Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Crystal Structures of 6-Phosphogluconate Dehydrogenase from Corynebacterium glutamicum

  • Hyeonjeong Yu (School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University) ;
  • Jiyeon Hong (KNU Institute for Microorganisms, Kyungpook National University) ;
  • Jihye Seok (School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University) ;
  • Young-Bae Seu (School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University) ;
  • Il-Kwon Kim (KNU Institute for Microorganisms, Kyungpook National University) ;
  • Kyung-Jin Kim (School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University)
  • Received : 2023.05.04
  • Accepted : 2023.06.16
  • Published : 2023.10.28
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Abstract

Corynebacterium glutamicum (C. glutamicum) has been considered a very important and meaningful industrial microorganism for the production of amino acids worldwide. To produce amino acids, cells require nicotinamide adenine dinucleotide phosphate (NADPH), which is a biological reducing agent. The pentose phosphate pathway (PPP) can supply NADPH in cells via the 6-phosphogluconate dehydrogenase (6PGD) enzyme, which is an oxidoreductase that converts 6-phosphogluconate (6PG) to ribulose 5-phosphate (Ru5P), to produce NADPH. In this study, we identified the crystal structure of 6PGD_apo and 6PGD_NADP from C. glutamicum ATCC 13032 (Cg6PGD) and reported our biological research based on this structure. We identified the substrate binding site and co-factor binding site of Cg6PGD, which are crucial for understanding this enzyme. Based on the findings of our research, Cg6PGD is expected to be used as a NADPH resource in the food industry and as a drug target in the pharmaceutical industry.

Keywords

Acknowledgement

This work was supported by the Cooperative Research Program for Agricultural Science & Technology Development (Project No. PJ01492602), Rural Development Administration, Republic of Korea. And this work is further supported by the Development of next-generation biorefinery platform technologies for leading bio-based chemicals industry project (2022M3J5A1056072) and by Development of platform technologies of microbial cell factories for the next-generation biorefineries project (2022M3J5A1056117) from National Research Foundation supported by the Korean Ministry of Science and ICT.

