| ribose-5-phosphate isomerase | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 D-Ribose-5-phosphate isomerase homotetramer, Pyrococcus horikoshii | |||||||||
| Identifiers | |||||||||
| EC no. | 5.3.1.6 | ||||||||
| CAS no. | 9023-83-0 | ||||||||
| Databases | |||||||||
| IntEnz | IntEnz view | ||||||||
| BRENDA | BRENDA entry | ||||||||
| ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDBPDBePDBsum | ||||||||
| Gene Ontology | AmiGO /QuickGO | ||||||||
| |||||||||
Ribose-5-phosphate isomerase (Rpi) encoded by the RPIA gene is anenzyme (EC5.3.1.6) thatcatalyzes the conversion betweenribose-5-phosphate (R5P) andribulose-5-phosphate (Ru5P). It is a member of a larger class ofisomerases which catalyze the interconversion of chemicalisomers (in this case structural isomers ofpentose). It plays a vital role in biochemical metabolism in both thepentose phosphate pathway and theCalvin cycle. Thesystematic name of this enzyme class isD-ribose-5-phosphate aldose-ketose-isomerase.
RpiA in human beings is encoded on the secondchromosome on the short arm (p arm) at position 11.2. Its encoding sequence is nearly 60,000 base pairs long.[1] The only known naturally occurring genetic mutation results inribose-5-phosphate isomerase deficiency, discussed below. The enzyme is thought to have been present for most of evolutionary history. Knock-out experiments conducted on the genes of various species meant to encode RpiA have indicated similar conserved residues and structural motifs, indicating ancient origins of the gene.[2]
Rpi exists as two distinct proteins, termed RpiA and RpiB. Although RpiA and RpiB catalyze the same reaction, they show no sequence or overall structuralhomology. According to Jung et al.,[3] an assessment of RpiA usingSDS-PAGE shows that the enzyme is ahomodimer of 25 kDa subunits. The molecular mass of the RpiA dimer was found to be 49 kDa[3] bygel filtration. Recently, the crystal structure of RpiA was determined. (please see[2])
Due to its role in thepentose phosphate pathway and theCalvin cycle, RpiA is highly conserved in most organisms, such as bacteria, plants, and animals. RpiA plays an essential role in the metabolism of plants and animals, as it is involved in theCalvin cycle which takes place in plants, and thepentose phosphate pathway which takes place in plants as well as animals.
All orthologs of the enzyme maintain an asymmetrictetramerquaternary structure with a cleft containing the active site. Each subunit consists of a five stranded β-sheet. These β-sheets are surrounded on both sides by α-helices.[4] This αβα motif is not uncommon in other proteins, suggesting possible homology with other enzymes.[5] The separate molecules of the enzyme are held together by highly polar contacts on the external surfaces of the monomers. It is presumed that the active site is located where multiple β-sheet C termini come together in the enzymatic cleft. This cleft is capable of closing upon recognition of the phosphate on the pentose (or an appropriate phosphate inhibitor). The active site is known to contain conserved residues equivalent to the E. coli residues Asp81, Asp84, and Lys94. These are directly involved in catalysis.[6]
In the reaction, the overall consequence is the movement of acarbonyl group from carbon number 1 to carbon number 2; this is achieved by the reaction going through anenediol intermediate (Figure 1).[6] Throughsite-directed mutagenesis, Asp87 of spinach RpiA was suggested to play the role of a general base in the interconversion of R5P to Ru5P.[7]
The first step in the catalysis is the docking of the pentose into the active site in the enzymatic cleft, followed byallosteric closing of the cleft. The enzyme is capable of bonding with the open-chain or ring form of the sugar-phosphate. If it does bind thefuranose ring, it next opens the ring. Then the enzyme forms the eneldiol which is stabilized by alysine orarginine residue.[6][8] Calculations have demonstrated that this stabilization is the most significant contributor to the overall catalytic activity of this isomerase and a number of others like it.[9]
