The active site pocket can accommodate either dribulose 5‐phosphate or d‐xylulose 5‐phosphate without causing any noticeable movement of the side chains of the catalytic residues. Interestingly, RPE has been shown to protect cells from oxidative stress via its participation in PPP for the production of NADPH (6–8). In the structure of hRPE, amino acids positioned between stands β2 and β3 and between β3 and β4 are seen engaged in intermolecular interactions. 1) (1). Xylulose 5-phosphate is always required to produce ribose 5-phosphate. ribose phosphates are intermediates in pentose phosphate pathway. Finally, the dihydroxy‐acetone phosphate was converted to glycerol phosphate using a glycerophosphate dehydrogenase. Interestingly, the activity of the S. pyogenes RPE stripped off its metal ion by treatment with EDTA and did not increase on addition of Fe2+ ions. Our structural, mutagen‐esis, and functional studies on hRPE suggest a highly conserved mechanism of catalysis. Inspection of the anomalous difference electron density map around the Fe binding site confirmed the presence of Fe2+ in the crystal. The enzyme from potato chloroplasts was expressed in Escherichia coli, isolated and crystallized. Accordingly, 9 amino acids were mutated to alanine and expressed under identical conditions in E. coli (Fig. RPE was PCR amplified from human brain cDNA library and cloned into pMD‐18T vector (Takara, Beijing, China). Blue indicates positive potential; red, negative potential. Induction was carried out at 16°C for 20 h by adding 0.2 mM IPTG. Crystals were frozen in liquid nitrogen prior to diffraction testing and data collection. The loop is seen capping the active site and therefore the binding of the ligand might have caused the movement of the loop. The deproto‐nated Asp37 abstracts a proton from the C3 atom of d‐ ribulose 5‐phosphate, resulting in a cis‐enediolate intermediate. These subtle differences in the configuration of the C4 atom have implications for the mechanism of catalysis. Ribulose 5-phosphate values were 3.4 +/- 0.3, 5.8 +/- 0.2, and 37.1 +/- 5.3 nmol/g. The D‐xylulose 5‐phosphate formed was first converted to glyceraldehyde 3‐phosphate and sedoheptulose 7‐phosphate using a transketolase. [2], InChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3,5-8,10H,1-2H2/t3-,5-/m1/s1, InChI=1/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3,5-8,10H,1-2H2/t3-,5-/m1/s1, Except where otherwise noted, data are given for materials in their, https://en.wikipedia.org/w/index.php?title=Ribulose&oldid=968494603, Chemical articles with multiple compound IDs, Multiple chemicals in an infobox that need indexing, Chemical articles with multiple CAS registry numbers, Chemical articles with multiple PubChem CIDs, Articles with changed ChemSpider identifier, Pages using collapsible list with both background and text-align in titlestyle, Articles containing unverified chemical infoboxes, Creative Commons Attribution-ShareAlike License, This page was last edited on 19 July 2020, at 19:10. None of the mutants displayed any significant activity (Fig. Any queries (other than missing content) should be directed to the corresponding author for the article. Mutating either of them to alanine affected the solubility of the protein. d-Ribulose is the diastereomer of d-xylulose. Structural evidence supports binding ofa divalent metal ion into the density observed. Interestingly, mutating Ser‐10 to alanine almost abolished the enzymatic activity, while L12A and M72A mutations resulted in an almost 50% decrease in the activity. Structural, mutagenesis, and functional data suggest that RPE uses a highly conserved mechanism for catalysis. In enzymology, a L-ribulose-5-phosphate 4-epimerase (EC 5.1.3.4) is an enzyme that catalyzes the interconversion of ribulose 5-phosphate and xylulose 5-phosphate in the oxidative phase of the Pentose phosphate pathway. Due to these structural differences, ribose and ribulose have varied functions in the living system. The ribulose-5-P is isomerized to ribose-5-P and also epimerized to xylulose-5-P (Figure 3 ). This hydrogen bonding network of Ser‐10 is probably important for the relay of charge. These findings have implications for the role of RPE in oxidative stress. However, none of the structures have been determined in complex with the physiological