- Research article
- Open Access
Crystal structures from the Plasmodium peroxiredoxins: new insights into oligomerization and product binding
© Qiu et al; licensee BioMed Central Ltd. 2012
- Received: 28 October 2011
- Accepted: 19 March 2012
- Published: 19 March 2012
Plasmodium falciparum is the protozoan parasite primarily responsible for more than one million malarial deaths, annually, and is developing resistance to current therapies. Throughout its lifespan, the parasite is subjected to oxidative attack, so Plasmodium antioxidant defences are essential for its survival and are targets for disease control.
To further understand the molecular aspects of the Plasmodium redox system, we solved 4 structures of Plasmodium peroxiredoxins (Prx). Our study has confirmed Pv Trx-Px1 to be a hydrogen peroxide (H2O2)-sensitive peroxiredoxin. We have identified and characterized the novel toroid octameric oligomer of Py Trx-Px1, which may be attributed to the interplay of several factors including: (1) the orientation of the conserved surface/buried arginine of the NNLA(I/L)GRS-loop; and (2) the C-terminal tail positioning (also associated with the aforementioned conserved loop) which facilitates the intermolecular hydrogen bond between dimers (in an A-C fashion). In addition, a notable feature of the disulfide bonds in some of the Prx crystal structures is discussed. Finally, insight into the latter stages of the peroxiredoxin reaction coordinate is gained. Our structure of Py Prx6 is not only in the sulfinic acid (RSO2H) form, but it is also with glycerol bound in a way (not previously observed) indicative of product binding.
The structural characterization of Plasmodium peroxiredoxins provided herein provides insight into their oligomerization and product binding which may facilitate the targeting of these antioxidant defences. Although the structural basis for the octameric oligomerization is further understood, the results yield more questions about the biological implications of the peroxiredoxin oligomerization, as multiple toroid configurations are now known. The crystal structure depicting the product bound active site gives insight into the overoxidation of the active site and allows further characterization of the leaving group chemistry.
- Disulfide Bond
- Active Site Pocket
- Sulfinic Acid
- High Order Oligomer
There are at least 500 million clinical episodes of malaria annually with more than a million Africans dying each year, most of whom are children under 5 years of age . The causative agent for the most lethal form of malaria is a protozoan parasite, Plasmodium falciparum, while P. vivax causes a less severe form, P. knowlesi is responsible for macaque malaria (but it can also infect humans [2, 3]), and P. yoelii and berghei infect rodents. Plasmodium parasites are frequently subject to oxidative attack, for example, in the erythrocyte from H2O2 release during heme metabolism and from NO and reactive oxygen species (ROS) generation during the host immune response [4, 5]. In addition, oxidative stress is sustained during the sexual maturation of the parasite within the Anopheles mosquito midgut and salivary gland prior to transmission [6, 7]. As such, Plasmodium antioxidant defences are essential to its survival, and thus are expected to be targets for the effective control of the disease [8, 9].
Plasomodium peroxiredoxin orthologues and corresponding PDB codes for solved structures
2-Cys (C50, C170)
2-Cys (C50, C170)
2-Cys (C50, C170)
2-Cys (C50, C169)
2-Cys (C50, C170)
2-Cys (C67, C187)
2-Cys (C67, C187)
2-Cys (C67, C187)
2-Cys (C59, C179)
2-Cys (C67, C187)
All peroxiredoxins contain a conserved cysteine residue at the N-terminus that is referred to as the peroxidatic cysteine (CP). During catalysis, it is oxidized by the ROS substrate (generally H2O2 or an alkyl hydroperoxide) to sulfenic acid (Cys-S-OH). Typical 2-Cys Prx contain 2 conserved cysteines, including the CP and a C-terminal cysteine (termed the resolving Cys (CR)). During catalysis, the CP sulfenic acid reacts with the CR of the adjacent monomer to form the intermolecular disulfide of the homodimer that is subsequently reduced by another (undetermined) thiol. In 1-Cys Prx, the CP sulfenic acid is directly reduced by an unidentified redox partner.
