Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome

Nicholas M. Fleischman, Debanu Das, Abhinav Kumar, Qingping Xu, Hsiu Ju Chiu, Lukasz Jaroszewski, Mark W. Knuth, Heath E. Klock, Mitchell D. Miller, Marc André Elsliger, Adam Godzik, Scott A. Lesley, Ashley M. Deacon, Ian A. Wilson, Michael D. Toney

Research output: Contribution to journalArticle

4 Scopus citations

Abstract

Pyridoxal-5'-phosphate or PLP, the active form of vitamin B6, is a highly versatile cofactor that participates in a large number of mechanistically diverse enzymatic reactions in basic metabolism. PLP-dependent enzymes account for ∼1.5% of most prokaryotic genomes and are estimated to be involved in ∼4% of all catalytic reactions, making this an important class of enzymes. Here, we structurally and functionally characterize three novel PLP-dependent enzymes from bacteria in the human microbiome: Two are from Eubacterium rectale, a dominant, nonpathogenic, fecal, Gram-positive bacteria, and the third is from Porphyromonas gingivalis, which plays a major role in human periodontal disease. All adopt the Type I PLP-dependent enzyme fold and structure-guided biochemical analysis enabled functional assignments as tryptophan, aromatic, and probable phosphoserine aminotransferases.

Original languageEnglish (US)
Pages (from-to)1060-1076
Number of pages17
JournalProtein Science
Volume23
Issue number8
DOIs
StatePublished - 2014

Keywords

  • Biochemical characterization
  • Crystal structure
  • Human microbiome
  • PLP-dependent enzymes
  • Protein structure initiative
  • Structural genomics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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  • Cite this

    Fleischman, N. M., Das, D., Kumar, A., Xu, Q., Chiu, H. J., Jaroszewski, L., Knuth, M. W., Klock, H. E., Miller, M. D., Elsliger, M. A., Godzik, A., Lesley, S. A., Deacon, A. M., Wilson, I. A., & Toney, M. D. (2014). Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome. Protein Science, 23(8), 1060-1076. https://doi.org/10.1002/pro.2493