Kinases that catalyze phosphorylation of sugars, called here sugar kinases, can be divided into at least three distinct nonhomologous families. The first is the hexokinase family, which contains many prokaryotic and eukaryotic sugar kinases with diverse specificities, including a new member, rhamnokinase from Salmonella typhimurium. The three-dimensional structure of hexokinase is known and can be used to build models of functionally important regions of other kinases in this family. The second is the ribokinase family, of unknown three-dimensional structure, and comprises pro- and eukaryotic ribokinases, bacterial fructokinases, the minor 6-phosphofructokinase 2 from Escherichia coli, 6-phosphotagatokinase, 1-phosphofructokinase, and, possibly, inosine-guanosine kinase. The third family, also of unknown three-dimensional structure, contains several bacterial and yeast galactokinases and eukaryotic mevalonate and phosphomevalonate kinases and may have a substrate binding region in common with homoserine kinases. Each of the three families of sugar kinases appears to have a distinct three-dimensional fold, since conserved sequence patterns are strikingly different for the three families. Yet each catalyzes chemically equivalent reactions on similar or identical substrates. The enzymatic function of sugar phosphorylation appears to have evolved independently on the three distinct structural frameworks, by convergent evolution. In addition, evolutionary trees reveal that (1) fructokinase specificity has evolved independently in both the hexokinase and ribokinase families and (2) glucose specificity has evolved independently in different branches of the hexokinase family. These are examples of independent Darwinian adaptation of a structure to the same substrate at different evolutionary times. The flexible combination of active sites and three-dimensional folds observed in nature can be exploited by protein engineers in designing and optimizing enzymatic function.

/pdf/convergent-evolution-of-similar-enzymatic-function-on-9e77fub4le.pdf

Convergent Evolution of Similar Enzymatic Function on Different Protein Folds: The Hexokinase, Ribokinase, and Galactokinase Families of Sugar Kinases

A family of bacterial regulators homologous to Gal and Lac repressors.

Ribokinase (RK) and adenosine kinase (AK) catalyze the phosphorylation of ribose and adenosine to ribose-5-phosphate and AMP, respectively. Belonging to the RK family of proteins, these enzymes share a number of unique structural and functional elements. Extensive work has been carried out on many aspects of these enzymes in recent years, and we summarize the wealth of information currently available on them. The topics covered include descriptions of the primary and three-dimensional structures of AK and RK, their phylogenetic relationships, biochemical aspects of these enzymes including their reaction mechanisms and ionic requirements, and also work on certain inhibitors of these enzymes. The cellular metabolism and transport of ribose and adenosine are also briefly discussed, as well as the beneficial effects of ribose and adenosine in physiology and how these effects can be harnessed for pharmacological purposes.

Adenosine kinase and ribokinase--the RK family of proteins.

It is quite important to understand the overall metabolic regulation mechanism of bacterial cells such as Escherichia coli from both science (such as biochemistry) and engineering (such as metabolic engineering) points of view. Here, an attempt was made to clarify the overall metabolic regulation mechanism by focusing on the roles of global regulators which detect the culture or growth condition and manipulate a set of metabolic pathways by modulating the related gene expressions. For this, it was considered how the cell responds to a variety of culture environments such as carbon (catabolite regulation), nitrogen, and phosphate limitations, as well as the effects of oxygen level, pH (acid shock), temperature (heat shock), and nutrient starvation.

/pdf/metabolic-regulation-of-a-bacterial-cell-system-with-1f87wicf1a.pdf

Metabolic Regulation of a Bacterial Cell System with Emphasis on Escherichia coli Metabolism

The Zymomonas mobilis genes encoding the glucose facilitator (glf), glucokinase (glk), or fructokinase (frk) were cloned and expressed in a lacIq-Ptac system using Escherichia coli K-12 mutants deficient in uptake and phosphorylation of glucose and fructose. Growth on glucose or fructose was restored when the respective genes (glf-glk or glf-frk) were expressed. In E. coli glf+ strains, both glucose and fructose were taken up via facilitated diffusion (Km, 4.1 mM for glucose and 39 mM for fructose; Vmax at 15 degrees C, 75 and 93 nmol min-1 mg-1 [dry weight] for glucose and fructose, respectively). For both substrates, counterflow maxima were observed.

Functional expression of the glucose transporter of zymomonas mobilis leads to restoration of glucose and fructose uptake in escherichia coli mutants and provides evidence for its facilitator action

Summary Sucrose-positive derivatives of Escherichia coli K-12, containing the plasmid pUR400, and of Kiebsieiia pneumoniae hydrolyse intracellular sucrose 6-phosphate by means of an invertase into D-glucose 6phosphate and free D-fructose. The latter is phosphorylated by an ATP-dependent fruclokinase (gene scrK of an ser reguion) to D-fructose 6-phosphate. The lack of ScrK does not cause any visible phenotype in wildtype strains of both organisms. Using genes and enzymes normally involved in D-arabinitoi metabolism from E. coli C and K. pneumoniae, derivatives of E. coii K-12 vi/ere constructed which allowed the identification of scr/C mutations on conventional indicator plates. Cloning and sequencing of scrK from sucrose ptasmid pUR400 and from the chromosome of K. pneumoniae revealed an open reading frame of 924 bp in both cases — the equivalent of a peptide containing 307 amino acid residues {M, 39 and 34 kDa, respectively, on sodium dodecyl sulphate gels). The sequences showed overall identity among each other (69% identical residues) and to a kinase from Vibrio alginoiyticus (57%) also involved in sucrose metabolism, iower overall identity (39%) to a Dribose-kinase from E. coli, and local similarity to prokaryotic, and eukaryotic phosphofructokinases at the putative ATP-binding sites.

Molecular analysis of two fructokinases involved in sucrose metabolism of enteric bacteria

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Molecular analysis of two fructokinases involved in sucrose metabolism of enteric bacteria