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Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate

Abstract

Sugar binding proteins and binders of intermediate sugar metabolites derived from microbes are increasingly being used as reagents in new and expanding areas of biotechnology. The fixation of carbon dioxide at emission source has recently emerged as a technology with potentially significant implications for environmental biotechnology. Carbon dioxide is fixed onto a five carbon sugar D-ribulose-1,5-bisphosphate. We present a review of enzymatic and non-enzymatic binding proteins, for 3-phosphoglycerate (3PGA), 3-phosphoglyceraldehyde (3PGAL), dihydroxyacetone phosphate (DHAP), xylulose-5-phosphate (X5P) and ribulose-1,5-bisphosphate (RuBP) which could be potentially used in reactors regenerating RuBP from 3PGA. A series of reactors combined in a linear fashion has been previously shown to convert 3-PGA, (the product of fixed CO2 on RuBP as starting material) into RuBP (Bhattacharya et al., 2004; Bhattacharya, 2001). This was the basis for designing reactors harboring enzyme complexes/mixtures instead of linear combination of single-enzyme reactors for conversion of 3PGA into RuBP. Specific sugars in such enzyme-complex harboring reactors requires removal at key steps and fed to different reactors necessitating reversible sugar binders. In this review we present an account of existing microbial sugar binding proteins and their potential utility in these operations.

Review

Rapid industrialization has led to a dramatically accelerated consumption of fossil fuels with a consequent increase in atmospheric levels of the greenhouse gas carbon dioxide (CO2). This sustained increase of atmospheric CO2 has already initiated a chain of events with negative ecological consequences [13]. Failure to reduce these greenhouse gas emissions will have a catastrophic impact upon both the environment and the economy on a global scale [4, 5]. The reduction has to be brought about by global concerted effort by all countries in order to be effective and meaningful.

At one end of the spectrum – that of generation and utilization of energy resulting in generation of carbon dioxide – hydrocarbons serve as intermediaries for energy storage. Hydrocarbons are not energy by themselves but store energy in their bonds, which is released during combustion. They are thus intermediates for obtaining stored bond energy within them and carbon dioxide is emitted as a consequence of combustion to extract this stored energy. In recent times hydrogen has received renewed attention as the potential replacement for hydrocarbons [610]. However, hydrogen too is an intermediary for obtaining stored bond energy. Recent reports suggest that hydrogen as intermediary may not be entirely free from problems. Also, the problems from use of hydrogen as fuel are yet to be fully realized or foreseen [11, 12]. In all these endeavors a key question, that whether the hydrocarbons will be still retained as intermediaries in energy utilization and the problem of air pollution caused as a result of their combustion can be technologically ameliorated, has not been looked in as much detail as perhaps it should have been. This can possibly be achieved by contained handling of carbon dioxide. The contained handling and fixation of CO2 can be achieved biotechnologically, chemically or by a combination of both.

Sugar binding proteins derived from microbial and other sources have been used for various applications such as diagnostics and affinity purification [13, 14], however they have not been used in environmental biotechnological applications. The possibility of their potential application in environmental biotechnology and review of a few potential candidates is presented here.

The methods in environmental biotechnology that enables efficient capture [15] and fixation of CO2 at emission source/site into concatenated carbon compounds has been pioneered by our group [1619]. The first part in the biocatalytic carbon dioxide fixation is the capture of gaseous CO2. We have pioneered novel reactors employing immobilized carbonic anhydrase for this purpose [15]. Subsequent to capture the carbon dioxide becomes solublized (as carbonic acid or bicarbonate). After adjustment of pH using controllers and pH-stat the solution is fed to immobilized Rubisco reactors [18] where acceptor D-Ribulose-1,5-bisphosphate (RuBP) after CO2 fixation is converted into 3-phosphoglycerate [16, 17]. However, inasmuch as the recycling of acceptor RuBP is central to continuous CO2 fixation, we have invented a novel scheme (Figure 1), which proceeds with no loss of CO2 (unlike cellular biochemical systems) in 11 steps in a series of bioreactors [20]. This scheme is very different from generation of RuBP from D-glucose for start-up process [21] and employing 11 steps in different reactors requiring large volume and weight. The linear combination of reactors with large volume and weight are unsuitable for use with mobile CO2 emitters leaving only the stationary source of emission to be controlled using this technology [17]. To circumvent these problems we have devised a new scheme presented in Figure 2[22]. Based on this scheme, we have designed enzymes as functionally interacting complexes/interactomes or successive conversion in radial flow with layers of uniformly oriented enzymes in concentric circle with axial collection flow system for three enzymes in first reactor for the scheme presented in Figure 2. The four reactors harboring enzymatic complexes/mixtures replace the current 11 reactors. This leads to a faster conversion rate and requires less volume and material weight. However, 4 sugar moieties [3-phosphoglyceraldehyde (3PGAL), Dihydroxyacetone phosphate (DHAP), Xylulose-5-phosphate (X5P) and Ribulose-1, 5-bisphosphate (RuBP)] must be separated at four key steps, as illustrated in Figure 2. In figure 2, using four symbols with solid for bound state and empty for released state, for potential binders: plus for 3PGA, circle for DHAP, cylinder for X5P and box for RuBP, the possible place for utility of these binders have been depicted. In the course of this review, we will consider the availability of enzymatic proteins and non-enzymatic proteins that would be potentially useful as specific binders for these sugar molecules. With a recombinant mutant enzyme we illustrate that such an approach has potential to be used as an in-situ reversible binding matrix for sugar binding and release.

Figure 1
figure1

Scheme for generation of D-ribulose-1,5-bisphosphate (RuBP) from 3-phosphoglycerate (3PGA) obtained from fixation of CO2 on RuBP. The continuous regeneration of RuBP in this scheme enables continuous fixation of CO2 at stationary emission sites.

Figure 2
figure2

An alternate arrangement of enzymes in the scheme outlined in Fig. 1. This schemes harbors four reactors with indicated enzyme complexes enabling internal channeling, greatly reduces volume and weight for regenerating reactors with faster overall conversion rate to RuBP starting with 3PGA making the system compatible for application in mobile devices in addition to stationary emitters. The reactors may use the sugar binding entities at indicated positions, the hollow and solid symbols represent binding and release phase of the binding-molecules, the plus, circle, cylinder and box are symbols for 3PGA, DHAP, X5P and RuBP binders respectively.