Building on the dimer formation, the 2-Cys Prx enzymes organize themselves into higher order oligomers, such as decamers, which have higher peroxidase activity. Formation of the higher order oligiomers is dependent on the redox state of CP (and CR), as well as other factors [22, 23]. Both Trx-Px1 and Trx-Px2 have been identified as typical 2-Cys Prx enzymes; and a crystal structure of P. falciparum Trx-Px2 (PDB ID: 2C0D) has been published . Distinguishing these two Plasmodium thioredoxin peroxidases is their cellular location, as Trx-Px1 is predicted to be cytosolic and Trx-Px2 has a mitochondrial targeting sequence . Both features were recently confirmed . Like the Plasmodium 1-Cys Prx from subfamily Prx6, AOP is also a 1-Cys Prx; and the P. falciparum AOP structure has been solved (PDB ID: 1XIY) . AOP is thought to be an apicoplast enzyme due to its N-terminal signal motif, while the other Plasmodium 1-Cys Prx is cytosolic. Both predictions were recently confirmed experimentally . Prx enzymes are highly expressed in Plasmodium (0.5% of cellular protein) and have been predicted from competitive kinetic analysis with human cells to be responsible for the reduction of 90% of mitochondrial H2O2 and nearly 100% of cytoplasmic H2O2.
In order to further the understanding of the molecular details of the Plasmodium redox system, we solved the crystal structures of Trx-Px1 from P. vivax (Pv Trx-Px1) in the reduced and oxidized forms, Trx-Px1 from P. yoelii (Py Trx-Px1) in the oxidized form, and a 1-Cys Prx from P. yoelii (termed Py Prx6, herein) with CP oxidized to the sulfinic acid and with glycerol bound within the active site pocket. In addition, we have structurally confirmed and characterized the Pv Trx-Px1 as a H2O2-sensitive peroxiredoxin; Py Trx-Px1 as forming an octamer (instead of the typical decamer and dodecamer arrangements); and Py Prx6 as a product bound complex revealing some interesting features of these enzymes.
Expression and initial characterization of Trx-Px1 from P. falciparum, P. vivax, P. yoelii, and P. knowlesi and Prx6 from P. yoelii
Mass spectroscopy of reduced and oxidized Plasmodium Trx-Px-1 orthologues
Expected MW of
Expected MW of
Purifed Enzyme +
20 mM DTT (Da)
23729.32 (trace) a
By analytical gel filtration, all of the purified Trx-Px1 constructs (oxidized form and at high μM concentrations) eluted primarily as the higher order oligomer (i.e. octamer or decamer or dodecamer) (data not shown). Oligomerization has been shown to be dependent on numerous factors including ionic strength, pH, concentration of divalent metals, and most importantly redox state . In our gel filtration, a small amount of presumably aggregated protein was followed by the oligomeric protein around (corresponding to a calculated mass of 272 or 314 kDa). In the case of Pf Trx-Px1, some presumably dimeric protein was also observed, which was not noticed in previous gel filtration analyses of Pf Trx-Px1 by Akerman and coworkers. . These authors only observed higher order oligomers corresponding to 400 and 250 kDa for Pf Trx-Px-1 and further detected the (α2)5 quaternary form by electron microscopy.
Py Prx6 was expressed in two ways: Py Prx6 expressed from our typical protocol was purified in the reduced form according to mass spectroscopy (27189.1 Da) without addition of exogenous reducing agents (with the expected molecular weight after cleavage of the N-terminal Met weight being 27188.2 Da), while Py Prx6 expressed from Studier auto-induction media was purified in the sulfinic acid form (see below). From a calibrated gel filtration column, the enzyme eluted at 220 mL (corresponding to a calculated gel filtration mass of 62 kDa) which is consistent with the expected behaviour of a dimer.
