Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily

Frank H. Wallrapp, Jian Jung Pan, Gurusankar Ramamoorthy, Daniel E. Almonacid, Brandan S. Hillerich, Ronald Seidel, Yury Patskovsky, Patricia C. Babbitt, Steven C. Almo, Matthew P. Jacobson, C. Dale Poulter

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

The number of available protein sequences has increased exponentially with the advent of high-throughput genomic sequencing, creating a significant challenge for functional annotation. Here, we describe a large-scale study on assigning function to unknown members of the trans-polyprenyl transferase (E-PTS) subgroup in the isoprenoid synthase superfamily, which provides substrates for the biosynthesis of the more than 55,000 isoprenoid metabolites. Although the mechanism for determining the product chain length for these enzymes is known, there is no simple relationship between function and primary sequence, so that assigning function is challenging. We addressed this challenge through large-scale bioinformatics analysis of >5,000 putative polyprenyl transferases; experimental characterization of the chain-length specificity of 79 diverse members of this group; determination of 27 structures of 19 of these enzymes, including seven cocrystallized with substrate analogs or products; and the development and successful application of a computational approach to predict function that leverages available structural data through homology modeling and docking of possible products into the active site. The crystallographic structures and computational structural models of the enzyme-ligand complexes elucidate the structural basis of specificity. As a result of this study, the percentage of E-PTS sequences similar to functionally annotated ones (BLAST e-value ≤ 1e-70) increased from 40.6 to 68.8%, and the percentage of sequences similar to available crystal structures increased from 28.9 to 47.4%. The high accuracy of our blind prediction of newly characterized enzymes indicates the potential to predict function to the complete polyprenyl transferase subgroup of the isoprenoid synthase superfamily computationally.

Original languageEnglish (US)
JournalProceedings of the National Academy of Sciences of the United States of America
Volume110
Issue number13
DOIs
StatePublished - Mar 26 2013

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Terpenes
Transferases
Enzymes
Structural Models
Computational Biology
Catalytic Domain
Ligands
Proteins

Keywords

  • Chain-elongation
  • Prenyltransferase

ASJC Scopus subject areas

  • General

Cite this

Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. / Wallrapp, Frank H.; Pan, Jian Jung; Ramamoorthy, Gurusankar; Almonacid, Daniel E.; Hillerich, Brandan S.; Seidel, Ronald; Patskovsky, Yury; Babbitt, Patricia C.; Almo, Steven C.; Jacobson, Matthew P.; Poulter, C. Dale.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 110, No. 13, 26.03.2013.

Research output: Contribution to journalArticle

Wallrapp, FH, Pan, JJ, Ramamoorthy, G, Almonacid, DE, Hillerich, BS, Seidel, R, Patskovsky, Y, Babbitt, PC, Almo, SC, Jacobson, MP & Poulter, CD 2013, 'Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily', Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 13. https://doi.org/10.1073/pnas.1300632110
Wallrapp, Frank H. ; Pan, Jian Jung ; Ramamoorthy, Gurusankar ; Almonacid, Daniel E. ; Hillerich, Brandan S. ; Seidel, Ronald ; Patskovsky, Yury ; Babbitt, Patricia C. ; Almo, Steven C. ; Jacobson, Matthew P. ; Poulter, C. Dale. / Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. In: Proceedings of the National Academy of Sciences of the United States of America. 2013 ; Vol. 110, No. 13.
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