Potential utilizable sugar binding proteins in RuBP regeneration

Three categories of binding proteins can be potentially employed for differential absorption of sugars and for subsequent elution and feeding the reactors downstream in conversion cascade. These are: mutant enzymatic proteins that retain the ability of binding but completely lack any catalytic activity, lectins or proteins of non-immunogenic origin [23] having more than one binding site for the sugar (in nature they cause agglutination of due to sugar binding at multiple sites) and mutant or wild type receptors that binds sugars but are incapable of eliciting further biological activities. The desirable proteins in all these categories are those for which binding affinity is high in a condition close to pH of the emanating solution from the reactor and other conditions for reactor effluent, ability to bind reversibly with respect to some simple but easily manipulable physicochemical parameter (such as temperature, pH, salt concentration), and the ability to be easily attached to a matrix using simple chemistry without loss of binding ability and a long shelf life.

We undertook this review because, although the comprehensive information on a large number of enzymes have been accumulated in BRENDA database [24, 25], but the systematic information on their mutants is lacking and non-enzymatic binders of sugar ligands are not identified / listed in the database.

Proteins that bind 3-phosphoglycerate/3-phosphoglyceraldehye

Both enzymatic and non-enzymatic proteins bind these sugar entities. A number of mutants of many enzymes that bind to either 3-phosphoglycerate or 3-phosphoglyceraldehyde are also known, for example, Phosphoglyceromutase (EC 5.4.2.1), Enolase (EC 4.2.1.11), Mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70), Mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217), Phosphoglycerate kinase, (EC 2.7.2.3), Bisphosphoglycerate mutase (EC 5.4.2.4), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.1), D-3-phosphoglycerate dehydrogenase 2 (EC 1.1.1.95), Cyclic 2,3-diphosphoglycerate-synthetase, Phosphoglycerate dehydrogenase, Transketolase, and Triosephosphate isomerase, BRENDA database shows only three enzymes: Phosphoglycerate dehydrogenase, Mannosyl-3-phosphoglycerate synthase and Phosphoglycerate kinase. A number of mutants of enzymes that binds 3-phosphoglycerate and shows some change in enzymatic activity or kinetic parameters are listed in Table 1. Many of these proteins are reported to retain ligand binding ability with varying degree of loss in catalytic ability (inactive mutants are in bold face), the non-enzymatic protein that also has been reported in literature has been placed towards the bottom part of Table 1. The proteins which retain binding ability but with complete loss in catalytic activity are the ones which warrant further investigation in batch and continuous processes for exploring their suitability as binding proteins in continuous RuBP regenerating reactors (Figure 2). A number of non-enzymatic protein summarized in Table 1 also warrant further exploration. The only binding entity of significance for 3-phosphoglyceraldehyde is 3-phosphoglyceraldehyde dehydrogenase (EC 1.2.1.12) and has not been reviewed.

Table 1 Proteins that bind 3-phosphoglycerate

Proteins that bind dihydroxyacetone phosphate

Several enzymes: dihydroxyacetone phosphate acyltransferase, Glycerol-3-phosphate dehydrogenase, Aldolase A, fructose-bisphosphatase, Aldolase B, fructose-bisphosphatase, L-aspartate oxidase, Quinolinate synthetase A, Dihydroxyacetone kinase 1 (Glycerone kinase 1), Glycerol-3-phosphate acyltransferase, NAD(P)H-dependent dihydroxyacetone-phosphate reductase, Dihydroxyacetone phosphate acyltransferase, Alkyl-dihydroxyacetonephosphate synthase, Dihydroxyacetone kinase isoenzyme I, Alpha-glycerophosphate oxidase and Triose phosphate isomerase binds DHAP (Table 2), however, BRENDA shows only four of these proteins, glycerol-3-phosphate dehydrogenase (EC 1.1.1.8), acylglycerone-phosphate reductase (EC 1.1.1.101), glycerone-phosphate O-acyltransferase (EC 2.3.1.42) and alkylglycerone-phosphate synthase (2.5.1.26). The mutants of enzymes with no chemical conversion ability but with high affinity for binding dihydroxyacetone phosphate but very low affinity for other proteins and reversible binding with respect to temperature, salt or pH are desirable properties for the binders.

Table 2 Proteins that bind Dihydroxyacetone phosphate

Proteins binding xylulose-5-phosphate

As shown in Table 3 several enzymatic proteins binds to xylulose-5-phosphate. Xylulose-5-phosphate phosphoketolase, Dihydroxyacetone synthase, xylulose kinase, Protein phosphatase 2A B alpha isoform, Xylulose 5-phosphate-activated protein phosphatase, 1-deoxy-D-xylulose 5-phosphate reductoisomerase, 1-deoxy-D-xylulose 5-phosphate synthase 1 and 2 are examples of such enzymes. The non-enzymatic xylulose-5-phosphate binders are shown in the bottom part of Table 3. BRENDA database shows following five proteins, 1-deoxy-D-xylulose-5-phosphate reductoisomerase (EC 1.1.1.267), formaldehyde transketolase (EC 2.2.1.3), 1-deoxy-D-xylulose 5-phosphate synthase (EC 2.2.1.7), Phosphoketolase (EC 4.1.2.9), Ribulose-phosphate 3-epimerase (EC 5.1.3.1).

Table 3 Proteins that bind Xylulose-5-phosphate

Proteins binding D-Ribulose-1,5-bisphosphate

A number of Ribulose-1,5-bisphosphate and metabolizing enzymes such as Ribulose phosphate kinase and their mutants binds D-ribulose-1,5-bisphosphate. The RuBP binding entities devoid of any enzymatic activities are very valuable in reactors necessitating extraction and separation of RuBP from other sugar compounds (Table 4). Very few non-enzymatic proteins bind RuBP and none of them are microbial sources, and hence have not been incorporated in this review, Rubisco associated protein from soybean is one of them, that show significant RuBP binding [137].

Table 4 Enzymes that bind D-Ribulose-1,5-bisphosphate

Illustrating example

In order to illustrate the utility of non-catalytic enzymatic mutants as specific sugar binders for in-situ separation in reactors, recombinant Saccharomyces cerevisiae 3-phosphoglycerate kinase mutant R38Q [41] was prepared. Mutagenesis was carried out using wild type protein construct in plasmid pET19b as a template. The R38Q mutant was constructed with the Quickchange/Chameleon site-directed mutagenesis kit from stategene using primers as described elsewhere [41]. DNA sequencing of the plasmid identified the mutant. Recombinant wild-type and mutant (R38Q) 3-phosphoglycerate kinase (PGK) were purified to apparent homogeneity as described previously [20] have been shown in Figure 3A. The wild-type and mutant protein was incubated with 10 mM 3-phosphoglycerate barium salt (3PGA) in 50 mM Tris-Cl buffer, pH 7.5 containing 50 mM NaCl for overnight at room temperature. No modification of 3PGA was observed after incubation with R38Q mutant protein (data not shown). The R38Q was coupled with Protein A sepharose beads using dimethylpimelimidate. The recombinant R38Q mutant protein beads (R38Q-PGK) was incubated overnight at room temperature with a mixture of sugars, 3-phosphoglycerate, barium salt (3PGA), ribulose-5-phosphate (R5P), Glucose-6-phosphate (G6P) and Fructose-6-posphate (F1,6-bP) each at a concentration of 10 mM in a volume of 200 μl. After incubation they were washed with 1.5 ml of 180 mM NaCl in 50 mM Tris-Cl buffer, pH 7.5. They were subjected to elution with 1 M NaCl. Lane 1, mixture of sugar prior to incubation with R38Q-PGK and Lane-2 after elution with 1 M NaCl.