Crystal structures of Trx-Px1 from P. vivax and P. yoelii
The structures of each (Pv Trx-Px1_red, Pv Trx-Px1_ox, and Py Trx-Px1_ox) contain the typical thioredoxin-fold found in known peroxiredoxins. There is a central 7-stranded β-sheet comprised of β2-β1-β5-β4-β3-β6-β7 with β1 and β6 running anti-parallel relative to the other strands. This β-sheet is sandwiched by α1 and α4 on one side and α2, α3, and α5 on the other side. The root mean square deviation (rmsd) between Pv Trx-Px1_ox, and Py Trx-Px1_ox is 0.91 Å when superimposing over the monomer encompassing Cα's from residues 2 to 177. The remaining residues of the C-terminus are disordered (from 178 to 195) in the Pv Trx-Px1_ox structure.
Pv Trx-Px1 and Py Trx-Px1 are H2O2-sensitive peroxiredoxins
Disulfide bonds in the Pv Trx-Px1_ox and Py Trx-Px1_ox structures
Oligomeric organization of Pv Trx-Px1 and Py Trx-Px1
Crystal structure of Py Prx6 with product bound
The Py Prx6-SO2H crystal structure has been solved at 2.3 Å (PDB ID: 3TB2). It is 47% identical to its closest human orthologue and shares 76% sequence identity with its P. falciparum orthologue. The closest available structure by sequence (at 48% sequence identity) is Arenicola marina peroxiredoxin 6 which was further identified as a 2-Cys Prx , but it also shares 47% sequence identity with a solved structure for a human 1-Cys Prx . Overall, the human (PDB ID: 1PRX) and P. yoelii structures are very similar with a core thioredoxin-fold and a C-terminal domain connected by both an extended helix α5 and a loop. The core rmsd is 1.38A for 401 aligned residues in both structures. The C-terminal domain of Py Prx6 that comprised of 3 β-strands and a α-helix is larger than the C-terminal domain from the Prx1 subfamily (Figure 1D). This domain from each monomer extends over the other forming a domain swapped dimer.
In order to understand the reaction mechanism, our focus is on the comparison of structures with substrate (H2O2) or glycerol bound. The binding of H2O2 to Aeropyrum pernix Tpx (thiol peroxidase) has been structural characterized (PDB: 3A2W and 3A2V) . Further work on these structures and comparisons to other ligand bound peroxiredoxin structures previously showed that oxygen atoms of the ligands overlap with the proximal (relative to CP) oxygen atom (OA) and/or the distal oxygen atom (OB) of bound H2O2. Interestingly, the glycerol molecule found in these structures can adopt all three possibilities: (1) in one monomer of Ap Trx (PDB: 3A2W) it is found with a single oxygen atom overlapping OA (Figure 7C, pink); (2) in another monomer of Ap Trx (PDB: 3A2W), it is found to overlap with both OA and OB (Figure 7C, pink); and (3) reported for the first time, in our structure of Py Prx6, the glycerol is observed to overlay with only OB (Figure 7C, purple). Previously, only 2 anionic ligands (sulfate and citrate) were observed to occupy OB alone (see PDB: 1TP9 and 3DRN) . Despite variations in the backbone orientation of the glycerol in our structure (which is also seen in the Ap Trx glycerol bound chains and presumably due to its conformational flexibility), the binding of all 4 glycerol molecules shows that each binds with the terminal hydroxyl in a similar position overlapping with OB site (Figure 7B). Oxygen atoms at position OA are postulated to be a mimetic for the substrate bound in a Michaelis complex ready for attack by the nucleophilic CP, while oxygen atoms at position OB are indicative of the leaving group (H2O or alcohol) . As such, it can be suggested that the glycerol positioned with its terminal hydroxyl at OB is in a product bound configuration. Although there is variability in the binding of the remainder of the glycerol molecule, the alkyl group is always directed away from the active site pocket and the oxygen of the leaving group is in close proximity to a conserved threonine (Thr44). This arrangement suggests that it may be the proton donor, although others have suggested that this threonine functions as a hydrogen bond acceptor as it deprotonates the incoming substrate for attack by the CP thiolate and that bulk solvent is responsible for the protonation of the leaving group . Therefore, the active site pocket is adapted to accommodate different substrates (and thus products), which is exemplified through the structural flexibility exhibited in the product bound glycerol shown herein. As well, the OB position appears to be designated for the oxygen of the leaving group and is well positioned for protonation by a conserved threonine.