ligands. Although we are reporting for the first time that hRPE might be Fe2+ dependent or at least be able to bind and use Fe2+ for activity, the nature of the divalent metal ion preferred by RPE under physiological conditions needs to be investigated. Use the link below to share a full-text version of this article with your friends and colleagues. Therefore, the methionines are more likely to play a role in imparting substrate specificity by constricting the active site rather than participate directly in catalysis. In the binary complexes of hRPE with d‐ribulose 5‐phosphate and d‐xylulose 5‐phosphate, these methionines are at least 3.5 Å from the ligands. We have used one of these, xylulose 1,5-bisphosphate as an analogue of the natural substrate and co-crystallized it with the enzyme. For clarity, the coordination of Fe2+ with the hydroxyl group of C3 and the carboxyl oxygen of Asp37 has not been shown. 5A). After buffer exchange to remove the imidazole, the His tag was removed by treating the protein with TEV protease. Fructose, ribulose and xylulose, erythrulose, tagatose, sorbose, psicose are some of the prominent examples of ketose sugars. The positions of C1, O1, C2, O2, and the phosphate group of d‐ribulose 5‐phosphate and d‐xylulose 5‐phosphate are identical in the binary complexes. In other words, it is the stereoisomer formed by removing a proton from the chiral alpha position of xylulose-5-phosphate and putting it back on the wrong side. Isotope exchange studies, mutagenesis, and structural studies on RPE homologues reported previously (15, 16) suggest the participation of a pair of aspartic acids, with one acting as a proton donor and the other as a proton acceptor (Fig. A central β sheet made up of 8 parallel strands makes up the core barrel. The overall structure of hRPE closely mirrors the structures of RPE homologues reported previously (10–14). The reaction mixture consisted of 2 mM of D‐ribulose 5‐phosphate in 50 mM glycylglycine (pH 7.7), 0.001 mg cocarboxylase/thiamine pyrophosphate, 0.0625 mM NADH, 0.01 U transketolase, 0.01 Uofα‐glycerophosphate dehydrogenase/TIM, 7.5 mM MgCl2, and appropriate dilution of the enzyme. These results suggest that RPE may not be able to use Fe2+ or Mg2+ for catalysis. CD analysis of all three mutants revealed that the mutation altered the content of the secondary structural elements of the protein. To gain insights into the mode of ligand binding and the nature of the active site residues of hRPE, we soaked the crystals of apo‐RPE with the substrate d‐ribulose 5‐phosphate. Since the Fe2+ ion binds the enzyme tightly, hRPE is probably able to catalyze the reaction using Fe2+ ion. D-ribulose and 1,5-bisphosphate combines with carbon dioxide initially in the photosynthesis process in green plants. Here, using structural, biochemical, and functional studies, we show that human D‐ribulose 5‐phosphate 3‐epimerase (hRPE) uses Fe2+ for catalysis. Cells were harvested by centrifugation and lysed by sonication. Fe2+ is shown as a sphere. This work was funded by the Ministry of Science and Technology of China (grants 2006AA02A316, 2009DFB30310, and 2006CB910901), the National Natural Science Foundation of China (grants 30670427 and 30721003), the Ministry of Health of China (grant 2008ZX10404), a Chinese Academy of Sciences (CAS) research grant (KSCX2‐YW‐R‐127 and INFO‐115‐D01–2009), and a CAS fellowship for young international scientists (grant 2010Y1SA1). Leu12 is highly conserved among the orthologs of RPE. RPE, ribulose 5‐phosphate 3‐epimerase; RPI, ribose 5‐phosphate isomerase; TK, transketolase; TA, transaldolase. The only structure of a RPE homologue solved in complex with a ligand to date, the structure of RPE from S. pyogenes in complex with a substrate analog d‐xylitol 5‐phosphate (10), confirms results of mutagenesis and isotope exchange studies that implicate a pair of aspar‐tates as the acid/base catalysts (15, 16). Native diffraction data were collected at a wavelength of 0.979 Å at beamline 19‐ID of the APS (Argonne National Laboratory). 