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J Biol Chem. 2015 Nov 27;290(48):28963-76. doi: 10.1074/jbc.M115.686857. Epub 2015 Oct 15.

ATP-binding Cassette (ABC) Transport System Solute-binding Protein-guided Identification of Novel d-Altritol and Galactitol Catabolic Pathways in Agrobacterium tumefaciens C58.

Author information

1
From the Departments of Biochemistry and Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and.
2
the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461.
3
From the Departments of Biochemistry and Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and j-gerlt@illinois.edu.

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 solute-binding 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.

KEYWORDS:

ABC transporter; Agrobacterium tumefaciens C58; D-altritol catabolism; bioinformatics; carbohydrate metabolism; enzyme; genome neighborhood networks; sequence similarity networks; transcriptomics

PMID:
26472925
PMCID:
PMC4661409
DOI:
10.1074/jbc.M115.686857
[Indexed for MEDLINE]
Free PMC Article

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