Pseudomonas cichorii D-tagatose 3-epimerase (PcDTE), which has a broad substrate specificity, efficiently catalyzes the epimerization of not only D-tagatose to D-sorbose but also D-fructose to D-psicose (D-allulose) and also recognizes the deoxy sugars as substrates. In an attempt to elucidate the substrate recognition and catalytic reaction mechanisms of PcDTE for deoxy sugars, the X-ray structures of the PcDTE mutant form with the replacement of Cys66 by Ser (PcDTE_C66S) in complexes with deoxy sugars were determined. These X-ray structures showed that substrate recognition by the enzyme at the 1-, 2-, and 3-positions is responsible for enzymatic activity and that substrate-enzyme interactions at the 4-, 5-, and 6-positions are not essential for the catalytic reaction of the enzyme leading to the broad substrate specificity of PcDTE. They also showed that the epimerization site of 1-deoxy 3-keto D-galactitol is shifted from C3 to C4 and that 1-deoxy sugars may bind to the catalytic site in the inhibitor-binding mode. The hydrophobic groove that acts as an accessible surface for substrate binding is formed through the dimerization of PcDTE. In PcDTE_C66S/deoxy sugar complex structures, bound ligand molecules in both the linear and ring forms were detected in the hydrophobic groove, while bound ligand molecules in the catalytic site were in the linear form. This result suggests that the sugar-ring opening of a substrate may occur in the hydrophobic groove and also that the narrow channel of the passageway to the catalytic site allows a substrate in the linear form to pass through.
This is a preview of subscription content, log in to check access.
Buy single article
Instant access to the full article PDF.
Price includes VAT for USA
Subscribe to journal
Immediate online access to all issues from 2019. Subscription will auto renew annually.
This is the net price. Taxes to be calculated in checkout.
Brunger AT (1993) X-PLOR 3.1: a system for X-ray crystallography and NMR. Yale University Press, New Haven and London
Carrell HL, Glusker JP, Burger V, Manfre F, Tritsch D, Biellmann JF (1989) X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator. Proc Natl AcadSci USA 86:4440–4444
Carrell HL, Hoier H, Glusker JP (1994) Modes of binding substrates and their analogues to the enzyme D-xylose isomerase. Acta Crystallogr Sect D 50:113–123. doi:10.1107/S0907444993009345
Collyer CA, Henrick K, Blow DM (1990) Mechanism for aldose-ketose interconversion by D-xylose isomerase involving ring opening followed by a 1,2-hydride shift. J Mol Biol 212:211–235. doi:10.1016/0022-2836(90)90316-E
Emsley P, Lohkamp B, Scott W, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486–501. doi:10.1107/S0907444910007493
Fenn TD, Ringe D, Petsko GA (2004) Xylose isomerase in substrate and inhibitor michaelis states: atomic resolution studies of a metal-mediated hydride shift. Biochemistry 43:6464–6474. doi:10.1021/bi049812o
Gullapalli P, Yoshihara A, Morimoto K, Rao D, Akimitsu K, Jenkinson SF, Fleet GWJ, Izumori K (2010) Conversion of l-rhamnose into ten of the sixteen 1- and 6-deoxyketohexoses in water with three reagents: d-tagatose-3-epimerase equilibrates C3 epimers of deoxyketoses. Tetrahedron Lett 51(6):895–898. doi:10.1016/j.tetlet.2009.12.024
Hayashi N, Iida T, Yamada T, Okuma K, Takehara I, Yamamoto T, Yamada K, Tokuda M (2010) Study on the postprandial blood glucose suppression effect of D-psicose in borderline diabetes and the safety of long-term ingestion by normal human subjects. Biosci Biotechnol Biochem 74:510–519. doi:10.1271/bbb.90707
