Abstract
The gene for a Nudix enzyme (SP_1669) was found to code for a UDP-X diphosphatase. The SP_1669 gene is localized among genes encoding proteins that participate in cell division in Streptococcus pneumoniae. One of these genes, MurF, encodes an enzyme that catalyzes the last step of the Mur pathway of peptidoglycan biosynthesis. Mur pathway substrates are all derived from UDP-glucosamine and all are potential Nudix substrates. We showed that UDP-X diphosphatase can hydrolyze the Mur pathway substrates UDP-N-acetylmuramic acid and UDP-N-acetylmuramoyl-L-alanine. The 1.39 Å resolution crystal structure of this enzyme shows that it folds as an asymmetric homodimer with two distinct active sites, each containing elements of the conserved Nudix box sequence. In addition to its Nudix catalytic activity, the enzyme has a 3′5′ RNA exonuclease activity. We propose that the structural asymmetry in UDP-X diphosphatase facilitates the recognition of these two distinct classes of substrates, Nudix substrates and RNA. UDP-X diphosphatase is a prototype of a new family of Nudix enzymes with unique structural characteristics: two monomers, each consisting of an N-terminal helix bundle domain and a C-terminal Nudix domain, form an asymmetric dimer with two distinct active sites. These enzymes function to hydrolyze bacterial cell wall precursors and degrade RNA.
Highlights
Peptidoglycan is an essential component of cell walls that allows bacteria to maintain shape and structural integrity under conditions of osmotic stress
Pneumoniae genome, was shown using the DOOR database [34] to be located within an operon containing the gene encoding Dalanine-D-alanine synthetase A (Ddl), the enzyme that joins two Dalanines to form a dipeptide, and the gene encoding MurF, the enzyme that carries out the addition of a D-alanine-D-alanine dipeptide to UDP-N-acetylmuramoyl-L-alanine-D-glutamate-Llysine in the peptidoglycan biosynthesis pathway
The operon containing SP_1669 is upstream of another operon containing genes that code for proteins involved in cell division including DivIVA, YlmH, YlmG, YlmF, FtsZ, and FtsA (Figure 1)
Summary
Peptidoglycan is an essential component of cell walls that allows bacteria to maintain shape and structural integrity under conditions of osmotic stress. The genomic localization of the gene SP_1669 and its Nudix hydrolase sequence, suggest that the protein may hydrolyze, for example, UDP-N-acetylmuramoyl-L-alanine-D-glutamate-L-lysine and other substrates of the Mur pathway.
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