4B). The structure of the apo form of hRPE was solved by molecular replacement using the structure of the rice RpE (Oryza sativa; PDB code 1H1Y) as a search model. These results suggest that the enzyme may not be able to utilize Fe2+ to catalyze the reaction. The tagless protein was exchanged into a buffer containing 20 mM Tris‐HCl (pH 7.5) and 150 mM NaCl, using a Superdex G75 size‐exclusion column (GE Healthcare, Piscataway, NJ, USA). Further, we have probed the role of residues surrounding the ligands in catalysis by site‐directed mu‐tagenesis and functional assays. These methionines are highly conserved, with Met72 being absolutely conserved among the orthologs of RPE (Fig. These observations serve to establish that there is a structural link between between the active site geometry of the epimerase and the aldolase. www.fasebj.org. 5B). C) Octahedral coordination of the Fe2+ ion. The ligands bind deep inside a narrow tunnel just above the β barrel (Fig. The final model, containing residues 4–223 of the enzyme and 282 water molecules, was refined to 1.70‐Å resolution. While the ε1 carbon atom of Phe147 was 3.9 Å from the 7 carbon atom of Pro45 in the apo structure, the minimum distance between any of the atoms of Phe147 and Pro45 is now > 4.44 Å in the binary complexes. RPE functions in the PPP, catalyzing the reversible conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate and is an important enzyme for cellular response against oxidative stress. Human RPE consistently bound Fe2+ when produced under conditions mentioned in Materials and Methods. While some protein could be salvaged to perform activity assays for H35A, D37A, and D175A mutants, H70A mutant was completely insoluble and therefore could not be tested for activity. The pathway produces precursors for the synthesis of nucleic acids, aromatic amino acids, and energy via the glycolytic pathway. In the binary complex of xylulose 5‐phosphate with RPE, the hydroxyl oxygen of Ser‐10 is hydrogen bonded to the C4 oxygen, which is forming a hydrogen bond with Wat30. The results of the scan suggested that hRPE bound Fe2+ predominantly under the conditions mentioned in Materials and Methods. The statistics of the anomalous data are listed in Supplemental Table S1, and the anomalous difference electron density map is shown in Supplemental Fig. Further, side chains of Met39, Met72, and Met141 constrict the active site around the O1 and C1 atoms, preventing any movement of the ligands around this region. Summary: The protein encoded by this gene is a transketolase that acts as a homodimer and catalyzes the conversion of sedoheptulose 7-phosphate and D-glyceraldehyde 3-phosphate to D-ribose 5-phosphate and D-xylulose 5-phosphate. Next, the glyceraldehyde 3‐phosphate was converted to dihydroxyacetone phosphate by the action of triosephosphate isomerase (TIM). RPE probably helps alleviate this damage by binding free Fe2+ ions, thereby making them unavailable for reaction with H2O2. In summary, the structures of hRPE reported here provide a clear picture of the architecture of the active site. Learn about our remote access options, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, Graduate University of Chinese Academy of Sciences, Beijing, China, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois, USA. However, addition of Zn2+, Mn2+, and Co2+ under identical conditions resulted in an increase in activity of the enzyme (10). The excess charge on the O2 atom ofthe intermediate is probably stabilized by the interactions of the atom with Fe2+ and His70. Secondary structure of hRPE is annotated at bottom. 4A). 1) (3, 4). Nonoxidative Segment. Because of the change in configuration of C3, the positions of C4 and the hydroxyl group at C4 changes. It has chemical formula C5H10O5. RPE functions in the PPP, catalyzing the reversible conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate and is an important enzyme for cellular response against oxidative stress. Transfer of the top two carbons as a unit from the xylulose-5-P to ribose-5-P, catalyzed by transketolase, yields seven-carbon-containing sedoheptulose-7-P and glyceraldehyde-3-P. D-Ribulose | C5H10O5 | CID 151261 - structure, chemical names, physical and chemical properties, classification, patents, literature, biological activities, safety/hazards/toxicity information, supplier lists, and more. One unit of activity is defined as the amount of enzyme required to convert 1 µmol of D‐ribulose 5‐phosphate to D‐xylulose 5‐phosphate under the assay conditions. The βα loops connecting the strands with helices have been known to impart substrate specificities to a wide range of enzymes catalyzing diverse reactions employing the TIM‐barrel fold. The overlap PCR product was ligated into pMCSG7 as described earlier. Two enantiomers are possible, D-ribulose (D-erythro-pentulose) and L-ribulose (L-erythro-pentulose). Ribulose-5-phosphate is just the epimer of xylulose-5-phosphate. The monomers within the dimer are identical. Analytical ultracentrifugation analysis confirmed that hRPE exists as a dimer in solution. 