Figure 3
figure3

The recombinant his-tagged wild-type and R38Q mutant 3-phosphoglycerate kinase was subjected to affinity purification on Ni-NTA column as described previously [20]. A. SDS-PAGE of recombinant wild-type and R38Q mutant S. cerevisiae 3-phosphoglycerate kinase. The proteins (1 and 1.8 μg respectively) was separated in 10% polyacrylamide gel and stained with Coommassie blue R250. B. TLC analysis of sugars prior to and after in-situ separation with R38Q. The recombinant R38Q mutant (R38Q-PGK) was coupled with Protein A sepharose beads and incubated overnight with a mixture of sugars, 3-phosphoglycerate (3PGA), ribulose-5-phosphate (R5P), Glucose-6-phosphate (G6P) and Fructose-6-posphate (F1,6-bP). After washing with 180 mM NaCl, the sugars were eluted with 1 M NaCl. Lane 1, mixture of sugar prior to incubation with R38Q-PGK and Lane-2 after elution with 1 M NaCl.

Conclusion

The enzyme-mutants lacking catalytic activity represent an important group of proteins that could be used for development of sugar-binding proteins reversible with respect to physicochemical parameters such as pH or salt concentration. Nevertheless, the non-enzymatic proteins also represent a suitable repertoire of such potential scaffolds, which could be used for development as sugar-binding proteins to be used in reactors for simultaneous separation of sugars that would be used in subsequent conversion steps. We have developed a RuBP production scheme from 3PGA [16, 17] and also a de novo RuBP production scheme from D-glucose [21] for continuous CO2 fixation and for start-up of the fixation respectively employing series of reactors. Both systems for production of RuBP will benefit from specific sugar binders but besides their use in environmental biotechnology, they will find application in diagnostics, separation technologies and also as research reagents.

References

  1. 1.

    Victor DG: Strategies for cutting Carbon. Nature. 1998, 395: 837-838. 10.1038/27532.

  2. 2.

    Joos F, Plattner G-K, Stocker TF, Marchal O, Schmittner A: Global warming and marine carbon cycle feedbacks on future atmospheric CO2. Science. 1999, 284: 464-467. 10.1126/science.284.5413.464.

  3. 3.

    Schnur R: The investment Forecast. Nature. 2002, 415: 483-484. 10.1038/415483a.

  4. 4.

    De Leo GA, Gatto M, Caizzi A, Cellina F: The ecological and economic consequences of global climate change. In Recent Research Developments in Biotechnol. Bioengg. Edited by: Bhattacharya SK, Chakrabarti S, Mal TK. 2002, 163-183. Research Signpost, Kerala

  5. 5.

    De Leo GA, Rizzi L, Caizzi A, Gatto M: Carbon emissions. The economic benefits of the Kyoto Protocol. Nature. 2001, 413: 478-479. 10.1038/35097156.

  6. 6.

    Cortright RD, Davda RR, Dumesic JA: Hydrogen from catalytic reforming of biomass-derived hydrocarbons in liquid water. Nature. 2002, 418: 964-967. 10.1038/nature01009.

  7. 7.

    Service RF: Fuel cells. Biofuel cells. Science. 2002, 296: 1223-10.1126/science.296.5571.1223.

  8. 8.

    Schultz MG, Diehl T, Brasseur GP, Zittel W: Air pollution and climate-forcing impacts of a global hydrogen economy. Science. 2003, 302: 624-627. 10.1126/science.1089527.

  9. 9.

    Prather MJ: Atmospheric science. An environmental experiment with H2?. Science. 2003, 302: 581-582. 10.1126/science.1091060.

  10. 10.

    Brumfiel G: Hydrogen cars fuel debate on basic research. Nature. 2003, 422: 104-10.1038/422108a.

  11. 11.

    Rahn T, Eiler JM, Boering KA, Wennberg PO, McCarthy MC, Tyler S, Schauffler S, Donnelly S, Atlas E: Extreme deuterium enrichment in stratospheric hydrogen and the global atmospheric budget of H2. Nature. 2003, 424: 918-921. 10.1038/nature01917.

  12. 12.

    Tromp TK, Shia RL, Allen M, Eiler JM, Yung YL: Potential environmental impact of a hydrogen economy on the stratosphere. Science. 2003, 300: 1740-1742. 10.1126/science.1085169.

  13. 13.

    Raphael SJ: The meanings of markers: ancillary techniques in diagnosis of thyroid neoplasia. Endocr Pathol. 2002, 13: 301-311. 10.1385/EP:13:4:301.

  14. 14.

    Jackson A, Kemp P, Giddings J, Sugar R: Development and validation of a lectin-based assay for the quantitation of rat respiratory mucin. Novartis Found Symp. 2002, 248: 94-105. 10.1002/0470860790.ch7.

  15. 15.

    Bhattacharya S, Nayak A, Schiavone M, Bhattacharya SK: Solubilization and Concentration of Carbon dioxide: Novel Spray reactors with immobilized Carbonic anhydrase. Biotechnol Bioeng. 2004, 86: 37-46. 10.1002/bit.20042.

  16. 16.

    Bhattacharya SK: Conversion of carbon dioxide from ICE exhausts by fixation. US patent number 6258335. 2001, 1-18.

  17. 17.

    Bhattacharya S, Chakrabarti S, Bhattacharya SK: Bioprocess for recyclable CO2 fixation: A general description. In Recent Research Developments in Biotechnol. Bioengg. Edited by: Bhattacharya SK, Chakrabarti S, Mal TK. 2002, 109-120. Research Signpost, Kerala,

  18. 18.

    Chakrabarti S, Bhattacharya S, Bhattacharya SK: Immobilization of D-ribulose-1, 5-bisphosphate carboxylase/oxygenase: A step toward carbon dioxide fixation bioprocess. Biotechnol Bioengg. 2003, 81: 705-711. 10.1002/bit.10515.

  19. 19.

    Chakrabarti S, Bhattacharya S, Bhattacharya SK: Biochemical engineering: cues from cells. Trends Biotechnol. 2003, 21: 204-209. 10.1016/S0167-7799(03)00077-5.

  20. 20.

    Bhattacharya S, Schiavone M, Gomes J, Bhattacharya SK: Cascade of bioreactors in series for conversion of 3-phospho-D-glycerate into D-ribulose-1, 5-bisphosphate: Kinetic parameters of enzymes and operation variables. J Biotechnol. 2004

  21. 21.

