Abstract
The enzyme 4-hydroxy-tetrahydrodipicolinate synthase (DapA) is involved in the production of lysine and precursor molecules for peptidoglycan synthesis. In a multistep reaction, DapA converts pyruvate and L-aspartate-4-semialdehyde to 4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid. In many organisms, lysine binds allosterically to DapA, causing negative feedback, thus making the enzyme an important regulatory component of the pathway. Here, the 2.1 Å resolution crystal structure of DapA from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV is reported. The enzyme crystallized as a contaminant of a protein preparation from native biomass. Genome analysis reveals that M. fumariolicum SolV utilizes the recently discovered aminotransferase pathway for lysine biosynthesis. Phylogenetic analyses of the genes involved in this pathway shed new light on the distribution of this pathway across the three domains of life.
Highlights
Animals rely on prokaryotes and plants for the production of the essential amino acid lysine
In the DAP pathway, lysine biosynthesis is initiated by the enzyme 4-hydroxytetrahydrodipicolinate synthase (DapA; EC 4.3.3.7), which catalyses a multistep reaction
THDP is converted into mesoDAP, the direct precursor for lysine and for the peptidoglycan synthesis pathway (Pillai et al, 2009), via a variety of routes
Summary
Animals rely on prokaryotes and plants for the production of the essential amino acid lysine. In the first step of this reaction, a conserved catalytic lysine residue in the active site of DapA reacts with pyruvate, forming a Schiff base linkage and resulting in a covalent enamine intermediate (Blickling & Knablein, 1997) This enamine subsequently reacts with l-aspartate-4-semialdehyde (ASA), creating a second covalent intermediate. Liu et al, 2010) In this pathway, the enzyme l,l-diaminopimelate (ll-DAP) aminotransferase (DapL; EC 2.6.1.83) converts THDP into ll-DAP in a single step (Hudson et al, 2006, 2008). We report the first crystal structure of DapA from a methanotroph, Methylacidiphilum fumariolicum SolV This thermoacidophile was isolated from a hot and extremely acidic volcanic ecosystem and belongs to the phylum Verrucomicrobia, which mainly represents (volcanic) soil bacteria. Phylogenetic analyses were conducted to assess the phylogenies of DapA and DapL among prokaryotic and eukaryotic phyla
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