babbitt, Steven C. Almo, John A. Gerlt, Matthew P. Jacobson

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

We have developed a computational approach to aid the assignment of enzymatic function for uncharacterized proteins that uses homology modeling to predict the structure of the binding site and in silico docking to identify potential substrates. We apply this method to proteins in the functionally diverse enolase superfamily that are homologous to the characterized L-Ala-D/L-Glu epimerase from Bacillus subtilis. In particular, a protein from Thermotoga martima was predicted to have different substrate specificity, which suggests that it has a different, but as yet unknown, biological function. This prediction was experimentally confirmed, resulting in the assignment of epimerase activity for L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His, whereas the enzyme is annotated incorrectly in GenBank as muconate cycloisomerase. Subsequently, crystal structures of the enzyme were determined in complex with three substrates, showing close agreement with the computational models and revealing the structural basis for the observed substrate selectivity.

Original languageEnglish (US)
Pages (from-to)1668-1677
Number of pages10
JournalStructure
Volume16
Issue number11
DOIs
StatePublished - Nov 12 2008

Fingerprint

Racemases and Epimerases
Dipeptides
muconate cycloisomerase
Proteins
Phosphopyruvate Hydratase
Structural Models
Nucleic Acid Databases
Enzymes
Substrate Specificity
Bacillus subtilis
Binding Sites

Keywords

  • PROTEINS

ASJC Scopus subject areas

  • Molecular Biology
  • Structural Biology

Cite this

Kalyanaraman, C., Imker, H. J., Fedorov, A. A., Fedorov, E. V., Glasner, M. E., Babbitt, P. C., ... Jacobson, M. P. (2008). Discovery of a Dipeptide Epimerase Enzymatic Function Guided by Homology Modeling and Virtual Screening. Structure, 16(11), 1668-1677. https://doi.org/10.1016/j.str.2008.08.015

Discovery of a Dipeptide Epimerase Enzymatic Function Guided by Homology Modeling and Virtual Screening. / Kalyanaraman, Chakrapani; Imker, Heidi J.; Fedorov, Alexander A.; Fedorov, Elena V.; Glasner, Margaret E.; Babbitt, Patricia C.; Almo, Steven C.; Gerlt, John A.; Jacobson, Matthew P.

In: Structure, Vol. 16, No. 11, 12.11.2008, p. 1668-1677.

Research output: Contribution to journalArticle

Kalyanaraman, C, Imker, HJ, Fedorov, AA, Fedorov, EV, Glasner, ME, Babbitt, PC, Almo, SC, Gerlt, JA & Jacobson, MP 2008, 'Discovery of a Dipeptide Epimerase Enzymatic Function Guided by Homology Modeling and Virtual Screening', Structure, vol. 16, no. 11, pp. 1668-1677. https://doi.org/10.1016/j.str.2008.08.015
Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC et al. Discovery of a Dipeptide Epimerase Enzymatic Function Guided by Homology Modeling and Virtual Screening. Structure. 2008 Nov 12;16(11):1668-1677. https://doi.org/10.1016/j.str.2008.08.015
Kalyanaraman, Chakrapani ; Imker, Heidi J. ; Fedorov, Alexander A. ; Fedorov, Elena V. ; Glasner, Margaret E. ; Babbitt, Patricia C. ; Almo, Steven C. ; Gerlt, John A. ; Jacobson, Matthew P. / Discovery of a Dipeptide Epimerase Enzymatic Function Guided by Homology Modeling and Virtual Screening. In: Structure. 2008 ; Vol. 16, No. 11. pp. 1668-1677.
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