The protein encoded by RPIA gene is an enzyme, which catalyzes the reversible conversion betweenribose-5-phosphate andribulose-5-phosphate in thepentose-phosphate pathway. This gene is highly conserved in most organisms. The enzyme plays an essential role in thecarbohydrate metabolism.Mutations in this gene causeribose 5-phosphate isomerase deficiency. Apseudogene is found onchromosome 18.[10]
In the non-oxidative part of thepentose phosphate pathway, RPIA converts Ru5P to R5P which then is converted byribulose-phosphate 3-epimerase toxylulose-5-phosphate (figure 3).[11] The result of the reaction essentially is the conversion of the pentose phosphates to intermediates used in the glycolytic pathway. In the oxidative part of the pentose phosphate pathway, RpiA converts Ru5P to the final product, R5P through the isomerization reaction (figure 3). The oxidative branch of the pathway is a major source forNADPH which is needed for biosynthetic reactions and protection against reactive oxygen species.[12]
In theCalvin cycle, the energy from the electron carriers is used in carbon fixation, the conversion of carbon dioxide and water into carbohydrates. RPIA is essential in the cycle, as Ru5P generated from R5P is subsequently converted toribulose-1,5-bisphosphate (RuBP), the acceptor of carbon dioxide in the first dark reaction of photosynthesis (Figure 3).[13] The direct product of RuBP carboxylase reaction isglyceraldehyde-3-phosphate; these are subsequently used to make larger carbohydrates.[14]Glyceraldehyde-3-phosphate is converted to glucose which is later converted by the plant to storage forms (e.g., starch or cellulose) or used for energy.[15]
Ribose-5-phosphate isomerase deficiency is mutated in a rare disorder,Ribose-5-phosphate isomerase deficiency. The disease has only one known affected patient, diagnosed in 1999.[16] It has been found to be caused by a combination of two mutations. The first is an insertion of a prematurestop codon into the gene encoding the isomerase, and the second is amissense mutation. The molecular pathology is, as yet, unclear.[17]
Human ribose-5-phosphate isomerase A (RpiA) plays a role in humanhepatocellular carcinoma (HCC).[18] A significant increase in RpiA expression was detected both in tumor biopsies of HCC patients and in aliver cancer tissue array. Importantly, the clinicopathological analysis indicated that RpiAmRNA levels were highly correlated with clinical stage, grade, tumor size, types, invasion andalpha-fetoprotein levels in the HCC patients. In addition, the ability of RpiA to regulate cell proliferation and colony formation in different liver cancer cell lines requiredERK signaling as well as the negative modulation ofPP2A activity and that the effects of RpiA could be modulated by the addition of either a PP2A inhibitor or activator. It suggests that RpiA overexpression can induceoncogenesis in HCC.[19]
RpiA generated attention when the enzyme was found to play an essential role in the pathogenesis of the parasitePlasmodium falciparum, the causative agent ofmalaria. Plasmodium cells have a critical need for a large supply of the reducing power ofNADPH via PPP in order to support their rapid growth. The need forNADPH is also required to detoxifyheme, the product ofhemoglobin degradation.[20] Furthermore, Plasmodium has an intense requirement for nucleic acid production to support its rapid proliferation. The R5P produced via increased pentose phosphate pathway activity is used to generate 5-phospho-D-ribose α-1-pyrophosphate (PRPP) needed fornucleic acid synthesis. It has been shown that PRPP concentrations are increased 56 fold in infectederythrocytes compared with uninfected erythrocytes.[17] Hence, designing drugs that target RpiA in Plasmodium falciparum could have therapeutic potential for patients that suffer from malaria.
RPIA has been shown tointeract withPP2A.[19]
As of late 2007, 15structures have been solved for this class of enzymes, withPDB accession codes1LK5,1LK7,1LKZ,1M0S,1NN4,1O1X,1O8B,1UJ4,1UJ5,1UJ6,1USL,1XTZ,2BES,2BET, and2F8M.
