Escherichia coli YrbH is a D-arabinose 5-phosphate isomerase

A gene encoding for arabinose 5-phosphate isomerase (API), which catalyzes the interconversion of D-ribulose 5-phosphate (Ru5P) and D-arabinose 5-phosphate (A5P), has been identified from the genome of Escherichia coli K-12. API is the first enzyme in the biosynthesis of 3-deoxy-D-manno-octulosonate (KDO), a sugar moiety located in the lipopolysaccharide layer of most Gram-negative bacteria. The API gene yrbH is located next to the recently identified specific KDO 8-P phosphatase gene, yrbI. The 328-amino acid open reading frame yrbH was cloned, overexpressed, and characterized. The purified recombinant enzyme is a tetramer and is sensitive to inhibition by zinc cations. API has optimal activity at pH 8.4 and catalytic residues with estimated pK_a values of 6.55 ± 0.04 and 10.34 ± 0.07. The enzyme is specific for A5P and Ru5P, with apparent K_m values of 0.61 ± 0.06 mM for A5P and 0.35 ± 0.08 mM for Ru5P. The apparent k _cat in the A5P to Ru5P direction is 157 ± 4 s^-1, and in the Ru5P to A5P direction it is 255 ± 16 s^-1. The value of K_eq (Ru5P/A5P) is 0.50 ± 0.06. Homology searches of the E. coli genome suggest yrbH may be one of multiple genes that encode proteins with API activity.