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Rubisco*, an Old Challenge with New Perspectives Günter F Invited Trends Article: Rubisco*, an Old Challenge with New Perspectives Günter F. Wildner3, Jürgen Schlitterh and Matthias Müllerb a Ruhr-Universität Bochum, Lehrstuhl für Biochemie der Pflanzen b Ruhr-Universität Bochum, Lehrstuhl für Biophysik Universitätsstraße 150, D-44780 Bochum Z. Naturforsch. 51c, 263-276 (1996) received March 18, 1995 Rubisco, Photoassimilation, Specificity, MD Simulation, Protein Engineering I. Introduction of site-specific mutagenesis, structural analysis and The importance of Rubisco derives from its spe­ chemical analysis of side and abortive reaction cial role as the main catalyst for the flow of carbon products. Recent advances in comprehending the dioxide from the inorganic sphere to the plant mechanisms of catalysis of both reactions make it kingdom. Since its discovery as fraction I protein feasible to develop strategies for „improvement“ fifty years ago (Wildman and Bonner, 1947) and of the enzyme with respect to its relative specific­ its role as the key enzyme in the Calvin cycle forty ity for C 0 2 as opposed to O?, and its catalytic years ago (Quaile et al ., 1954; Weissbach et al., turnover rates in organisms with low specificity or 1954) it attracted attention for a series of specific low turnover rates. Genetic engineering can be reasons concerning its enzyme mechanism, its reg­ used to manipulate partitioning of carbon flow be­ ulation and its structural features. Twentyfive tween photosynthesis and photorespiration in years ago the bifunctionality of this enzyme was those organisms. discovered by the fact that it catalyses not only The key to these challenges is the evolutionary C 0 2 fixation but also the RuBP oxygenase reac­ variety of Rubiscos with different properties. The tion, and therefore, Rubisco is also the key en­ enzyme from the nonsulfur purple bacteria Rho- zyme for the photorespiration (Bowes et al., 1971). dospirillum rubrum consists of only two large su­ Since photorespiration is generally considered a bunits (type II Rubisco) whereas the enzyme of wasteful process due to the loss of fixed carbon cyanobacteria, green algae and higher plants are and the additional consumption of energy, parti­ assembled of eight large subunits and eight small tioning of carbon between Calvin cycle and the subunits (type I Rubisco). The bifunctional en­ photorespiratory pathways plays a crucial role in zyme changed its specificity toward a better car­ the efficiency of photosynthesis (Zelitch, 1973). boxylase during the evolution of photosynthetic The predominant role of this enzyme as an im­ organisms. The lowest values for the ratio of portant research area in plant biochemistry can be VC.KQ / V0.KC (specificity factor, abbreviated: SF; illustrated by the vast and still growing number of see Scheme 1) is found with the enzyme isolated communications of sequence data (above 1500) from R. rubrum (SF values of 10 to 15), whereas and of twelve reports of X-ray structures (enzymes high values (SF of about 80) were obtained with from photosynthetic bacteria, cyanobacteria and enzymes isolated from higher plants (Jordan and higher plants). The recent renaissance of Rubisco Ogren, 1981). The price for the better carboxyl­ research should lead to a better understanding of ase / oxygenase ratio of enzyme activities is paid its mechanisms of function by a combined effort for by a parallel drop in the kcat of the carboxylase reaction (Bainbridge et al., 1995). Negative corre­ lation between specificity and turnover rates must be seen, it seems, in conjunction with both en­ Reprint requests to Prof. Wildner. zyme mechanisms. Fax: 0234/7094322. The question why the enzyme of unicellular or­ * Rubisco: ribulose 1,5-bisphosphate carboxylase/oxy­ ganisms has a lower specificity factor compared to genase; E.C. 4.1.1.39. multicellular organisms, still needs to be answered. 0939-5075/96/0500-0263 $ 06.00 © 1996 Verlag der Zeitschrift für Naturforschung. All rights reserved. D 264 Trends Article • G. F. Wildner et al. ■ Rubisco, an Old Challenge with New Perspectives RuBP Intermediate PGA + CABP PGA o- i o = p -o - I 0 1 H C;H O- i1 / HO-C,----- -C.B H C r O H O C r O H 13 Ii H C r O H H-C.-O H 14 XuBP I 4 Intermediate HC;H HC;H 15 o- 15 o- 0 I 0 i 1 o = p - o - 1 o = p - o - o = p -o - I I I 0 o = pI -o - 0 o- 1 O- 1 H C;H H C;H PGlyc I 1 HX> 11 c,=o H O - C r O -O - + 12 12 H 0 -C ;H C =0 PGA 13 13 H-C.