Plasmodium lacks the two major antioxidant enzymes of eukaryotic cells, namely glutathione peroxidase and catalase . As such, the parasite is likely to rely on the peroxiredoxin family to control peroxide production (as well as other reactive oxygen and nitrogen species) during critical stages of its lifecycle, for example during erythrocyte invasion when heme metabolism and immune response pathways ensue. During the trophozoite stage (feeding period), Prx enzymes accounts for 0.5% of the total expressed protein . One recent study suggests that Pf nPrx, the P. falciparium nuclear peroxiredoxin might be essential in the erthyrocyte stage, as neither P. falciparum or P. berghei knock-out lines could be generated despite several attempts and success with generating tagged nPrx-GFP fusion cell lines . Analysis of the growth of a P. berghei Trx-Px1 knockout also suggests that Trx-Px1 is not essential for growth, but P. falciparum and P. bergei show differences in their lifecycles . There is a possibility that Trx-Px1 is essential during the asexual growth of P. falciparum. Expression of Pf 1-Cys Prx is elevated during the trophozoite and early schizont stages (when the parasites are maturing during the liver phase) suggesting that this subfamily detoxifies ROS, like those released during heme metabolism . Despite the important roles of peroxiredoxins, whether inhibitors targeting Plasmodium peroxiredoxins will lead to parasite death remains to be determined.
Structural characterization of the 2-Cys Prx enzymes has shown that the C-terminal tail (referred to as the CR) is essential for stabilizing the octameric/decameric arrangement of peroxiredoxins. When Trx-Px1 (or another 2-Cys Prx) is oxidized to the disulfide form, the CR loop is unfolded; and structural support of the octamer/decamer/dodecamer interfaces are weakened giving rise to dimer formation (as seen in part when our oxidized Pf Trx-Px1 is run on a gel filtration column). When the CR loop is folded as in the reduced form, the higher order oligomer is favoured because of increased stabilization for the B-type interface which supports oligomerization. The dramatic rearrangement of the C-terminal tail and ensuing changes in stability are clearly demonstrated in our structures from Py Trx-Px1 and Pv Trx-Px1 (both oxidized and reduced forms). However, the high concentrations of protein used in crystallizing the enzyme (and also apparently during most of our gel filtration experiments) may account for the trapping of the disulfide forms of these peroxiredoxins in their predicted unfavoured octameric/decameric/dodecameric forms. Factors associated with the oligomeric forms primarily include reduction of the active site disulfide, but also, high or low ionic strength, low pH, high magnesium or calcium concentrations, and overoxidation of the peroxidatic cysteine (Cys-SO2H) . At physiologically relevant concentrations, peroxiredoxins can be expected to exist as dimers awaiting reduction; and upon reduction, the catalytic cycle is complete and the reduced peroxiredoxin oligomerizes . With data from the novel octameric configuration of Py Trx-Prx1 studied herein, other specific structural features affecting oligomerization are considered. The molecular basis for octamer formation relies on the hydrogen bond between the dimers which is facilitated by the positioning of the C-terminal tail which in turn rests on interplay between the surface/buried arginine of the NNLA(I/L)GRS-loop and possibly the N-terminal tail. In vivo work directed at the further characterization of the different sizes and configurations of the oligomers will be necessary to fully understand the biological implications.