    Bhattacharya S, Nayak A, Gomes J, Bhattacharya SK: A continuous process for production of D-ribulose-1, 5-bisphosphate from D-glucose. Biochem Engg J. 2004, 19: 229-235.

  22. 22.

    Bhattacharya SK.: Use of enzyme mixtures for complex biosynthesis. Curr Opin Biotechnol. 2004

  23. 23.

    Hart DA: Lectins in biological systems: applications to microbiology. Am J Clin Nutr. 1980, 33: 2416-2425.

  24. 24.

    Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D: BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res. 2004, 32: D431-D433. 10.1093/nar/gkh081.

  25. 25.

    Pharkya P, Nikolaev EV, Maranas CD: Review of the BRENDA Database. Metab Eng. 2003, 5: 71-73. 10.1016/S1096-7176(03)00008-9.

  26. 26.

    Lin K, Li L, Correia JJ, Pilkis SJ: Arg-257 and Arg-307 of 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase bind the C-2 phospho group of fructose-2, 6-bisphosphate in the fructose-2, 6-bisphosphatase domain. J Biol Chem. 1992, 267: 19163-19171.

  27. 27.

    Garel MC, Arous N, Calvin MC, Craescu CT, Rosa J, Rosa R: A recombinant bisphosphoglycerate mutase variant with acid phosphatase homology degrades 2, 3-diphosphoglycerate. Proc Natl Acad Sci U S A. 1994, 91: 3593-3597.

  28. 28.

    White MF, Fothergill-Gilmore LA: Development of a mutagenesis, expression and purification system for yeast phosphoglycerate mutase. Investigation of the role of active-site His181. Eur J Biochem. 1992, 207: 709-714.

  29. 29.

    Walter RA, Nairn J, Duncan D, Price NC, Kelly SM, Rigden DJ, Fothergill-Gilmore LA: The role of the C-terminal region in phosphoglycerate mutase. Biochem J. 1999, 337: 89-95. 10.1042/0264-6021:3370089.

  30. 30.

    Rigden DJ, Lamani E, Mello LV, Littlejohn JE, Jedrzejas MJ: Insights into the catalytic mechanism of cofactor-independent phosphoglycerate mutase from X-ray crystallography, simulated dynamics and molecular modeling. J Mol Biol. 2003, 328: 909-920. 10.1016/S0022-2836(03)00350-4.

  31. 31.

    Nairn J, Price NC, Kelly SM, Rigden D, Fothergill-Gilmore LA, Krell T: Phosphoglycerate mutase from Schizosaccharomyces pombe: development of an expression system and characterisation of three histidine mutants of the enzyme. Biochim Biophys Acta. 1996, 1296: 69-75. 10.1016/0167-4838(96)00046-5.

  32. 32.

    Brewer JM, Glover CV, Holland MJ, Lebioda L: Significance of the enzymatic properties of yeast S39A enolase to the catalytic mechanism. Biochim Biophys Acta. 1998, 1383: 351-355. 10.1016/S0167-4838(98)00004-1.

  33. 33.

    Vinarov DA, Nowak T: Role of His159 in yeast enolase catalysis. Biochemistry. 1999, 38: 12138-12149. 10.1021/bi990760q.

  34. 34.

    Brewer JM, Holland MJ, Lebioda L: The H159A mutant of yeast enolase 1 has significant activity. Biochem Biophys Res Commun. 2000, 276: 1199-1202. 10.1006/bbrc.2000.3618.

  35. 35.

    Gulick AM, Hubbard BK, Gerlt JA, Rayment I: Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli. Biochemistry. 2001, 40: 10054-10062. 10.1021/bi010733b.

  36. 36.

    Holland MJ, Yokoi T, Holland JP, Myambo K, Innis MA: The GCR1 gene encodes a positive transcriptional regulator of the enolase and glyceraldehyde-3-phosphate dehydrogenase gene families in Saccharomyces cerevisiae. Mol Cell Biol. 1987, 7: 813-820.

  37. 37.

    Wilson CA, Hardman N, Fothergill-Gilmore LA, Gamblin SJ, Watson HC: Yeast phosphoglycerate kinase: investigation of catalytic function by site-directed mutagenesis. Biochem J. 1987, 241: 609-614.

  38. 38.

    Walker PA, Littlechild JA, Hall L, Watson HC: Site-directed mutagenesis of yeast phosphoglycerate kinase. The 'basic-patch' residue arginine 168. Eur J Biochem. 1989, 183: 49-55.

  39. 39.

    Fairbrother WJ, Hall L, Littlechild JA, Walker PA, Watson HC, Williams RJ: Site-directed mutagenesis of histidine 62 in the 'basic patch' region of yeast phosphoglycerate kinase. FEBS Lett. 1989, 258: 247-250. 10.1016/0014-5793(89)81665-5.

  40. 40.

    Ballery N, Minard P, Desmadril M, Betton JM, Perahia D, Mouawad L, Hall L, Yon JM: Introduction of internal cysteines as conformational probes in yeast phosphoglycerate kinase. Protein Eng. 1990, 3: 199-204.

  41. 41.

    Sherman MA, Szpikowska BK, Dean SA, Mathiowetz AM, McQueen NL, Mas MT: Probing the role of arginines and histidines in the catalytic function and activation of yeast 3-phosphoglycerate kinase by site-directed mutagenesis. J Biol Chem. 1990, 265: 10659-10665.

  42. 42.

    Sherman MA, Dean SA, Mathiowetz AM, Mas MT: Site-directed mutations of arginine 65 at the periphery of the active site cleft of yeast 3-phosphoglycerate kinase enhance the catalytic activity and eliminate anion-dependent activation. Protein Eng. 1991, 4: 935-940.

  43. 43.

    Joao HC, Taddei N, Williams RJ: Investigating interdomain region mutants Phe194Leu and Phe194Trp of yeast phosphoglycerate kinase by 1H-NMR spectroscopy. Eur J Biochem. 1992, 205: 93-104.

  44. 44.

    Tougard P, Le TH, Minard P, Desmadril M, Yon JM, Bizebard T, Lebras G, Dumas C: Structural and functional properties of mutant Arg203Pro from yeast phosphoglycerate kinase, as a model of phosphoglycerate kinase-Uppsala. Protein Eng. 1996, 9: 181-187.

  45. 45.

    Wikner C, Meshalkina L, Nilsson U, Nikkola M, Lindqvist Y, Sundstrom M, Schneider G: Analysis of an invariant cofactor-protein interaction in thiamin diphosphate-dependent enzymes by site-directed mutagenesis. Glutamic acid 418 in transketolase is essential for catalysis. J Biol Chem. 1994, 269: 32144-32150.

