Ribose-5-phosphate isomerase

ribose-5-phosphate isomerase
Identifiers
EC number 5.3.1.6
CAS number 9023-83-0
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO

Ribose-5-phosphate isomerase (Rpi) is an enzyme that catalyzes the conversion between ribose-5-phosphate (R5P) and ribulose-5-phosphate (Ru5P). It is a member or a larger class of isomerases which catalyze the interconversion of chemical isomers (in this case structural isomers of pentose). It plays a vital role in biochemical metabolism in both the pentose phosphate pathway and the Calvin cycle. The systematic name of this enzyme class is D-ribose-5-phosphate aldose-ketose-isomerase.

Structure

Gene

RpiA in human beings is encoded on the second chromosome 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 in ribose-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 motiffs, indicating ancient origins of the gene. [2]

Protein

A structural diagram of the enzyme ribose-5-phosphate isomerase by Zhang, et al.

Rpi exists as two distinct proteins forms, termed RpiA and RpiB. Although RpiA and RpiB catalyze the same reaction, they show no sequence or overall structural homology.2 According to Jung et al.,[3] an assessment of RpiA using SDS-PAGE shows that the enzyme is a homodimer of 25 kDa subunits. The molecular weight of the RpiA dimer was found to be 49 kDa [3] by gel filtration. Recently, the crystal structure of RpiA was determined. (please see http://www3.interscience.wiley.com/cgi-bin/fulltext/97516673/PDFSTAR)

Due to its role in the pentose phosphate pathway and the Calvin 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 the Calvin cycle which takes place in plants, and the pentose phosphate pathway which takes place in plants as well as animals.

All orthologs of the enzyme maintain an asymmetric tetramer quaternary 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 motiff 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 resides Asp81, Asp84, and Lys94. These are directly involved in catalysis.[6]

Mechanism

In the reaction, the overall consequence is the movement of a carbonyl group from carbon number 1 to carbon number 2; this is achieved by the reaction going through an enediol intermediate (Figure 1).[6] Through site-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 by allosteric 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 the furanose ring, it next opens the ring. Then the enzyme forms the eneldiol which is stabilized by an lysine or arginine 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 other like it.[9]

Function

The protein encoded by RPIA gene is an enzyme, which catalyzes the reversible conversion between ribose-5-phosphate and ribulose-5-phosphate in the pentose-phosphate pathway. This gene is highly conserved in most organisms. The enzyme plays an essential role in the carbohydrate metabolism. Mutations in this gene cause ribose 5-phosphate isomerase deficiency. A pseudogene is found on chromosome 18.[10]

Pentose phosphate pathway

In the non-oxidative part of the pentose phosphate pathway, RPIA converts Ru5P to R5P which then is converted by ribulose-phosphate 3-epimerase to xylulose-5-phosphate (figure 3).[11] The end 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 for NADPH which is needed for biosynthetic reactions and protection against reactive oxygen species.[12]

Calvin cycle

In the Calvin 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 to ribulose-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 is glyceraldehyde-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]

Clinical significance

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 premature stop codon into the gene encoding the isomerase, and the second is a missense mutation. The molecular pathology is, as yet, unclear.[17]

RpiA and hepatocarcinogenesis

Human ribose-5-phosphate isomerase A (RpiA) plays a role in human hepatocellular carcinoma (HCC).[18] A significant increase in RpiA expression was detected both in tumor biopsies of HCC patients and in a liver cancer tissue array. Importantly, the clinicopathological analysis indicated that RpiA mRNA levels were highly correlated with clinical stage, grade, tumor size, types, invasion and alpha-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 required ERK signaling as well as the negative modulation of PP2A 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 induce oncogenesis in HCC.[19]

RpiA and the malaria parasite

RpiA generated attention when the enzyme was found to play an essential role in the pathogenesis of the parasite Plasmodium falciparum, the causative agent of malaria. Plasmodium cells have a critical need for a large supply of the reducing power of NADPH via PPP in order to support their rapid growth. The need for NADPH is also required to detoxify heme, the product of hemoglobin 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 for nucleic acid synthesis. It has been shown that PRPP concentrations are increased 56 fold in infected erythrocytes compared with uninfected erythrocytes.[21] Hence, designing drugs that target RpiA in Plasmodium falciparum could have therapeutic potential for patients that suffer from malaria.

Interactions

RPIA has been shown to interact with PP2A.[19]

Structural studies

As of late 2007, 15 structures have been solved for this class of enzymes, with PDB accession codes 1LK5, 1LK7, 1LKZ, 1M0S, 1NN4, 1O1X, 1O8B, 1UJ4, 1UJ5, 1UJ6, 1USL, 1XTZ, 2BES, 2BET, and 2F8M.

