Crystal structure of the YjeE protein from Haemophilus influenzae: A putative Atpase involved in cell wall synthesis

Abstract

A hypothetical protein encoded by the gene YjeE of Haemophilus influenzae was selected as part of a structural genomics project for X-ray analysis to assist with the functional assignment. The protein is considered essential to bacteria because the gene is present in virtually all bacterial genomes but not in those of archaea or eukaryotes. The amino acid sequence shows no homology to other proteins except for the presence of the Walker A motif G-X-X-X-X-G-K-T that indicates the possibility of a nucleotide-binding protein. The YjeE protein was cloned, expressed, and the crystal structure determined by the MAD method at 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. Crystallization of YjeE in the presence of ATP and Mg2+ resulted in the structure with ADP bound in the P-loop. The ATPase activity of YjeE was confirmed by kinetic measurements. The distribution of conserved residues suggests that the protein may work as a "molecular switch" triggered by ATP hydrolysis. The phylogenetic pattern of YjeE suggests its involvement in cell wall biosynthesis.

Deficiency of BrpB causes major defects in cell division, stress responses and biofilm formation by Streptococcus mutans

“…c-proteobacteria, the yjeE locus is closely linked to genes encoding proteins with potential functions in DNA repair and peptidoglycan remodelling, which is consistent with a role for YjeE in stress tolerance and cell envelope biogenesis (Handford et al, 2009;Teplyakov et al, 2002 Kawai et al, 2011;Over et al, 2011;Wen et al, 2006). This highly conserved genetic linkage, along with the characteristic phenotypes of the BrpB-deficient mutants, all support a role for BrpB and its streptococcal homologues in cell wall biogenesis/homeostasis.…”

“…The YjeE-like proteins are a unique, new family of P-loop ATP/GTPase proteins widespread in virtually all eubacteria, but not in archaea and eukaryotes (Teplyakov et al, 2002), although their exact function in cellular physiology remains unclear (Allali-Hassani et al, 2004;Karst et al, 2009). In Escherichia coli, YjeE is required for growth, and strains with decreased expression of YjeE had an elongated lag phase and a decreased growth rate (Allali-Hassani et al, 2004).…”

“…Unlike E. coli, however, Bacillus subtilis deficient of YdiB orthologue was shown to be viable, but had a much reduced growth rate, when compared to the wild-type (Karst et al, 2009). Recombinant proteins of YjeE from E. coli and Haemophilus influenzae, and YdiB from B. subtilis, all possessed low ATPase activity (Allali-Hassani et al, 2004;Karst et al, 2009;Teplyakov et al, 2002), and in B. subtilis ATPase activity was shown to be essential for the function of YdiB protein in vivo (Karst et al, 2009). More recently, an in vitro study has also provided evidence that in E. coli YjeE is part of a three essential protein complex required for biosynthesis of threonylcarbamoyl adenosine (t 6 A), a modified tRNA nucleoside involved in codon decoding (Deutsch et al, 2012).…”

Functional analysis of 11 putative essential genes in Bacillus subtilis

“…Its homologues in E. coli and H. influenzae (YjeE) have been studied more extensively than YdiB (Teplyakov et al, 2002;Allali-Hassani et al, 2004). yjeE has been shown to be essential in E. coli (Freiberg et al, 2001;Allali-Hussani et al, 2004), and it has been proposed that YjeE is involved in cell wall synthesis, based on its conservation in all bacteria except Mycoplasma and Ureaplasma, and the position of the gene next to amiB (a cell wall amidase) in E. coli (Teplyakov et al, 2002). Depletion of YjeE in E. coli results in a morphology that is consistent with defective cell wall synthesis (J. Handford, personal communication).…”

Anabaena sp. Strain PCC 7120 hetY Gene Influences Heterocyst Development

“…A search against PDB resulted in a significant hit (E value, 8eϪ13) with YjeE, an ATPase from Haemophilus influenzae, which has been implicated in cell wall biosynthesis (16). HetY and YjeE showed 31.6% identity and 62.4% similarity.…”