ATP-binding cassette (ABC) transport system solute-binding protein-guided identification of novel D-altritol and galactitol catabolic pathways in Agrobacterium tumefaciens C58

Daniel J. Wichelecki, Matthew W. Vetting, Liyushang Chou, Nawar Al-Obaidi, Jason T. Bouvier, Steven C. Almo, John Alan Gerlt

Research output: Contribution to journalArticle

Abstract

Innovations in the discovery of the functions of uncharacterized proteins/enzymes have become increasingly important as advances in sequencing technology flood protein databases with an exponentially growing number of open reading frames. This study documents one such innovation developed by the Enzyme Function Initiative (EFI; U54GM093342), the use of solutebinding proteins for transport systems to identify novel metabolic pathways. In a previous study, this strategy was applied to the tripartite ATP-independent periplasmic transporters. Here, we apply this strategy to the ATP-binding cassette transporters and report the discovery of novel catabolic pathways for D-altritol and galactitol in Agrobacterium tumefaciens C58. These efforts resulted in the description of three novel enzymatic reactions as follows: 1) oxidation of D-altritol to D-tagatose via a dehydrogenase in Pfam family PF00107, a previously unknown reaction; 2) phosphorylation of D-tagatose to D-tagatose 6-phosphate via a kinase in Pfam family PF00294, a previously orphan EC number; and 3) epimerization of D-tagatose 6-phosphate C-4 to D-fructose 6-phosphate via a member of Pfam family PF08013, another previously unknown reaction. The epimerization reaction catalyzed by a member of PF08013 is especially noteworthy, because the functions of members of PF08013 have been unknown. These discoveries were assisted by the following two synergistic bioinformatics web tools made available by the Enzyme Function Initiative: the EFI-Enzyme Similarity Tool and the EFI-Genome Neighborhood Tool.

Original languageEnglish (US)
Pages (from-to)28963-28976
Number of pages14
JournalJournal of Biological Chemistry
Volume290
Issue number48
DOIs
StatePublished - Nov 27 2015

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Galactitol
Agrobacterium tumefaciens
Carrier Proteins
Adenosine Triphosphate
Enzymes
Innovation
Protein Databases
Phosphorylation
Proteins
ATP-Binding Cassette Transporters
Protein Transport
Bioinformatics
Metabolic Networks and Pathways
Computational Biology
Open Reading Frames
Oxidoreductases
Phosphotransferases
Genes
Genome
Technology

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

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ATP-binding cassette (ABC) transport system solute-binding protein-guided identification of novel D-altritol and galactitol catabolic pathways in Agrobacterium tumefaciens C58. / Wichelecki, Daniel J.; Vetting, Matthew W.; Chou, Liyushang; Al-Obaidi, Nawar; Bouvier, Jason T.; Almo, Steven C.; Gerlt, John Alan.

In: Journal of Biological Chemistry, Vol. 290, No. 48, 27.11.2015, p. 28963-28976.

Research output: Contribution to journalArticle

Wichelecki, Daniel J. ; Vetting, Matthew W. ; Chou, Liyushang ; Al-Obaidi, Nawar ; Bouvier, Jason T. ; Almo, Steven C. ; Gerlt, John Alan. / ATP-binding cassette (ABC) transport system solute-binding protein-guided identification of novel D-altritol and galactitol catabolic pathways in Agrobacterium tumefaciens C58. In: Journal of Biological Chemistry. 2015 ; Vol. 290, No. 48. pp. 28963-28976.
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