References

  1. Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, et al. 2003. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J. Biotechnol. 104: 5-25.  https://doi.org/10.1016/S0168-1656(03)00154-8
  2. Becker J, Giesselmann G, Hoffmann SL, Wittmann C. 2018. Corynebacterium glutamicum for sustainable bioproduction: from metabolic physiology to systems metabolic engineering. Adv. Biochem. Eng. Biotechnol. 162: 217-263.  https://doi.org/10.1007/10_2016_21
  3. Lee JY, Na YA, Kim E, Lee HS, Kim P. 2016. The Actinobacterium Corynebacterium glutamicum, an industrial workhorse. J. Microbiol. Biotechnol. 26: 807-822.  https://doi.org/10.4014/jmb.1601.01053
  4. Eikmanns BJ, Eggeling L, Sahm H. 1993. Molecular aspects of lysine, threonine, and isoleucine biosynthesis in Corynebacterium glutamicum. Antonie Van Leeuwenhoek. 64: 145-163.  https://doi.org/10.1007/BF00873024
  5. Baumgart M, Unthan S, Ruckert C, Sivalingam J, Grunberger A, Kalinowski J, et al. 2013. Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 for use as a platform strain for basic research and industrial biotechnology. Appl. Environ. Microbiol. 79: 6006-6015.  https://doi.org/10.1128/AEM.01634-13
  6. Xu JZ, Yang HK, Zhang WG. 2018. NADPH metabolism: a survey of its theoretical characteristics and manipulation strategies in amino acid biosynthesis. Crit. Rev. Biotechnol. 38: 1061-1076.  https://doi.org/10.1080/07388551.2018.1437387
  7. Takeno S, Hori K, Ohtani S, Mimura A, Mitsuhashi S, Ikeda M. 2016. l-Lysine production independent of the oxidative pentose phosphate pathway by Corynebacterium glutamicum with the Streptococcus mutans gapN gene. Metab. Eng. 37: 1-10.  https://doi.org/10.1016/j.ymben.2016.03.007
  8. Sheng Q, Wu XY, Xu X, Tan X, Li Z, Zhang B. 2021. Production of l-glutamate family amino acids in Corynebacterium glutamicum: physiological mechanism, genetic modulation, and prospects. Synth. Syst. Biotechnol. 6: 302-325.  https://doi.org/10.1016/j.synbio.2021.09.005
  9. Ma YC, Ma Q, Cui Y, Du LH, Xie XX, Chen N. 2019. Transcriptomic and metabolomics analyses reveal metabolic characteristics of L-leucine- and L-valine-producing Corynebacterium glutamicum mutants. Ann. Microbiol. 69: 457-468.  https://doi.org/10.1007/s13213-018-1431-2
  10. Ma WJ, Wang JL, Li Y, Hu XQ, Shi F, Wang XY. 2016. Enhancing pentose phosphate pathway in Corynebacterium glutamicum to improve L-isoleucine production. Biotechnol. Appl. Biochem. 63: 877-885.  https://doi.org/10.1002/bab.1442
  11. Pfefferle W, Mockel B, Bathe B, Marx A. 2003. Biotechnological manufacture of lysine. Adv. Biochem. Eng. Biotechnol. 79: 59-112.  https://doi.org/10.1007/3-540-45989-8_3
  12. Kimura E. 2003. Metabolic engineering of glutamate production. Adv. Biochem. Eng. Biotechnol. 79: 37-57.  https://doi.org/10.1007/3-540-45989-8_2
  13. Ikeda M. 2003. Amino acid production processes. Adv. Biochem. Eng. Biotechnol. 79: 1-35.  https://doi.org/10.1007/3-540-45989-8_1
  14. Schnarrenberger C, Flechner A, Martin W. 1995. Enzymatic evidence for a complete oxidative pentose phosphate pathway in chloroplasts and an incomplete pathway in the cytosol of spinach leaves. Plant Physiol. 108: 609-614.  https://doi.org/10.1104/pp.108.2.609
  15. Xia W, Wang Z, Wang Q, Han J, Zhao C, Hong Y, et al. 2009. Roles of NAD(+) / NADH and NADP(+) / NADPH in cell death. Curr. Pharm. Des. 15: 12-19.  https://doi.org/10.2174/138161209787185832
  16. Park SH, Kim HU, Kim TY, Park JS, Kim SS, Lee SY. 2014. Metabolic engineering of Corynebacterium glutamicum for L-arginine production. Nat. Commun. 5: 4618. 
  17. Chen YY, Ko TP, Chen WH, Lo LP, Lin CH, Wang AH. 2010. Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: implications for enzyme mechanism. J. Struct. Biol. 169: 25-35.  https://doi.org/10.1016/j.jsb.2009.08.006
  18. Lin R, Elf S, Shan C, Kang HB, Ji Q, Zhou L, et al. 2015. 6-phosphogluconate dehydrogenase links oxidative PPP, lipogenesis and tumour growth by inhibiting LKB1-AMPK signalling. Nat. Cell Biol. 17: 1484-1496.  https://doi.org/10.1038/ncb3255
  19. Ruda GF, Alibu VP, Mitsos C, Bidet O, Kaiser M, Brun R, et al. 2007. Synthesis and biological evaluation of phosphate prodrugs of 4-phospho-D-erythronohydroxamic acid, an inhibitor of 6-phosphogluconate dehydrogenase. ChemMedChem. 2: 1169-1180.  https://doi.org/10.1002/cmdc.200700040
  20. Hanau S, Rinaldi E, Dallocchio F, Gilbert IH, Dardonville C, Adams MJ, et al. 2004. 6-phosphogluconate dehydrogenase: a target for drugs in African trypanosomes. Curr. Med. Chem. 11: 2639-2650.  https://doi.org/10.2174/0929867043364441
