title: Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome.
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.
authors.affiliation: Department of Chemistry, University of California, Davis, California, 95616.
authors.forename: Nicholas M
authors.initials: NM
authors.lastname: Fleischman
authors.forename: Debanu
authors.initials: D
authors.lastname: Das
authors.forename: Abhinav
authors.initials: A
authors.lastname: Kumar
authors.forename: Qingping
authors.initials: Q
authors.lastname: Xu
authors.forename: Hsiu-Ju
authors.initials: HJ
authors.lastname: Chiu
authors.forename: Lukasz
authors.initials: L
authors.lastname: Jaroszewski
authors.forename: Mark W
authors.initials: MW
authors.lastname: Knuth
authors.forename: Heath E
authors.initials: HE
authors.lastname: Klock
authors.forename: Mitchell D
authors.initials: MD
authors.lastname: Miller
authors.forename: Marc-André
authors.initials: MA
authors.lastname: Elsliger
authors.forename: Adam
authors.initials: A
authors.lastname: Godzik
authors.forename: Scott A
authors.initials: SA
authors.lastname: Lesley
authors.forename: Ashley M
authors.initials: AM
authors.lastname: Deacon
authors.forename: Ian A
authors.initials: IA
authors.lastname: Wilson
authors.forename: Michael D
authors.initials: MD
authors.lastname: Toney
mesh_terms: D018360:Crystallography, X-Ray; D005051:Eubacterium / Q000201:enzymology*; D006801:Humans; D064307:Microbiota; D008958:Models, Molecular; D010088:Oxidoreductases / Q000737:chemistry / Q000378:metabolism*; D016966:Porphyromonas gingivalis / Q000201:enzymology*; D011487:Protein Conformation; D011732:Pyridoxal Phosphate / Q000737:chemistry / Q000378:metabolism*; D000637:Transaminases / Q000737:chemistry / Q000378:metabolism*
chemical_list: D011732:Pyridoxal Phosphate; D010088:Oxidoreductases; D000637:Transaminases
keywords: PLP-dependent enzymes; Protein Structure Initiative; biochemical characterization; crystal structure; human microbiome; structural genomics