References

  1. ↑ U.S. National Library of Medicine http://ghr.nlm.nih.gov/gene/RPIA
  2. ↑ SØRENSEN, Kim. I (February 1996). "Ribose Catabolism of Escherichia coli : Characterization of the rpiB Gene Encoding Ribose Phosphate Isomerase B and of the rpiR Gene, Which Is Involved in Regulation of rpiB Expression". Journal of Bacteriology 178 (4): 1003–1011. PMC 177759. PMID 8576032.
  3. 1 2 Jung, Ch; Hartman, Fc; Lu, Ty; Larimer, Fw (Jan 2000). "D-ribose-5-phosphate isomerase from spinach: heterologous overexpression, purification, characterization, and site-directed mutagenesis of the recombinant enzyme". Archives of Biochemistry and Biophysics 373 (2): 409–17. doi:10.1006/abbi.1999.1554. ISSN 0003-9861. PMID 10620366.
  4. ↑ Zhang, Rong-Guang; et al. (3 October 2003). "The 2.2 Å Resolution Structure of RpiB/AlsB from Escherichia coli Illustrates a New Approach to the Ribose-5-phosphate Isomerase Reaction". J. Mol. Biol. 332 (5): 1083–94. doi:10.1016/j.jmb.2003.08.009. PMC 2792017. PMID 14499611.
  5. ↑ Rossmann, MG; Morris, D.; Olsen, KW (1974). "Chemical and biological evolution of a nucleotide-binding protein". Nature 250 (5463): 194–9. doi:10.1038/250194a0. PMID 4368490.
  6. 1 2 3 Zhang, R; Andersson, CE; Savchenko, A; Skarina, T; Evdokimova, E; Beasley, S; Arrowsmith, CH; Edwards, AM; et al. (2003). "Structure of Escherichia coli Ribose-5-Phosphate Isomerase: A Ubiquitous Enzyme of the Pentose Phosphate Pathway and the Calvin Cycle". Structure 11 (1): 31–42. doi:10.1016/S0969-2126(02)00933-4. PMC 2792023. PMID 12517338.
  7. ↑ Gengenbacher, M; Fitzpatrick, Tb; Raschle, T; Flicker, K; Sinning, I; Müller, S; Macheroux, P; Tews, I; Kappes, B (Feb 2006). "Vitamin B6 biosynthesis by the malaria parasite Plasmodium falciparum: biochemical and structural insights" (Free full text). The Journal of Biological Chemistry 281 (6): 3633–41. doi:10.1074/jbc.M508696200. ISSN 0021-9258. PMID 16339145.
  8. ↑ Woodruff, William W.; Wolfenden, Richard (18 July 1978). "Inhibition of ribose-5-phosphate by 4-phosphoerythronate". Journal of Biological Chemistry 254 (13). Retrieved 6 March 2013.
  9. ↑ Feierberg I, Åqvist (2002). "Computational modeling of enzymatic keto–enol isomerization reactions.". Theor Chem Accts 108.
  10. ↑ "Entrez Gene: RPIA ribose 5-phosphate isomerase A".
  11. ↑ Berg, Jeremy M. (2012). Biochemistry. New York: W.H. Freeman and Company. ISBN 1-4292-2936-5.
  12. ↑ Struzyńska, L; Chalimoniuk, M; Sulkowski, G (Sep 2005). "The role of astroglia in Pb-exposed adult rat brain with respect to glutamate toxicity". Toxicology 212 (2–3): 185–94. doi:10.1016/j.tox.2005.04.013. ISSN 0300-483X. PMID 15955607.
  13. ↑ Martin, William; Henze, K; Kellerman, J; Flechner, A; Schnarrenberger, C (1996). "Microsequecing and cDNA cloning of the Calvin cycle/OPPP enzyme ribose-5-phosphate isomerase (EC 5.3.1.6) from spinach chloroplasts". Plant Molecular Biology 30 (4): 795–805. doi:10.1007/BF00019012. PMID 8624410.
  14. ↑ A. A. Benson; J. A. Bassham; M. Calvin; T. C. Goodale; V. A. Haas; W. Stepka (1950). "The Path of Carbon in Photosynthesis. V. Paper Chromatography and Radioautography of the Products1". Journal of the American Chemical Society 72 (4): 1710–1718. doi:10.1021/ja01160a080.
  15. ↑ Nelson, David L. (2005). Principles of Biochemistry. New Yord: W.H Freeman and Company. ISBN 0-7167-4339-6.
  16. ↑ Huck, JH; Verhoeven, NM; Struys, EA; Salomons, GS; Jakobs, C; van der Knaap, MS (Apr 2004). "Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy". Am J Hum Genet 74 (4): 745–51. doi:10.1086/383204. PMC 1181951. PMID 14988808.
  17. ↑ Riganti, C; Gazzano, E; Polimeni, M; Aldieri, E; Ghigo, D (1 August 2012). "The pentose phosphate pathway: an antioxidant defense and a crossroad in tumor cell fate.". Free radical biology & medicine 53 (3): 421–36. doi:10.1016/j.freeradbiomed.2012.05.006. PMID 22580150.
  18. 1 2 Ciou, SC; Chou, YT; Liu, YL; Nieh, YC; Lu, JW; Huang, SF; Chou, YT; Cheng, LH; Lo, JF; Chen, MJ; Yang, MC; Yuh, CH; Wang, HD (1 July 2015). "Ribose-5-phosphate isomerase A regulates hepatocarcinogenesis via PP2A and ERK signaling.". International Journal of Cancer. Journal International Du Cancer 137 (1): 104–15. doi:10.1002/ijc.29361. PMID 25429733.
  19. ↑ Becker, K; Rahlfs, S; Nickel, C; Schirmer, Rh (Apr 2003). "Glutathione--functions and metabolism in the malarial parasite Plasmodium falciparum". Biological chemistry 384 (4): 551–66. doi:10.1515/BC.2003.063. ISSN 1431-6730. PMID 12751785.
  20. ↑ Huck, Jh; Verhoeven, Nm; Struys, Ea; Salomons, Gs; Jakobs, C; Van, Der, Knaap, Ms (Apr 2004). "Ribose-5-Phosphate Isomerase Deficiency: New Inborn Error in the Pentose Phosphate Pathway Associated with a Slowly Progressive Leukoencephalopathy". American Journal of Human Genetics 74 (4): 745–51. doi:10.1086/383204. ISSN 0002-9297. PMC 1181951. PMID 14988808.
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