5A). His35, His70, Asp37, Asp175, and oxygens O2 and O3 of the ligand are coordinated to the Fe2+ ion (Fig. Plant Physiol. Although the level of expression was similar to that of the wild‐type enzyme, > 90% ofthe mutant enzyme was insoluble, suggesting that the mutations affected the secondary structure of the protein. This assists in the reversal of role for the catalytic aspartates during the conversion of d‐xylulose 5‐phosphate to d‐ribulose 5‐phosphate. The conversion of xylulose 5-phosphate is catalyzed by ribulose phosphate epimerase; this reaction proceeds via a keto-enol isomerization and a 2,3-enediol intermediate. S1. 4A). We compared the structure of the binary complexes with the structure of the apo enzyme. The pentose phosphate pathway (PPP) confers protection against oxidative stress by supplying NADPH necessary for the regeneration of glutathione, which detoxifies H2O2 into H2O and O2. RPE is a metalloenzyme and requires a divalent metal ion for its activity. Nucleic acids (RNA) Ribozymes. An octahedral coordination and the charge of the groups involved in coordination support building of a positively charged divalent ion in the electron density (Fig. d -Ribulose is the diastereomer of d - xylulose. If the volume of the xylulose-5-phosphate epimerase added is small (0.01 ml. Accumulation of hydrogen peroxide during stress has deleterious effects and can lead to cell damage and death. RPE catalyzes the epimerization of ribulose 5‐phos‐phate to xylulose 5‐phosphate via a cis‐enediolate intermediate employing an acid‐base type of catalytic mechanism. A similar tetrahedral coordination for a Zn2+ ion has been reported for the apo form of RpE homologs from Plasmodium falciparum, potato, and rice (11, 13, 14). RPE functions in the PPP, catalyzing the reversible conversion of D‐ribulose 5‐phosphate to D‐xylulose 5‐phosphate and is an important enzyme for cellular response against oxidative stress. A number of amino acids are interacting with the ligands (Fig. M39A retained 90% of its activity when compared to that of the wild‐type enzyme. The asymmetric unit consists of 2 molecules of hRPE. After concentration using 10‐kDa‐cutoff centrifugal concentrators, the protein (15–20 mg/ml) was immediately screened for crystallization. The protection against reactive oxygen species is exerted by NADPH's ability to reduce glutathione, which detoxifies H2O2 into H2O (Fig. In addition, they probably assist in docking of the substrate into the active site under optimal orientation for catalysis. Catalyzes the interconversion of L-ribulose 5-phosphate (LRu5P) and D-xylulose 5-phosphate (D-Xu5P) via a retroaldol/aldol mechanism (carbon-carbon bond cleavage analogous to a class II aldolase reaction). Using the structures of the binary complexes of RPE and primary sequence alignment of RPE orthologs as a guide, we carried out alanine scanning mutagenesis of amino acids surrounding the ligands to determine their role in catalysis (Fig. Search results for D-Xylulose at Sigma-Aldrich. Which statement about the conversion of ribulose 5-phosphate to fructose 6-phosphate is TRUE? More important, the enzyme could not use Fe2+ and Mg2+ for catalysis (10). To confirm the nature of the metal ion, we performed an X‐ray fluorescence scan of the protein crystal at the absorption edge of Zn2+,Mg2+, Co2+,Ca2+,Ni2+, and Fe2+. 