  21. Park S-Y, Ha S-C, Kim Y-G. 2017. The protein crystallography beamlines at the pohang light source II. Biodesign. 5: 30-34. 
  22. Otwinowski Z, Minor W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307-326.  https://doi.org/10.1016/S0076-6879(97)76066-X
  23. Matthews BW. 1968. Solvent content of protein crystals. J. Mol. Biol. 33: 491-497.  https://doi.org/10.1016/0022-2836(68)90205-2
  24. Collaborative Computational Project N. 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50: 760-763.  https://doi.org/10.1107/S0907444994003112
  25. Vagin A, Teplyakov A. 2010. Molecular replacement with MOLREP. Acta Crystallogr. D Biol. Crystallogr. 66: 22-25.  https://doi.org/10.1107/S0907444909042589
  26. Emsley P, Cowtan K. 2004. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol. Crystallogr. 60: 2126-2132.  https://doi.org/10.1107/S0907444904019158
  27. Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, et al. 2011. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67: 355-367.  https://doi.org/10.1107/S0907444911001314
  28. Murshudov GN, Vagin AA, Dodson EJ. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol Crystallogr. 53: 240-255.  https://doi.org/10.1107/S0907444996012255
  29. Sievers F, Higgins DG. 2014. Clustal omega. Curr. Protoc. Bioinformatics 48: 3 13 11-13 13 16.  https://doi.org/10.1002/0471250953.bi0313s48
  30. Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Res. 14: 1188-1190.  https://doi.org/10.1101/gr.849004
  31. Trott O, Olson AJ. 2010. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31: 455-461.  https://doi.org/10.1002/jcc.21334
  32. Cameron S, Martini VP, Iulek J, Hunter WN. 2009. Geobacillus stearothermophilus 6-phosphogluconate dehydrogenase complexed with 6-phosphogluconate. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65: 450-454.  https://doi.org/10.1107/S1744309109012767
  33. Rippa M, Giovannini PP, Barrett MP, Dallocchio F, Hanau S. 1998. 6-Phosphogluconate dehydrogenase: the mechanism of action investigated by a comparison of the enzyme from different species. Biochim. Biophys. Acta. 1429: 83-92.  https://doi.org/10.1016/S0167-4838(98)00222-2
  34. Sundaramoorthy R, Iulek J, Barrett MP, Bidet O, Ruda GF, Gilbert IH, et al. 2007. Crystal structures of a bacterial 6-phosphogluconate dehydrogenase reveal aspects of specificity, mechanism and mode of inhibition by analogues of high-energy reaction intermediates. FEBS J. 274: 275-286.  https://doi.org/10.1111/j.1742-4658.2006.05585.x
  35. Adams MJ, Ellis GH, Gover S, Naylor CE, Phillips C. 1994. Crystallographic study of coenzyme, coenzyme analog and substrate-Binding in 6-phosphogluconate dehydrogenase - implications for Nadp specificity and the enzyme mechanism (Vol. 2, Pg 651, 1994). Structure 2: 784-784.  https://doi.org/10.1016/S0969-2126(00)00066-6
  36. Lei Z, Chooback L, Cook PF. 1999. Lysine 183 is the general base in the 6-phosphogluconate dehydrogenase-catalyzed reaction. Biochemistry 38: 11231-11238.  https://doi.org/10.1021/bi990433i
  37. Li L, Dworkowski FSN, Cook PF. 2006. Importance in catalysis of the 6-phosphate-binding site of 6-phosphogluconate in sheep liver 6-phosphogluconate dehydrogenase. J. Biol. Chem. 281: 25568-25576.  https://doi.org/10.1074/jbc.M601154200
  38. Lou D, Wang B, Tan J, Zhu L, Cen X, Ji Q, et al. 2016. The three-dimensional structure of Clostridium absonum 7alpha-hydroxysteroid dehydrogenase: new insights into the conserved arginines for NADP(H) recognition. Sci. Rep. 6: 22885. 
  39. Dambe TR, Kuhn AM, Brossette T, Giffhorn F, Scheidig AJ. 2006. Crystal structure of NADP(H)-dependent 1,5-anhydro-D-fructose reductase from Sinorhizobium morelense at 2.2 A resolution: construction of a NADH-accepting mutant and its application in rare sugar synthesis. Biochemistry 45: 10030-10042.  https://doi.org/10.1021/bi052589q
  40. Kitatani T, Nakamura Y, Wada K, Kinoshita T, Tamoi M, Shigeoka S, et al. 2006. Structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942 complexed with NADP. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62: 315-319.  https://doi.org/10.1107/S1744309106007378
  41. Haeussler K, Fritz-Wolf K, Reichmann M, Rahlfs S, Becker K. 2018. Characterization of Plasmodium falciparum 6-phosphogluconate dehydrogenase as an antimalarial drug target. J. Mol. Biol. 430: 4049-4067.  https://doi.org/10.1016/j.jmb.2018.07.030
  42. Hua YH, Wu CY, Sargsyan K, Lim C. 2014. Sequence-motif detection of NAD(P)-binding proteins: discovery of a unique antibacterial drug target. Sci. Rep. 4: 6471.