Location of the ubiA gene on the physical map of Escherichia coli

Modeling the E. coli 4-hydroxybenzoic acid oligoprenyltransferase ( ubiA transferase) and characterization of potential active sites

4-hydroxybenzoate oligoprenyltransferase of E. coli, encoded in the gene ubiA, is an important key enzyme in the biosynthetic pathway to ubiquinone. It catalyzes the prenylation of 4-hydroxybenzoic acid in position 3 using an oligoprenyl diphosphate as a second substrate. Up to now, no X-ray structure of this oligoprenyltransferase or any structurally related enzyme is known. Knowledge of the tertiary structure and possible active sites is, however, essential for understanding the catalysis mechanism and the substrate specificity. With homology modeling techniques, secondary structure prediction tools, molecular dynamics simulations, and energy optimizations, a model with two putative active sites could be created and refined. One active site selected to be the most likely one for the docking of oligoprenyl diphosphate and 4-hydroxybenzoic acid is located near the N-terminus of the enzyme. It is widely accepted that residues forming an active site are usually evolutionary conserved within a family of enzymes. Multiple alignments of a multitude of related proteins clearly showed 100% conservation of the amino acid residues that form the first putative active site and therefore strongly support this hypothesis. However, an additional highly conserved region in the amino acid sequence of the ubiA enzyme could be detected, which also can be considered a putative (or rudimentary) active site. This site is characterized by a high sequence similarity to the aforementioned site and may give some hints regarding the evolutionary origin of the ubiA enzyme. Semiempirical quantum mechanical PM3 calculations have been performed to investigate the thermodynamics and kinetics of the catalysis mechanism. These results suggest a near S(N)1 mechanism for the cleavage of the diphosphate ion from the isoprenyl unit. The 4-hydroxybenzoic acid interestingly appears not to be activated as benzoate anion but rather as phenolate anion to allow attack of the isoprenyl cation to the phenolate, which appeared to be the rate limiting step of the whole process according to our quantum chemical calculations. Our models are a basis for developing inhibitors of this enzyme, which is crucial for bacterial aerobic metabolism. [figure: see text]. Structure of the model of ubiA oligoprenyltransferase derived from the photosynthetic reaction center (1PRC). Putative active amino acid residues and substrates are shown as capped sticks to describe their location and geometry in the putative active sites. The violet spheres identify Mg2+.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Characterization of polyprenyldiphosphate: 4-hydroxybenzoate polyprenyltransferase from Escherichia coli

Polyprenyldiphosphate: 4-hydroxybenzoate polyprenyltransferase (4-HB polyprenyltransferase) is a key enzyme in ubiquinone biosynthesis in E. coli, encoded by the gene ubiA. By overexpression of ubiA and isolation of the membrane fraction, the enzyme was enriched approx. 3000-fold and characterized. The enzyme is membrane-bound and could not be solubilized by hypotonic buffer or detergent treatment. The enzymatic activity is optimal at pH 7.8 and depends on the presence of magnesium ions. Geranyldiphosphate (GPP), all-trans-farnesyldiphosphate (FPP) and all-trans-solanesyldiphosphate (SPP) are accepted as side chain precursors. The apparent Km values for these substances are are 254 microM, 22 microM and 31 microM, respectively. No reaction was observed with omega-t2-c5-octaprenyldiphosphate, in which five double bounds have cis-configuration. The reaction is stimulated by 0.01% CHAPS, but strongly inhibited by sodiumdeoxycholate, Tween 80 and Triton X-100. The amino acid sequence shows striking similarities to 4-HB hexaprenyltransferase from yeast. Sequence homologies to other prenyltransferases are discussed.