6-P gluconate Glycogen Ribulose 5-P 6-P UDP-Glucose Galactose 1-P Ribose 5-P Glucose 1-P UDP-Galactose Xylulose 5-P Glucose 6-P Glucose Sedoheptulose 7-P Fructose 6-P Fructose 1,6-bis-PGlyceraldehydeFructose 1-P Glyceraldehyde 3-P Dihydroxyacetone-P 1,3-Bisphosphoglycerate 3-Phosphoglycerate 2-Phosphoglycerate Phosphoenolpyruvate Triacylglycerol Fatty acyl CoA ← -Fatty … Asp175 donates a proton to complete the epimerization and formation of d‐xylulose 5‐phosphate (Fig. In humans, this reaction drives the nonoxidative phase of the pentose phosphate pathway (PPP), which generates precursors such as erythrose 4‐phosphate, glyceraldehyde 3‐phos‐phate, and fructose 6‐phosphate that are necessary for the synthesis of aromatic amino acids and production of energy (Fig. The authors thank Dr. Keming Tan (Structural Biology Center, Argonne National Laboratory) for the help in collecting anomalous data at the edge of Fe. Mutating the methionines to alanine probably perturbs the structure around this region, affecting the optimal docking ofthe substrate into the active site. Mutating similar amino acids in the RPE from S. pyogenes resulted in a loss of catalytic activity (10). The binary complexes of hRPE with D‐ribulose 5‐phosphate and D‐xylulose 5‐phos‐phate were obtained by soaking the crystals with ligands in 50% PEG 3350 (Table 1). Interestingly, structural and biochemical evidence indicates that hRPE uses Fe2+ ion for catalysis. Learn more. COVID-19 is an emerging, rapidly evolving situation. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. This will also help answer the question whether the ability of RPE to bind Fe2+ ions plays a role in protection against oxidative stress. Xylulose 5-phosphate values were 3.8 +/- 0.3, 8.6 +/- 0.3, and 66.3 +/- 8.3 nmol/g. In contrast to the structure of the apo enzyme, the Fe2+ ion is coordinated octahedrally in the binary complexes of the hRPE with the substrate and product. Ribulose-5-phosphate 3-epimerase (EC 5.1.3.1) catalyzes the interconversion of ribulose-5-phosphate and xylulose-5-phosphate in the Calvin cycle and in the oxidative pentose phosphate pathway. Two enantiomers are possible, d-ribulose (d-erythro-pentulose) and l-ribulose (l-erythro-pentulose). 5A). Ribulose is a ketopentose — a monosaccharide containing five carbon atoms, and including a ketone functional group. Here, using structural, biochemical, and functional studies, we show that human D-ribulose 5-phosphate 3-epimerase (hRPE) uses Fe{sup 2+} for catalysis. Transfer of the top three carbon unit as a unit from the sedoheptulose-7-P to the glyceraldehyde-3-P, catalyzed by … These methionines are inside the active site pocket and are within the van der Waal's radii of the substrate. L12A mutation probably disrupts these interactions and decreases the hydrophobicity of the region, resulting in a > 55% loss of the enzymatic activity (Fig. The initial phase was improved with Oasis (19). The last step involves the oxidation of NADH to NAD, which can be monitored by reading the absorbance at 340 nm. Ribulose is known as ketopentose sugar due to the presence of a ketone functional group. It has chemical formula C5H10O5. Analysis of the total metal content was carried out using inductively coupled plasma mass spectrometry (ICP‐MS; Thermo, San Jose, CA, USA) at the Analysis Center of Tsinghua University (Beijing, China). As nouns the difference between xylose and xylulose is that xylose is xylose (wood sugar) while xylulose is (carbohydrate) the ketopentose (3r,4s)-1,3,4,5-tetrahydroxypentan-2-one . Ribulose is a ketopentose — a monosaccharide containing five carbon atoms, and including a ketone functional group. 5A). Briefly, the production of D‐xylulose 5‐phosphate was monitored using an enzyme‐coupled spectrophotometric assay. Ribulose sugars are composed in the pentose phosphate pathway from arabinose. The Fe2+ ion occupies an identical position in all three structures. 25, 497–504 (2011). Under normal conditions, the hydrogen peroxide is converted to H2O and O2 by peroxidases and catalases (25). To confirm the oligomerization state of the protein in solution, we carried out analytical ultracentrifugation analysis of RPE. pathways, the xylulose monophosphate pathway for yeasts and the ribulose monophosphate (RuMP) path-way for methylotrophic bacteria. ATP, NAD, NADP , flavoprotiens. The quality of the final model was validated with MolProbity (23). Except for the position of the loop connecting helice α3 with strand β 3, the structures of the apo and binary complexes of RPE with the substrate and product are identical. The mutations were confirmed by nucleotide sequencing. A reducing sugar is the sugar that can act as reducing agent as it has a free aldehyde group or a free ketone group. The enzymatic activity of hRPE was measured using a