Aside from being antioxidant proteins, 2-Cys Prx (Prx1) has also been implicated in H2O2-mediated signal transduction. Eukaryotic 2-Cys Prx enzymes are sensitive to oxidative inactivation, while their bacterial orthologues are robust with respect to overoxidation . The Plasmodium 2-Cys Prx enzymes accordingly have the 3 sequence motifs indicative of the H2O2-sensitive peroxiredoxins, and as shown herein are structurally identical with respect to sensitivity to H2O2 to known H2O2-sensitive 2-Cys Prx enzymes, thus allowing low resting levels of H2O2, while permitting higher levels during signal transduction.
The Py Prx6 structure presented herein has greatly enhanced our understanding of the chemistry of the peroxiredoxins. With a product bound configuration, the residues supporting the leaving group are further understood. There is flexibility for the alkyl chain, but the OB position is indeed designated for the oxygen of the leaving group. As well, the retention of hydrogen bonds about the active site thiol (even in an oxidized state) indicates that it is poised for further reaction, albeit at a reduced efficiency owing to the reduced activity of an oxidized thiol relative to a thiolate.
Our structural data and mass spectroscopy confirms that Pv Trx-Px1 is H2O2-sensitive peroxiredoxin. The characterization of the oligomerization of Py Trx-Px1 has identified structural features supporting its novel octameric oligomerization. Previously unreported abnormalities of the disulfide bond measurements in some of the Prx crystal structures are brought to the forefront. Finally, a crystal structure with an alcohol bound and the CP oxidized gives a view to the product bound complex providing insight into leaving group and the susceptibility of some peroxiredoxins to overoxidation. These results enhance our understanding of the structural variations of the peroxiredoxin oligomers and the nature of the catalysis by these remarkable enzymes. Further work will lend insight into the biological implications of the oligomerization and how to exploit the active site features in drug discovery programs.
Cloning, expression, and purification
Full-length P. falciparum Trx-Px1 encoded by PlasmoDB ID: PF14_0368 http://plasmodb.org/plasmo/ was cloned from P. falciparum 3D7 genomic DNA with a His6-tag with an integrated thrombin cleavage site (MGSSHHHHHHSSGLVPR*GS). Full-length P. knowlesi Trx-Px1 encoded by PlasmoDB ID: PKH_126740 was cloned from P. knowlesi H genomic DNA with a His6-tag with an integrated TEV cleavage site (MGSSHHHHHHSSGRENLYFQ*G). Full-length P. vivax protein encoded by PlasmoDB ID:PVX_118545 with an N-terminal His6-tag and TEV cleavage site (as above) was cloned from a P. vivax Salvador I cDNA library (generously provided by Prof. Liwang Cui of Penn State University). Full-length P. yoelii protein encoded by PlasmoDB ID: PY00414 (Trx-Px1) was cloned from P. yoelii 17XNL genomic DNA with an N-terminal His6-tag and integrated TEV protease site (as above). Full-length P. yoelii protein encoded by PlasmoDB ID: PY04285 (Prx6) was cloned from P. yoelii 17XNL genomic DNA with an N-terminal His6tag with different integrated TEV protease site (MGSSHHHHHHSSGRENLYFQ*GHM) and C-terminal addition (GS). All enzymes were expressed and purified according to methods described previously  except for Py Prx6 which was expressed from Studier auto-induction media .
All mass spectra were completed on an Agilent LC-MS-TOF (Model #G1969A) running in positive ion mode and integrated with an Agilent 1100 series HPLC using an Agilent Poroshell 300-SB-C3 column for fast binding/elution desalting. All gel filtration experiments were complete on a AKTA purifier chromatography system (GE Healthcare Life Sciences) equipped with a Superdex S200 gel filtration column that was calibrated with 4 samples (bovine thyroglobulin (670 kDa), bovine γ-globulin (158 kDa), chicken ovalbumin (44 kDa), and horse myoglobin (17 kDa) all from Bio-Rad) in 10 mM HEPES, pH 7.4 and 500 mM NaCl.