  46. 46.

    Wikner C, Meshalkina L, Nilsson U, Backstrom S, Lindqvist Y, Schneider G: His103 in yeast transketolase is required for substrate recognition and catalysis. Eur J Biochem. 1995, 233: 750-755.

  47. 47.

    Meshalkina L, Nilsson U, Wikner C, Kostikowa T, Schneider G: Examination of the thiamin diphosphate binding site in yeast transketolase by site-directed mutagenesis. Eur J Biochem. 1967, 244: 646-652.

  48. 48.

    Wikner C, Nilsson U, Meshalkina L, Udekwu C, Lindqvist Y, Schneider G: Identification of catalytically important residues in yeast transketolase. Biochemistry. 1997, 36: 5643-15649. 10.1021/bi971606b.

  49. 49.

    Nilsson U, Hecquet L, Gefflaut T, Guerard C, Schneider G: Asp477 is a determinant of the enantioselectivity in yeast transketolase. FEBS Lett. 1998, 424: 49-52. 10.1016/S0014-5793(98)00136-7.

  50. 50.

    Fiedler E, Golbik R, Schneider G, Tittmann K, Neef H, Konig S, Hubner G: Examination of donor substrate conversion in yeast transketolase. J Biol Chem. 2001, 276: 16051-16058. 10.1074/jbc.M007936200.

  51. 51.

    Al-Rabiee R, Lee EJ, Grant GA: The mechanism of velocity modulated allosteric regulation in D-3-phosphoglycerate dehydrogenase. Cross-linking adjacent regulatory domains with engineered disulfides mimics effector binding. J Biol Chem. 1996, 271: 13013-13017. 10.1074/jbc.271.22.13013.

  52. 52.

    Capitanio D, Merico A, Ranzi BM, Compagno C: Effects of the loss of triose phosphate isomerase activity on carbon metabolism in Kluyveromyces lactis. Res Microbiol. 2002, 153: 593-598. 10.1016/S0923-2508(02)01365-7.

  53. 53.

    Maithal K, Ravindra G, Balaram H, Balaram P: Inhibition of plasmodium falciparum triose-phosphate isomerase by chemical modification of an interface cysteine. Electrospray ionization mass spectrometric analysis of differential cysteine reactivities. J Biol Chem. 2002, 277: 25106-25114. 10.1074/jbc.M202419200.

  54. 54.

    Maithal K, Ravindra G, Nagaraj G, Singh SK, Balaram H, Balaram P: Subunit interface mutation disrupting an aromatic cluster in Plasmodium falciparum triosephosphate isomerase: effect on dimer stability. Protein Eng. 2002, 15: 575-584. 10.1093/protein/15.7.575.

  55. 55.

    Chanez-Cardenas ME, Fernandez-Velasco DA, Vazquez-Contreras E, Coria R, Saab-Rincon G, Perez-Montfort R: Unfolding of triosephosphate isomerase from Trypanosoma brucei: identification of intermediates and insight into the denaturation pathway using tryptophan mutants. Arch Biochem Biophys. 2002, 399: 117-129. 10.1006/abbi.2001.2749.

  56. 56.

    Lambeir AM, Backmann J, Ruiz-Sanz J, Filimonov V, Nielsen JE, Kursula I, Norledge BV, Wierenga RK: The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase. Eur J Biochem. 2000, 267: 2516-2524. 10.1046/j.1432-1327.2000.01254.x.

  57. 57.

    Compagno C, Boschi F, Daleffe A, Porro D, Ranzi BM: Isolation, nucleotide sequence, and physiological relevance of the gene encoding triose phosphate isomerase from Kluyveromyces lactis. Appl Environ Microbiol. 1999, 65: 4216-4219.

  58. 58.

    Alvarez M, Zeelen JP, Mainfroid V, Rentier-Delrue F, Martial JA, Wyns L, Wierenga RK, Maes D: Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. Kinetic and structural properties. J Biol Chem. 1998, 273: 2199-2206. 10.1074/jbc.273.4.2199.

  59. 59.

    Gomez-Puyou A, Saavedra-Lira E, Becker I, Zubillaga RA, Rojo-Dominguez A, Perez-Montfort R: Using evolutionary changes to achieve species-specific inhibition of enzyme action – studies with triosephosphate isomerase. Chem Biol. 1995, 2: 847-855. 10.1016/1074-5521(95)90091-8.

  60. 60.

    Lodi PJ, Chang LC, Knowles JR, Komives EA: Triosephosphate isomerase requires a positively charged active site: the role of lysine-12. Biochemistry. 1994, 33: 2809-2814.

  61. 61.

    Joseph-McCarthy D, Rost LE, Komives EA, Petsko GA: Crystal structure of the mutant yeast triosephosphate isomerase in which the catalytic base glutamic acid 165 is changed to aspartic acid. Biochemistry. 1994, 33: 2824-2829.

  62. 62.

    Brzovic PS, Hyde CC, Miles EW, Dunn MF: Characterization of the functional role of a flexible loop in the alpha-subunit of tryptophan synthase from Salmonella typhimurium by rapid-scanning, stopped-flow spectroscopy and site-directed mutagenesis. Biochemistry. 1993, 32: 10404-10413.

  63. 63.

    Borchert TV, Pratt K, Zeelen JP, Callens M, Noble ME, Opperdoes FR, Michels PA, Wierenga RK: Overexpression of trypanosomal triosephosphate isomerase in Escherichia coli and characterisation of a dimer-interface mutant. Eur J Biochem. 1993, 211: 703-710.

  64. 64.

    Raines RT, Sutton EL, Straus DR, Gilbert W, Knowles JR: Reaction energetics of a mutant triosephosphate isomerase in which the active-site glutamate has been changed to aspartate. Biochemistry. 1986, 25: 7142-7154.

  65. 65.

    Casal JI, Ahern TJ, Davenport RC, Petsko GA, Klibanov AM: Subunit interface of triosephosphate isomerase: site-directed mutagenesis and characterization of the altered enzyme. Biochemistry. 1987, 26: 1258-1264.

  66. 66.

    Nickbarg EB, Davenport RC, Petsko GA, Knowles JR: Triosephosphate isomerase: removal of a putatively electrophilic histidine residue results in a subtle change in catalytic mechanism. Biochemistry. 1988, 27: 5948-5960.

  67. 67.

    Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E: Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature. 2001, 413: 852-856. 10.1038/35101614.

  68. 68.

    Goldrick D, Yu G-Q, Jiang S-Q, Hong J-S: Nucleotide sequence and transcription start point of the phosphoglycerate transporter gene of Salmonella typhimurium. J Bacteriol. 1988, 170: 3421-3426.

  69. 69.

    Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A: Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature. 2003, 423: 87-91. 10.1038/nature01582.

  70. 70.

    Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR: The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature. 2003, 423: 81-86. 10.1038/nature01586.

  71. 71.

    Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MTG, Sebaihia M: Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature. 2001, 413: 848-852. 10.1038/35101607.

  72. 72.

    Deng W, Liou SR, Plunkett G, Mayhew GF, Rose DJ, Burland V, Kodoyianni V, Schwartz DC, Blattner FR: Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J Bacteriol. 2003, 185: 2330-2337. 10.1128/JB.185.7.2330-2337.2003.

  73. 73.

    Shimoji Y, Ng V, Matsumura K, Fischetti VA, Rambukkana A: A 21-kDa surface protein of Mycobacterium leprae binds peripheral nerve laminin-2 and mediates Schwann cell invasion. Proc Natl Acad Sci USA. 1999, 96: 9857-9862. 10.1073/pnas.96.17.9857.

  74. 74.

    Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N, Garnier T, Churcher C, Harris D, Mungall K, Basham D, Brown D, Chillingworth T, Connor R, Davies RM, Devlin K, Duthoy S, Feltwell T, Fraser A, Hamlin N, Holroyd S, Hornsby T, Jagels K, Lacroix C, Maclean J, Moule S, Murphy L, Oliver K, Quail MA, Rajandream MA, Rutherford KM, Rutter S, Seeger K, Simon S, Simmonds M, Skelton J, Squares R, Squares S, Stevens K, Taylor K, Whitehead S, Woodward JR, Barrell BG: Massive gene decay in the leprosy bacillus. Nature. 2001, 409: 1007-1011. 10.1038/35059006.

  75. 75.

    Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Barrell BG: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998, 393: 537-544. 10.1038/31159.

  76. 76.

    Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, DeBoy R, Dodson R, Gwinn M, Haft D, Hickey E, Kolonay JF, Nelson WC, Umayam LA, Ermolaeva M, Salzberg SL, Delcher A, Utterback T, Weidman J, Khouri H, Gill J, Mikula A, Bishai W, Jacobs WR, Venter JC, Fraser CM: Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol. 2002, 184: 5479-5490. 10.1128/JB.184.19.5479-5490.2002.

  77. 77.

    Keppel E, Schaller HC: A 33 kDa protein with sequence homology to the 'laminin binding protein' is associated with the cytoskeleton in hydra and in mammalian cells. J Cell Sci. 1991, 100: 789-797.

  78. 78.

    Hung M, Rosenthal ET, Boblett B, Benson S: Characterization and localized expression of the laminin binding protein/p40 (LBP/p40) gene during sea urchin development. Exp Cell Res. 1995, 221: 221-230. 10.1006/excr.1995.1370.

  79. 79.

    Rosenthal ET, Wordeman L: A protein similar to the 67 kDa laminin binding protein and p40 is probably a component of the translational machinery in Urechis caupo oocytes and embryos. J Cell Sci. 1995, 108: 245-256.

  80. 80.

    Tettelin H, Masignani V, Cieslewicz MJ, Eisen JA, Peterson S, Wessels MR, Paulsen IT, Nelson KE, Margarit I, Read TD, Madoff LC, Wolf AM, Beanan MJ, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Kolonay JF, Madupu R, Lewis MR, Radune D, Fedorova NB, Scanlan D, Khouri H, Mulligan S, Carty HA, Cline RT, Van Aken SE, Gill J, Scarselli M, Mora M, Iacobini ET, Brettoni C, Galli G, Mariani M, Vegni F, Maione D, Rinaudo D, Rappuoli R, Telford JL, Kasper DL, Grandi G, Fraser CM: Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc Natl Acad Sci USA. 2002, 99: 12391-12396. 10.1073/pnas.182380799.

  81. 81.

    Glaser P, Rusniok C, Buchrieser C, Chevalier F, Frangeul L, Msadek T, Zouine M, Couve E, Lalioui L, Poyart C, Trieu-Cuot P, Kunst F: Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease. Mol Microbiol. 2002, 45: 1499-1513. 10.1046/j.1365-2958.2002.03126.x.

  82. 82.

    Ferretti JJ, McShan WM, Ajdic D, Savic DJ, Savic G, Lyon K, Primeaux C, Sezate S, Suvorov AN, Kenton S, Lai HS, Lin SP, Qian Y, Jia HG, Najar FZ, Ren Q, Zhu H, Song L, White J, Yuan X, Clifton SW, Roe BA, McLaughlin R: Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci USA. 2001, 98: 4658-4663. 10.1073/pnas.071559398.

  83. 83.

    Granlund M, Michel F, Norgren M: Mutually exclusive distribution of IS1548 and GBSi1, an active group II intron identified in human isolates of group b streptococci. J Bacteriol. 2001, 183: 2560-2569. 10.1128/JB.183.8.2560-2569.2001.

  84. 84.

    Loehning C, Ciriacy M: The TYE7 gene of Saccharomyces cerevisiae encodes a putative bHLH-LZ transcription factor required for Ty1-mediated gene expression. Yeast. 1994, 10: 1329-1339.

  85. 85.

    Nishi K, Park CS, Pepper AE, Eichinger G, Innis MA, Holland MJ: The GCR1 requirement for yeast glycolytic gene expression is suppressed by dominant mutations in the SGC1 gene, which encodes a novel basic-helix-loop-helix protein. Mol Cell Biol. 1995, 15: 2646-2653.

  86. 86.

    Kurita O, Nishida Y: Involvement of mitochondrial aldehyde dehydrogenase ALD5 in maintenance of the mitochondrial electron transport chain in Saccharomyces cerevisiae. FEMS Microbiol Lett. 2003, 181: 281-287. 10.1016/S0378-1097(99)00523-6.

  87. 87.

    Valadi H, Larsson C, Gustafsson L: Improved ethanol production by glycerol-3-phosphate dehydrogenase mutants of Saccharomyces cerevisiae. Appl Microbiol Biotechnol. 1998, 50: 434-439. 10.1007/s002530051317.

  88. 88.

    van der Klei IJ, van der Heide M, Baerends RJ, Rechinger KB, Nicolay K, Kiel JA, Veenhuis M: The Hansenula polymorpha per6 mutant is affected in two adjacent genes which encode dihydroxyacetone kinase and a novel protein, Pak1p, involved in peroxisome integrity. Curr Genet. 1998, 34: 1-11. 10.1007/s002940050360.

  89. 89.

    Heath RJ, Rock CO: A missense mutation accounts for the defect in the glycerol-3-phosphate acyltransferase expressed in the plsB26 mutant. J Bacteriol. 1999, 181: 1944-1946.

  90. 90.

    Heath RJ, Rock CO: A conserved histidine is essential for glycerolipid acyltransferase catalysis. J Bacteriol. 1998, 180: 1425-1430.

  91. 91.