commercially available kit from Sigma (St. Louis, MO, USA). Conversion of D‐ribulose 5‐phosphate to D‐xylulose 5‐phosphate: new insights from structural and biochemical studies on human RPE. In addition, a majority of the NADPH used by the human body for biosynthetic purposes is supplied by the PPP (5). After verifying the DNA sequence, full‐length RPE (aa 1–228) was subcloned into pMCSG7 vector for expression in Escherichia coli BL 21 (DE3). Further functional studies are warranted to elucidate the physiological significance of this finding. Data were indexed and scaled to 1.70‐Å resolution using HKL2000 (17). The Fe2+ binds hRPE tightly, and density for the metal was visible even after treatment of the protein with 20 mM EDTA. Amino acids are shown as blue sticks; Fe2+ is shown as a sphere. RPE folds into a single domain with a classical TIM‐barrel α/β fold (Fig. Ribulose is produced in another reaction within the Calvin cycle, too. Involved in the degradation of L-arabinose (PubMed:13890280). These new interactions of the aromatic ring of Phe147 with Asn46 and that of Gly148 with Asn13 observed in the binary complexes result in the closure of the active site and isolation of the reactants from the aqueous environment (Fig. 2). The binary complexes of hRPE reported here will aid in the design of small molecules for modulating the activity of the enzyme and altering flux through the PPP.—Liang, W., Ouyang, S., Shaw, N., Joachimiak, A., Zhang, R., Liu, Z‐J. Also, as the 1,5-bisphosphate, d-ribulose combines with carbon dioxide at the start of the photosynthesis process in green plants (carbon dioxide trap). Human RPE crystallized as a dimer. FASEB J. 5A). Conservation has been colored according to Clustal W convention. All the mutants were purified to homogeneity using affinity and size‐exclusion chromatography, before being assayed for enzymatic activity under identical conditions. Electron density maps calculated from the anomalous differences were used to confirm identity of the metal ion. Numbers in parentheses represent values for the highest‐resolution shell. Results of the sedimentation velocity experiments suggest that hRPE exists as a dimer in solution. B) Reaction catalyzed by RPE. Uncut protein and TEV were removed by a second round of Ni‐affinity chromatography. Related Citations: The X-Ray Structure of Synechococcus Ribulose Bisphosphate Carboxylase(Slash)Oxygenase Activate Quaternary Complex at 2.2 Angstroms Resolution It is a ketose sugar formed from ribulose - 5 - phosphate. This conversion is important for the assimilation of CO2 by plants, which is carried out via the Calvin cycle (2). Soluble hRPE was purified by Ni‐affinity chromatography. Structures of the binary complexes of hRPE with D‐ribulose 5‐phosphate and D‐xylulose 5‐phosphate provide the first detailed molecular insights into the binding mode of physiological ligands and reveal an octa‐hedrally coordinated Fe2+ ion buried deep inside the active site. Additional data sets were collected near the absorption edge of Fe. A comparison of these structures seems to suggest that the overall structure of RPE is conserved. D-ribose biochem importance. Previously, RPE has been shown to carry out catalysis using Co2+,Mn2+, and Zn2+ ions. Further, to unravel the structural basis for the mechanism of catalysis at the molecular level and view the interaction of the product with the enzyme, we solved the structure of hRPE in complex with the product d‐xylulose 5‐phosphate by soaking the crystals of apo‐RPE with the product (Fig. Hanging drops (1 µl) containing 0.5 µl protein mixed with 0.5 µl mother liquor were equilibrated over 300 µl reservoir solution and incubated at 16°C. RPEs from yeast (1), rice (11), and Plasmodium (13) exist as dimers, while the RPEs from potato (14), Cyanobacterium synechocystis (12), and S. pyogenes (10) assemble into hexamers. 