-O H H C r O H I 4 14 HC;H HC;H 15 15 0 1 0I o = pI -o - 0 = pI —O- o- o- Scheme 1. In order to elucidate the crucial differences be­ a Rubisco with high specificity and an enzyme tween Rubisco enzymes of these two groups we molecule with low specificity. have compared the structure of enzymes with dif­ ferent specificity factor. Our analysis includes the II. How to Change Enzyme Specificity amino acid residues of the active center and the Any explanation for the Rubisco specificity has positions of the atoms of the transition state ana­ to take into account that the specificity factor of a log, CABP (2-carboxy-D-arabinitol 1,5-bisphos- pertinent enzyme is not an invariant property of phate), in relation to the active center. The active the molecule but can be altered. For example, it center is located in the C-terminal a/ß barrel do­ can be altered by replacement of the active-site main of the large subunit and residues from the metal ion, Mn2+, instead of Mg2+ (Wildner and N-terminal domain of the other large subunit of Henkel, 1978; Jordan and Ogren, 1983) or by sub­ the functional dimer are also part of the active stitution of amino acid residues (see for a review center (Schneider et al ., 1986; Chapman et al., Spreitzer, 1993), or simply by changing the reac­ 1988; Andersson et al ., 1989). The comparison of tion temperature (Jordan and Ogren, 1984). the primary sequences of Rubiscos from different organisms is not sufficient and has to be supple­ mented by structural comparison as achieved by II. I Rubisco-metal ion complex and specificity superimposition of the x-ray structure data sets Rubisco is activated by pretreatment with bicar­ (presented in Section IV). This analysis will lead bonate and Mg2+ ions forming an enzyme-carba- to stereotypic characterization of the interaction myl Mg2+ complex. The carbamvlation of the e - network between CABP and the protein shell for amino group of K 201 residue (respectively K 191 Trends Article • G. F. Wildner et al. ■ Rubisco, an Old Challenge with New Perspectives 265 in R.rubrum) is stabilized by the binding of Mg2+ of C-4 as observed with spinach Rubisco (Fig. lb). (Lorimer et al., 1976). The environment of the It seems that the Mg2+ ion has at least a double Me2+ in the ternary complex of spinach Rubisco role: it participates in both the binding and the (Knight et al ., 1990) is determined by a coordi­ conversion of substrate. Mg2+ directs the substrate nated octahedral complex with the following li­ into the correct binding position, because non-ac- gand residues (Fig. la): the hydroxyl groups of C- tivated enzyme molecules bind the substrate ana­ 2 and C-4 of the transition state analogue CABP, log (CABP) in an inverted fashion (Lundqvist and the carbamate of K 201, the residues D 203 and E Schneider, 1989). Beside the positioning effect, 204 and an additional ligand position for the reac­ Mg2+ serves also in the polarization of the car­ tion intermediate (-COO or -O-O ). The ligand bonyl group at C-2 to facilitate the enolization, field is similar for the Synechococcus enzyme and furthermore, stabilizes the reaction intermedi­ (Newman and Gutteridge, 1993), except for the ate by complexing either the carboxyl group or participation of the hydroxyl group of C-3 instead the hydroperoxide. The metal ion can be replaced by other divalent cations. The enzyme can accomodate in addition to a Mg2+ also Ca2+, Ni2+, Co2+, Cr2+, Fe2+, Cu2+, and Mn2+ (Andrews and Lorimer, 1987). The question whether the replacement of Mg2+ by redox-active metal ions such as Mn2+ or Co2+ could change the specificity of the Rubisco has been addressed. The E -C 0 2-Mn2+ complex of higher plants has a speci­ ficity factor value which is twenty times lower as the one for the appropriate E-C0 2-Mg2+ complex from the same Rubisco (Jordan and Ogren, 1983). The E -C 0 2-Co2+ complex in R.rubrum func­ tions only as an oxygenase without detectable car­ boxylase activity (Christeller, 1981). The interpre­ tation of the EPR spectra of the E-C0 2-Me2+- CABP complexes with Mn2+, Co2+, and Cu2+ fo­ b cussed on the highly distorted coordination system of the metal ion (Styring and Bränden, 1985). This structural distortion would be evident in X-ray studies of the activated enzymes, complexed with the substrate analog, CABP. Such investigations have not been carried out so far. Another explanation was offered (Chen and Spreitzer, 1992) for the Mn2+ effect on the specific­ ity, proposing the involvement of Mg2+ preferably in the carboxylation reaction (higher effective cat­ ionic charge) while the involvement of Mn2+ was preferred in the oxygenase reaction (facilitation of the activation of triplet 0 2 into singlet 0 2). A switch from a free-radical mechanism in presence of Mg2+ to a more favorable ionic mechanism in Fig. 1. Octahedral coordination complex of the active presence of Mn2+ was assumed. site Mg2+ with CABP and amino acid residues of spinach (Fig.
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