Ribokinase

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Introductions

Ribokinases (RK) belong to the phosphofructokinase B (PfkB) family of glucokinases. Other members of this family (also known as the RK family) include adenosine kinase (AK), inosine-guanosine kinase, fructokinase, and 1-phosphofructokinase. members of the PfkB/RK family are recognized by the presence of three conserved sequence motifs, and the enzymatic activity of this protein family typically exhibits a dependence on the presence of pentavalent ions. The conserved NXXE motif is a unique feature of the PfkB protein family that is associated with pentavalent ion dependence. The structure of RK and several other PfK protein families has been determined from many organisms. Although the sequence similarity between AdK and other PfkB protein families is low, these proteins are very similar at the structural level.

Figure 1. Ribokinase homodimer.

Overview of the RK family

RK genes are found in both prokaryotes and eukaryotes, and sequence comparisons indicate that they belong to the PfkB family of carbohydrate kinases, which phosphorylate the hydroxymethyl groups of various sugar molecules. Therefore, the PfkB family of enzymes, also known as the RK family, constitutes one of the three non-homologous branches of glycokinases along with the hexokinase family and the galactokinase family. Initially, the RK family consisted of a small number of evolutionarily related enzymes. In addition to RKs from E. coli and yeast, other members of this group included fructokinase, 1-phosphofructokinase, 6-phosphofructo-2-kinase (PfkB or PFK2), 6-phospho-taccharide kinase, and inositide kinase (INGK). Since then, many other enzymes have been added to the RK family, including AK and 2-dehydro-3-deoxyglucose kinase.

Structure of RK

The first three-dimensional crystal structure of RK was determined in 1998 for the E. coli protein. RK exists in solution as a homodimer, with each monomer consisting of two structural domains. The larger structural domain is formed by a nine-stranded b-sheet, which is flanked by 10 a-sheets. This ABA sandwich structure provides most of the specific binding of substrate, ribose and ATP. The smaller structural domain consists of four b-strands that serve as a cap for the active site. The outer surface of this b-sheet provides an interface for dimeric interactions through which the two b-sheets of the dimer are packed orthogonally to each other to form a flat b-barrel. The crossed segments of each subunit also contribute to the formation of the active site of the dimer partner.

Figure 2. Structure of an E. coli ribokinase subunit. ( Park J, et al.2008)

Gene structure of RK

RK gene has been characterized in human cells. The human RK gene is located on chromosome 2, approximately 110 Kb, and includes eight exons ranging from 63 to 189 nucleotides in length. Interestingly, human RK shows a higher degree of identity with RK sequences from protozoa (e.g. trypanosomes and amoebae) and various bacteria compared to plant (Arabidopsis) and fungal (Saccharomyces cerevisiae) homologs. These results were unexpected because fungi and plants are more closely related to animals than bacteria. Thus, RKs of plant and fungal species may have arisen independently of RKs of animal and protozoan species. It is also possible that plant and fungal RK sequences, which have not been biochemically characterized, may correspond to some other glyco-kinases.

Phosphate or pentavalent ion dependence of RK

Another important biochemical property of RKs is that their catalytic activity is almost entirely dependent on the presence of pentavalent ions (PVI), such as phosphate. In both cases, the addition of inorganic phosphate leads to an increase in the maximum velocity of the enzyme as well as a decrease in the Km of its substrate adenosine and ribose.