Crystallization and structure determination
Pv Trx-Px1_ox with the His6-tag intact was crystallized by mixing 1.5 μL of protein (at a concentration of 8 mg/mL in a buffer of 10 mM HEPES, pH 7.5, 500 mM NaCl) with 1.5 μL of reservoir solution containing 5% Peg 4 K, 50 mM NaAc, 100 mM NaAc, pH 4.6 in a hanging drop vapour diffusion setup with over 350 μL of reservoir solution at 18°C in VDXm plates (Hampton Research). Crystals appeared overnight and were flashed-cooled in liquid nitrogen (N2(l)) for data collection. Single wavelength data was collected at a synchrotron source (APS Beamline 17-ID) with a CCD detector (ADSC quantum 210). Pv Trx-Px1_red with the His6-tag intact was crystallized using the hanging drop vapour diffusion method in a VDXm plate with 350 μL of mother liquor at 18°C. 1.5 μL of the protein solution treated with 5 mM TCEP was mixed with 1.5 μL of the reservoir solution containing 19% PEG 3350, 150 mM lithium citrate. Crystals appeared overnight. Data for crystals flash frozen in N2(l) was collected at the synchrotron (APS Beamline 17-BM) with a CCD detector (MAR CCD 165 mm). Py Trx-Px1 with the His6-tag intact was crystallized at 4.3 mg/mL using the sitting drop vapour diffusion method in a Linbro plate with 300 μL of mother liquor at 18°C. 1.5 μL of the protein solution was mixed with 1.5 μL of the reservoir solution containing 1.6 M ammonium sulfate, 100 mM HEPES, pH 6.8, 200 mM NaAc, 20 mM NaBr, 5% ethylene glycol. Crystals appeared in 3-5 days and were flash frozen in N2(l) with data collected on a Rigaku FRE Superbright rotating anode with an RAXIS IV plate reader. Py Prx6 with the His6-tag intact at 15 mg/mL was crystallized by means of by hanging drop vapour diffusion in a VDXm plate. The plate was set with 1.5 μL protein plus1.5 μL buffer in each drop and 350 μL reservoir volume per well. Crystals emerged in 23% Peg 3350, 0.1 M Bis-Tris pH 5.5, 200 mM (NH4)2SO4 and 5% ethylene glycol at 20°C. MAD data from a crystal flash frozen in N2(l) was collected at the synchrotron (APS Beamline 17-ID) with a CCD detector (ADSC Quantum 4).
Data collection, phasing, and refinement statistics for the 2H66, 2I81, 2H01, and 3TB2
Number of Reflections
Test Set Reflection numbers
Number of Atoms (protein/ligand/water)
Ramachandran Favored (%)
Ramachandran Disallowed (%)
Bond length (Å)
Bond angle (°)
The authors would like to thank Jocelyne Lew for cloning of Trx-Px-1 from P. falciparum, P. vivax, P. yoelii, and P. knowseii and Prx6 from P. yoelii and Helen Ren, Michelle Melone, Zahoor Alam, Simon Houston, Mehrnaz Amani, and Greg Wasney for the large scale expression of these enzymes. The BL21(DE3)R3 strain of E. coli (which we subsequently modified adding pRARE2) used in expressing the proteins came from Opher Gileadi of the Structural Genomics Consortium (SGC) at the University of Oxford. The Structural Genomics Consortium is a registered charity (number 1097737) that receives funds from the Canadian Institutes for Health Research, the Canadian Foundation for Innovation, Genome Canada through the Ontario Genomics Institute, GlaxoSmithKline, the Knut and Alice Wallenberg Foundation, the Ontario Innovation Trust, the Ontario Ministry for Research and Innovation, Merck & Co., Inc., the Novartis Research Foundation, the Petrus and Augusta Hedlund's Foundation, the Swedish Agency for Innovation Systems, the Swedish Foundation for Strategic Research and the Wellcome Trust.
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