2B). Crystallographic data were collected at beamline 19‐ID of APS (Argonne National Laboratory). In the structure of the apo enzyme, the Fe2+ ion is tetrahedrally coordinated, with His35, His70, Asp37, and Asp175 participating in the coordination. If you do not receive an email within 10 minutes, your email address may not be registered, The apo enzyme from Streptococcus pyogenes could be activated by the addition of Zn2+, Mn2+, or Co2+ ions, but not Fe2+ or Mg2+ ions (10). This hydrogen bond is missing in the hRPE:d‐ribulose 5‐phosphate binary complex. Ribulose sugars are composed in the pentose phosphate pathway from arabinose. Mutants of yeast lacking a functional RPE were shown to be susceptible to oxidative stress (9). A) Residual activity of hRPE mutants. Human RPE folds into a typical (β/α)g triosephosphate isomerase (TIM) barrel with a loop regulating access to the active site. d‐ribulose 5‐phosphate 3‐epimerase (RPE) catalyzes the reversible conversion of d‐ribulose 5‐phosphate to d‐xylulose 5‐phosphate (Fig. Please check your email for instructions on resetting your password. d‐ribulose 5‐ phosphate 3‐ epimerase (RPE) catalyzes the reversible conversion of d ‐ribulose 5‐phosphate to d ‐xylulose 5‐phosphate (Fig. 5B). A) Cartoon representation of the structure. Asp37 is hydrogen bonded to Fe2+ and Ser‐10. This is the difference between Ribose and Ribulose. B) Alignment of the primary sequence of RPE orthologs deposited in PDB. RPEs have been reported to exist as dimers or hexam‐ers. The metal ion seems to have originated from the medium used for the production of RPE. Mechanism of catalysis. -D-ribulose and D-Xylulose (except the 3rd carbon is completely cut out) D-ribose where found. 4B). Error bars = sd. D-Ribulose is the diastereomer of D-xylulose." Crystallization screening was carried out using commercially available sparse matrix screens. HPS catalyzes For example, d-ribulose is an intermediate in the fungal pathway for d-arabitol production. The enzyme was active when assayed for activity using ribulose 5‐phosphate as a substrate. Glyceraldehyde 3-phosphate is formed after isomerization of CZ carbohydrates. Ribulose 1,5-bisphosphate (RuBP) is a colourless anion and a double phosphate ester of the ketopentose; Ribulose. structural elements of nucleic acids and coenzymes ,eg. B, C) Surface electrostatic potential representation of the apo‐hRPE (B) and the binary complex (C) showing the open and capped active site, respectively. The atomic coordinates and structure factor files of the apo‐hRPE, hRPE:D‐ribulose 5‐phosphate complex, and hRPE: D‐xylulose 5‐phosphate complex have been deposited in the PDB under the accession codes 3OVP, 3OVQ, and 3OVR, respectively. Please visit, © 2021 Federation of American Societies for Experimental Biology (FASEB), I have read and accept the Wiley Online Library Terms and Conditions of Use, Cloning of the amphibolic Calvin cycle/OPPP enzyme d‐ribulose‐5‐phosphate 3‐epimerase (EC 5.1.3.1) from spinach chloroplasts: functional and evolutionary aspects, The oxidative pentose phosphate pathway: structure and organisation, Physiological functions of the pentose phosphate pathway, Cells have distinct mechanisms to maintain protection against different reactive oxygen species: oxidative‐stress‐response genes, Mutants that show increased sensitivity to hydrogen peroxide reveal an important role for the pentose phosphate pathway in protection of yeast against oxidative stress, Cu, Zn superoxide dismutase and NADP(H) homeosta‐sis are required for tolerance ofendoplasmic reticulum stress in, d‐Ribulose 5‐phosphate 3‐epimerase: functional and structural relationships to members of the ribulose‐phosphate binding (β/α)8‐barrel superfamily, structure and catalytic mechanism of the cytosolic d‐ribulose‐5‐phosphate 3‐epimerase from rice, Structure of d‐ribulose 5‐phosphate 3‐epimerase from, Structure of a ribulose 5‐phosphate 3‐epimerase from, Structure and mechanism of the amphibolic enzyme ‐ribulose‐5‐phosphate 3‐epimerase from potato chloroplasts, Identification of a catalytic aspartyl residue of d‐ribulose 5‐phosphate 3‐epimerase by site‐directed mutagenesis, On the mechanism of the pentose phosphate epimerases, Processing of X‐ray diffraction data collected in oscillation mode, OASIS and molecular‐replacement model completion, Coot: model‐building tools for molecular graphics, Refinement of macromolecular structures by the maximum‐likelihood method, Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard, MolProbity: all‐atom contacts and structure validation for proteins and nucleic acids, Site‐directed mutagenesis by overlap extension using the polymerase chain reaction, Complex cellular responses to reactive oxygen species.

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