Hayashi N, Yamada T, Takamine S, Iida T, Okuma K, Tokuda M (2014) Weight reducing effect and safety evaluation of rare sugar syrup by a randomized double-blind, parallel-group study in human. J Funct Foods 11:152–159. doi:10.1016/j.jff.2014.09.020
Hossain A, Yamaguchi F, Matsunaga T, Hirata Y, Kamitori K, Dong Y, Sui L, Tsukamoto I, Ueno M, Tokuda M (2012) Rare sugar D-psicose protects pancreas β-islets and thus improves insulin resistance in OLETF rats. Biochem Biophys Res Commun 425:717–723. doi:10.1016/j.bbrc.2012.07.135
Hossain MA, Kitagaki S, N akano D, Nishiyama A, Funamoto Y, Matsunaga T, Tsukamoto I, Yamaguchi F, Kamitori K, Dong Y, Hirata Y, Murao K, Toyoda Y, Tokuda M (2011) Rare sugar D-psicose improves insulin sensitivity and glucose tolerance in type 2 diabetes Otsuka Long-Evans Tokushima Fatty (OLETF) rats. Biochem Biophys Res Commun 405:7–12. doi:10.1016/j.bbrc.2010.12.091
Iida T, Kishimoto Y, Yoshikawa Y, Hayashi N, Okuma K, Tohi M, Yagi K, Matsuo T, Izumori K (2008) Acute D-psicose administration decreases the glycemic responses to an oral maltodextrin tolerance test in normal adults. J Nutr Sci Vitaminol (Tokyo) 54:511–514. doi:10.3177/jnsv.54.511
Iida T, Yamada T, Hayashi N, Okuma K, Izumori K, Ishii R, Matsuo T (2013) Reduction of abdominal fat accumulation in rats by 8-week ingestion of a newly developed sweetener made from high fructose corn syrup. Food Chem 138(2–3):781–785. doi:10.1016/j.foodchem.2012.11.017
Ishida Y, Kamiya T, Izumori K (1997) Production of d-tagatose 3-epimerase of Pseudomonas cichorii ST-24 using recombinant Escherichia coli. J Ferment Bioeng 84:348–350. doi:10.1016/S0922-338X(97)89257-4
Itoh H, Okaya H, Khan AR, Tajima S, Hayakawa S, Izumori K (1994) Purification and characterization of D-tagatose 3-epimerase from Pseudomonas sp. ST-24. Biosci Biotechnol Biochem 58:2168–2171. doi:10.1271/bbb.58.2168
Itoh H, Sato T, Izumori K (1995) Preparation of D-psicose from D-fructose by immobilized D-tagatose 3-epimerase. J Ferment Bioeng 80:101–103. doi:10.1016/0922-338X(95)98186-O
Izumori K, Khan AR, Okaya H, Tsumura T (1993) A new enzyme, D-ketohexose 3-epimerase, from Pseudomonas sp. ST-24. Biosci Biotechnol Biochem 57:1037–1039. doi:10.1271/bbb.57.1037
Jia M, Mu WM, Chu FF, Zhang XM, Jiang B, Zhou LL, Zhang T (2014) A D-psicose 3-epimerase with neutral pH optimum from Clostridium bolteae for D-psicose production: cloning, expression, purification, and characterization. Appl Microbiol Biotechnol 98:717–725. doi:10.1007/s00253-013-4924-8
Kim HJ, Hyun EK, Kim YS, Lee YJ, Oh DK (2006a) Characterization of an Agrobacterium tumefaciens D-psicose 3-epimerase that converts D-fructose to D-psicose. Appl Environ Microbiol 72:981–985. doi:10.1128/AEM.72.2.981-985.2006
Kim K, Kim HJ, Oh DK, Cha SS, Rhee S (2006b) Crystal structure of D-psicose 3-epimerase from Agrobacterium tumefaciens and its complex with true substrate D-fructose: a pivotal role of metal in catalysis, an active site for the non-phosphorylated substrate, and its conformational changes. J Mol Biol 361:920–931. doi:10.1016/j.jmb.2006.06.069
Kovalevsky AY, Hanson L, Fisher SZ, Mustyakimov M, Mason SA, Forsyth VT, Blakeley MP, Keen DA, Wagner T, Carrell HL, Katz AK, Glusker JP, Langan P (2010) Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study. Structure 18:688–699. doi:10.1016/j.str.2010.03.011
Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774–797. doi:10.1016/j.jmb.2007.05.022
Langan P, Sangha AK, Wymore T, Parks JM, Yang ZK, Hanson BL, Fisher Z, Mason SA, Blakeley MP, Forsyth VT, Glusker JP, Carrell HL, Smith JC, Keen DA, Graham DE, Kovalevsky A (2014) L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study. Structure 22:1287–1300. doi:10.1016/j.str.2014.07.002
Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1992) PROCHECK v.2: programs to check the stereochemical quality of protein structures. Oxford Molecular Ltd, Oxford, England
Matsuo T, Izumori K (2009) D-Psicose inhibits intestinal alpha glucosidase and suppresses the glycemic response after ingestion of carbohydrates in rats. J Clin Biochem Nutr 45:202–206. doi:10.3164/jcbn.09-36
Matsuo T, Suzuki H, Hashiguchi M, Izumori K (2002) D-Psicose is a rare sugar that provides no energy to growing rats. J Nutr Sci Vitaminol 48:77–80. doi:10.3177/jnsv.48.77
Matsuo T (2006) Inhibitory effects of D-psicose on glycemic responses after oral carbohydrate tolerance test in rats. J Jpn Soc Nutr Food Sci 59:119–121. doi:10.4327/jsnfs.59.119
McRee DE (1999) XtalView/Xfit: a versatile program for manipulating atomic coordinate and electron density. J Struct Biol 125:156–165. doi:10.1006/jsbi.1999.4094
Mu W, Zhang W, Feng Y, Jiang B, Zhou L (2012) Recent advances on applications and biotechnological production of D-psicose. Appl Microbiol Biotechnol 94:1461–1467. doi:10.1007/s00253-012-4093-1
Mu WM, Chu FF, Xing QC, Yu SH, Zhou L, Jiang B (2011) Cloning, expression, and characterization of a D-psicose 3-epimerase from Clostridium cellulolyticum H10. J Agric Food Chem 59:7785–7792. doi:10.1021/jf201356q
Mu WM, Zhang WL, Fang D, Zhou L, Jiang B, Zhang T (2013) Characterization of a D-psicose-producing enzyme, D-psicose 3-epimerase, from Clostridium sp. Biotechnol Lett 35:1481–1486. doi:10.1007/s10529-013-1230-6
Munshi P, Snell EH, van der Woerd MJ, Judge RA, Myles DA, Ren Z, Meilleur F (2014) Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant. Acta Crystallogr D Biol Crystallogr 70:414–420. doi:10.1107/S1399004713029684
Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53:240–255. doi:10.1107/S0907444996012255
Nakajima Y, Gotanda T, Uchiyama H, Furukawa T, Haraguchi M, Ikeda R, Sumizawa T, Yoshida H, Akiyama S (2004) Inhibition of metastasis of tumor cells overexpressing thymidine phosphorylase by 2-deoxy-L-ribose. Cancer Res 64:1794–1801
Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Method in enzymology 276: macromolecular crystallography, part A, 307–326. doi:10.1016/S0076–6879(97)76066-X
Shompoosang S, Yoshihara A, Uechi K, Asada Y, Morimoto K (2014) Enzymatic production of three 6-deoxy-aldohexoses from L-rhamnose. Biosci Biotechnol Biochem 78:317–325. doi:10.1080/09168451.2014.878217
Shompoosang S, Yoshihara A, Uechi K, Asada Y, Morimoto K (2016) Novel process for producing 6-deoxy monosaccharides from l-fucose by coupling and sequential enzymatic method. J Biosci Bioeng 121:1–6. doi:10.1016/j.jbiosc.2015.04.017
Takahashi S, Ohta K, Furubayashi N, Yan B, Koga M, Wada Y, Yamada M, Inaka K, Tanaka H, Miyoshi H, Kobayashi T, Kamigaichi S (2013) JAXA protein crystallization in space: ongoing improvements for growing high-quality crystals. J Synchrotron Radiat 20(Pt 6):968–973. doi:10.1107/S0909049513021596
Terami Y, Yoshida H, Uechi K, Morimoto K, Takata G, Kamitori S (2015) Essentiality of tetramer formation of Cellulomonas parahominis L-ribose isomerase involved in novel L-ribose metabolic pathway. Appl Microbiol Biotechnol 99:6303–6313. doi:10.1007/s00253-015-6417-4
Vagin A, Teplyakov A (1997) MOLREP: an automated program for molecular replacement. J Appl Crystallogr 30:1022–1025. doi:10.1107/S0021889897006766
Whitlow M, Howard AJ, Finzel BC, Poulos TL, Winborne E, Gilliland GL (1991) A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 Å Streptomyces rubiginosus structures with xylitol and D-xylose. Proteins 9:153–173. doi:10.1002/prot.340090302
Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AGW, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67:235–242. doi:10.1107/S0907444910045749
Yoshida H, Yamada M, Nishitani T, Takada G, Izumori K, Kamitori S (2007) Crystal structures of D-tagatose 3-epimerase from Pseudomonas cichorii and its complexes with D-tagatose and D-fructose. J Mol Biol 374(2):443–453. doi:10.1016/j.jmb.2007.09.033
Yoshida H, Yamaji M, Ishii T, Izumori K, Kamitori S (2010) Catalytic reaction mechanism of Pseudomonas stutzeri L-rhamnose isomerase deduced from X-ray structures. FEBS J 277:1045–1057. doi:10.1111/j.1742-4658.2009.07548.x
Yoshida H, Yoshihara A, Teraoka M, Terami Y, Takata G, Izumori K, Kamitori S (2014) X-ray structure of a novel L-ribose isomerase acting on a non-natural sugar L-ribose as its ideal substrate. FEBS J 281:3150–3164. doi:10.1111/febs.12850
Yoshida H, Yoshihara A, Teraoka M, Yamashita S, Izumori K, Kamitori S (2012) Structure of L-rhamnose isomerase in complex with L-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site. FEBS Open Bio 3:35–40. doi:10.1016/j.fob.2012.11.008
Zhang L, Mu W, Jiang B, Zhang T (2009) Characterization of D-tagatose-3-epimerase from Rhodobacter sphaeroides that converts D-fructose into D-psicose. Biotechnol Lett 31:857–862. doi:10.1007/s10529-009-9942-3
Zhang W, Fang D, Xing Q, Zhou L, Jiang B, Mu WM (2013b) Characterization of a novel metal-dependent D-psicose 3-epimerase from Clostridium scindens 35704. PLoS One 8:e62987. doi:10.1371/journal.pone.0062987
Zhang W, Fang D, Zhang T, Zhou L, Jiang B, Mu W (2013a) Characterization of a metal-dependent D-psicose 3-epimerase from a novel strain, Desmospora sp. 8437. J Agric Food Chem 61:11468–11476. doi:10.1021/jf4035817
Zhang W, Zhang T, Jiang B, Mu W (2015) Biochemical characterization of a d-psicose 3-epimerase from Treponema primitia ZAS-1 and its application on enzymatic production of d-psicose. J Sci Food Agric 96:49–56. doi:10.1002/jsfa.7187
Zhu YM, Men Y, Bai W, Li XB, Zhang LL, Sun YX, Ma Y (2012) Overexpression of D-psicose 3-epimerase from Ruminococcus sp. in Escherichia coli and its potential application in D-psicose production. Biotechnol Lett 34:1901–1906. doi:10.1007/s10529-012-0986-4
We thank Mr. Y. Tahara, Ms. S. Kayahara, and Mr. S. Ohga for assisting with protein purification; Mr. K. Yube for his technical assistance with DNA sequencing; and Dr. K. Inaka, Dr. N. Furubayashi, Dr. M. Yamada, and Dr. K. Ohta for assisting with crystallizations under microgravity. This research was performed with the approval of the Photon Factory Advisory Committee and National Laboratory for High Energy Physics, Japan. This study is contributed by a part of “High-Quality Protein Crystal Growth Experiment on KIBO” promoted by JAXA (Japan Aerospace Exploration Agency). Russian spacecraft “Progress” and/or “Soyuz” provided by the Russian Federal Space Agency were used for space transportation. A part of space crystallization technology had been developed by the European Space Agency and University of Granada.
This study was funded in part by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (25440028, 23770122).
The authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
About this article
Cite this article
Yoshida, H., Yoshihara, A., Ishii, T. et al. X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates. Appl Microbiol Biotechnol 100, 10403–10415 (2016). https://doi.org/10.1007/s00253-016-7673-7
- Deoxy sugar
- Rare sugar
- X-ray structure