    Minskoff SA, Racenis PV, Granger J, Larkins L, Hajra AK, Greenberg ML: Regulation of phosphatidic acid biosynthetic enzymes in Saccharomyces cerevisiae. J Lipid Res. 1994, 35: 2254-2262.

  92. 92.

    Cho H, Oliveira MA, Tai HH: Critical residues for the coenzyme specificity of NAD+-dependent 15-hydroxyprostaglandin dehydrogenase. Arch Biochem Biophys. 2003, 419: 139-146. 10.1016/j.abb.2003.09.019.

  93. 93.

    Soundar S, Park JH, Huh TL, Colman RF.: Evaluation by mutagenesis of the importance of 3 arginines in alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase. J Biol Chem. 2003, 278: 52146-52153. 10.1074/jbc.M306178200.

  94. 94.

    Yamaguchi M, Stout CD: Essential glycine in the proton channel of Escherichia coli transhydrogenase. J Biol Chem. 2003, 278: 45333-45339. 10.1074/jbc.M308236200.

  95. 95.

    Klimacek M, Kavanagh KL, Wilson DK, Nidetzky B: On the role of Bronsted catalysis in Pseudomonas fluorescens mannitol 2-dehydrogenase. Biochem J. 2003, 375: 141-149. 10.1042/BJ20030733.

  96. 96.

    Saridakis V, Pai EF: Mutational, structural, and kinetic studies of the ATP-binding site of Methanobacterium thermoautotrophicum nicotinamide mononucleotide adenylyltransferase. J Biol Chem. 2003, 278: 34356-34363. 10.1074/jbc.M205369200.

  97. 97.

    Waterham HR, Titorenko VI, Swaving GJ, Harder W, Veenhuis M: Peroxisomes in the methylotrophic yeast Hansenula polymorpha do not necessarily derive from pre-existing organelles. EMBO J. 1993, 12: 4785-4794.

  98. 98.

    Liao HF, Lin LL, Chien HR, Hsu WH: Serine 187 is a crucial residue for allosteric regulation of Corynebacterium glutamicum 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase. FEMS Microbiol Lett. 2001, 194: 59-64. 10.1016/S0378-1097(00)00507-3.

  99. 99.

    Alvarez M, Wouters J, Maes D, Mainfroid V, Rentier-Delrue F, Wyns L, Depiereux E, Martial JA: Lys13 plays a crucial role in the functional adaptation of the thermophilic triose-phosphate isomerase from Bacillus stearothermophilus to high temperatures. J Biol Chem. 1999, 274: 19181-19187. 10.1074/jbc.274.27.19181.

  100. 100.

    Zheng Z, Zou J: The initial step of the glycerolipid pathway: identification of glycerol 3- phosphate/dihydroxyacetone phosphate dual substrate acyltransferases in Saccharomyces cerevisiae. J Biol Chem. 2001, 276: 41710-41716. 10.1074/jbc.M104749200.

  101. 101.

    Vilei EM, Frey J: Genetic and biochemical characterization of glycerol uptake in mycoplasma mycoides subsp. mycoides SC: its impact on H(2)O(2) production and virulence. Clin Diagn Lab Immunol. 2001, 8: 85-92. 10.1128/CDLI.8.1.85-92.2001.

  102. 102.

    Ferguson GP, Totemeyer S, MacLean MJ, Booth IR: Methylglyoxal production in bacteria: suicide or survival?. Arch Microbiol. 1998, 170: 209-218. 10.1007/s002030050635.

  103. 103.

    Williams SG, Greenwood JA, Jones CW: The effect of nutrient limitation on glycerol uptake and metabolism in continuous cultures of Pseudomonas aeruginosa. Microbiology. 1994, 140: 2961-2969.

  104. 104.

    Badia J, Gimenez R, Baldoma L, Barnes E, Fessner WD, Anguilar J: L-lyxose metabolism employs the L-rhamnose pathway in mutant cells of Escherichia coli adapted to grow on L-lyxose. J Bacteriol. 1991, 173: 5144-5150.

  105. 105.

    Zhu Y, Lin EC: A mutant crp allele that differentially activates the operons of the fuc regulon in Escherichia coli. J Bacteriol. 1988, 170: 2352-2358.

  106. 106.

    Hacking AJ, Lin EC: Disruption of the fucose pathway as a consequence of genetic adaptation to propanediol as a carbon source in Escherichia coli. J Bacteriol. 1976, 126: 1166-1172.

  107. 107.

    Miki K, Lin EC: Anaerobic energy-yielding reaction associated with transhydrogenation from glycerol 3-phosphate to fumarate by an Escherichia coli system. J Bacteriol. 1975, 124: 1282-1287.

  108. 108.

    Kuzuyama T, Takahashi S, Takagi M, Seto H: Characterization of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, an enzyme involved in isopentenyl diphosphate biosynthesis, and identification of its catalytic amino acid residues. J Biol Chem. 2000, 275: 19928-19932. 10.1074/jbc.M001820200.

  109. 109.

    Stevis PE, Ho NW: A novel xylB-based positive selection vector. Plasmid. 1988, 20: 92-95.

  110. 110.

    Faber KN, van Dijk R, Keizer-Gunnink I, Koek A, van der Klei IJ, Veenhuis M: Import of assembled PTS1 proteins into peroxisomes of the yeast Hansenula polymorpha: yes and no!. Biochim Biophys Acta. 2002, 1591: 157-162. 10.1016/S0167-4889(02)00274-4.

  111. 111.

    Salomons FA, Kiel JA, Faber KN, Veenhuis M, van der Klei IJ: Overproduction of Pex5p stimulates import of alcohol oxidase and dihydroxyacetone synthase in a Hansenula polymorpha Pex14 null mutant. J Biol Chem. 2000, 275: 12603-12611. 10.1074/jbc.275.17.12603.

  112. 112.

    Camus JC, Pryor MJ, Medigue C, Cole ST: Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology. 2002, 148: 2967-2973.

  113. 113.

    Eicks M, Maurino V, Knappe S, Flugge UI, Fischer K: The plastidic pentose phosphate translocator represents a link between the cytosolic and the plastidic pentose phosphate pathways in plants. Plant Physiol. 2002, 128: 512-522. 10.1104/pp.128.2.512.

  114. 114.

    Du YC, Peddi SR, Spreitzer RJ: Assessment of structural and functional divergence far from the large subunit active site of ribulose-1, 5-bisphosphate carboxylase/oxygenase. J Biol Chem. 2003, 278: 49401-49405. 10.1074/jbc.M309993200.

  115. 115.

    Spreitzer RJ, Thow G, Zhu G: Pseudoreversion substitution at large-subunit residue 54 influences the CO2/O2 specificity of chloroplast ribulose-bisphosphate carboxylase/oxygenase. Plant Physiol. 1995, 109: 681-685. 10.1104/pp.109.2.681.

  116. 116.

    Romanova AK, Zhen-Qi-Cheng Z, McFadden BA: Activity and carboxylation specificity factor of mutant ribulose 1, 5-bisphosphate carboxylase/oxygenase from Anacystis nidulans. Biochem Mol Biol Int. 1997, 42: 299-307.

  117. 117.

    Lee GJ, McDonald KA, McFadden BA: Leucine 332 influences the CO2/O2 specificity factor of ribulose-1, 5-bisphosphate carboxylase/oxygenase from Anacystis nidulans. Protein Sci. 1993, 2: 1147-1154.

  118. 118.

    Day AG, Chene P, Fersht AR: Role of phenylalanine-327 in the closure of loop 6 of ribulosebisphosphate carboxylase/oxygenase from Rhodospirillum rubrum. Biochemistry. 1993, 32: 1940-1944.

  119. 119.

    Chene P, Day AG, Fersht AR: Mutation of asparagine 111 of rubisco from Rhodospirillum rubrum alters the carboxylase/oxygenase specificity. J Mol Biol. 1992, 225: 891-896.

  120. 120.

    Read BA, Tabita FR: Amino acid substitutions in the small subunit of ribulose-1, 5-bisphosphate carboxylase/oxygenase that influence catalytic activity of the holoenzyme. Biochemistry. 1992, 31: 519-525.

  121. 121.

    Marcus Y, Altman-Gueta H, Finkler A, Gurevitz M: Dual role of cysteine 172 in redox regulation of ribulose 1, 5-bisphosphate carboxylase/oxygenase activity and degradation. J Bacteriol. 2003, 185: 1509-1517. 10.1128/JB.185.5.1509-1517.2003.

  122. 122.

    Zhu G, Spreitzer RJ: Directed mutagenesis of chloroplast ribulosebisphosphate carboxylase/oxygenase. Substitutions at large subunit asparagine 123 and serine 379 decrease CO2/O2 specificity. J Biol Chem. 1994, 269: 3952-3956.

  123. 123.

    Lee GJ, McFadden BA: Serine-376 contributes to the binding of substrate by ribulose-bisphosphate carboxylase/oxygenase from Anacystis nidulans. Biochemistry. 1992, 31: 2304-2308.

  124. 124.

    Chene P, Day AG, Fersht AR: Role of isoleucine-164 at the active site of rubisco from Rhodospirillum rubrum. Biochem Biophys Res Commun. 1997, 232: 482-486. 10.1006/bbrc.1997.6318.

  125. 125.

    Harpel MR, Larimer FW, Hartman FC: Multiple catalytic roles of His 287 of Rhodospirillum rubrum ribulose 1, 5-bisphosphate carboxylase/oxygenase. Protein Sci. 1998, 7: 730-738.

  126. 126.

    Terzaghi BE, Laing WA, Christeller JT, Petersen GB, Hill DF: Ribulose 1, 5-bisphosphate carboxylase. Effect on the catalytic properties of changing methionine-330 to leucine in the Rhodospirillum rubrum enzyme. Biochem J. 1986, 235: 839-846.

  127. 127.

    Spreitzer RJ, Esquivel MG, Du YC, McLaughlin PD: Alanine-scanning mutagenesis of the small-subunit beta A-beta B loop of chloroplast ribulose-1, 5-bisphosphate carboxylase/oxygenase: substitution at Arg-71 affects thermal stability and CO2/O2 specificity. Biochemistry. 2001, 40: 5615-5621. 10.1021/bi002943e.

  128. 128.

    Du YC, Spreitzer RJ: Suppressor mutations in the chloroplast-encoded large subunit improve the thermal stability of wild-type ribulose-1, 5-bisphosphate carboxylase/oxygenase. J Biol Chem. 2000, 275: 19844-19847. 10.1074/jbc.M002321200.

  129. 129.

    Runquist JA, Rios SE, Vinarov DA, Miziorko HM: Functional evaluation of serine/threonine residues in the P-Loop of Rhodobacter sphaeroides phosphoribulokinase. Biochemistry. 2001, 40: 14530-14537. 10.1021/bi010778c.

  130. 130.

    Runquist JA, Harrison DH, Miziorko HM: Rhodobacter sphaeroides phosphoribulokinase: identification of lysine-165 as a catalytic residue and evaluation of the contributions of invariant basic amino acids to ribulose 5-phosphate binding. Biochemistry. 1999, 38: 13999-14005. 10.1021/bi9910326.

  131. 131.

    Runquist JA, Harrison DH, Miziorko HM: Functional evaluation of invariant arginines situated in the mobile lid domain of phosphoribulokinase. Biochemistry. 1998, 37: 1221-1226. 10.1021/bi972052f.

  132. 132.

    Avilan L, Gontero B, Lebreton S, Ricard J: Information transfer in multienzyme complexes – 2. The role of Arg64 of Chlamydomonas reinhardtii phosphoribulokinase in the information transfer between glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase. Eur J Biochem. 1997, 250: 296-302.

  133. 133.

    Su X, Bogorad L: A residue substitution in phosphoribulokinase of Synechocystis PCC 6803 renders the mutant light-sensitive. J Biol Chem. 1991, 266: 23698-23705.

  134. 134.

    Sandbaken MG, Runquist JA, Barbieri JT, Miziorko HM: Identification of the phosphoribulokinase sugar phosphate binding domain. Biochemistry. 1992, 31: 3715-3719.

  135. 135.

    Charlier HA, Runquist JA, Miziorko HM: Evidence supporting catalytic roles for aspartate residues in phosphoribulokinase. Biochemistry. 1994, 33: 9343-9350.

  136. 136.

    Kung G, Runquist JA, Miziorko HM, Harrison DH: Identification of the allosteric regulatory site in bacterial phosphoribulokinase. Biochemistry. 1999, 38: 15157-15165. 10.1021/bi991033y.

  137. 137.

    Staswick PE, Crafts-Brandner SJ, Salvucci ME: cDNA sequence for the ribulose 1, 5 bisphosphate carboxylase/oxygenase complex protein. A protein that accumulates in soybean leaves in response to fruit removal. Plant Physiol. 1994, 105: 1445-1446. 10.1104/pp.105.4.1445.

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We thank Dr. Paramita Ray for help with literature search and Dr. Surabhi Choudhuri for her comments on the manuscript.

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Mahato, S., De, D., Dutta, D. et al. Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate. Microb Cell Fact 3, 7 (2004). https://doi.org/10.1186/1475-2859-3-7

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Keywords

  • Dihydroxyacetone Phosphate
  • Phosphoglycerate Mutase
  • Phosphoglycerate Dehydrogenase
  • Sugar Binding Protein
  • Dihydroxyacetone Kinase