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6-phosphogluconate dehydrogenase (6PGDH) participates in pentose phosphate pathway of glucose metabolism by catalyzing oxidative decarboxylation of 6-phsophogluconate (6PG) and its absence has been lethal for several eukaryotes. Despite being a validated drug target in many organisms like Plasmodium, the enzyme has not been explored in leishmanial parasites. In the present study, 6PGDH of Leishmania donovani (Ld6PGDH) is cloned and purified followed by its characterization using biochemical and structural approaches. Ld6PGDH lacks the glycine-serine-rich sequence at its C-terminal that is present in other eukaryotes including humans. Leishmanial 6PGDH possesses more affinity for substrate (6PG) and cofactor (NADP) in comparison to that of human. The enzymatic activity is inhibited by gentamicin and cefuroxime through competitive mode with functioning more potently towards leishmanial 6PGDH than its human counterpart. CD analysis has shown higher α-helical content in the secondary structure of Ld6PGDH, while fluorescence studies revealed that tryptophan residues are not completely accessible to solvent environment. The three-dimensional structure was generated through homology modelling and docked with substrate and cofactor. The docking studies demonstrated two separate binding pockets for 6PG and NADP with higher affinity for the cofactor binding, and Asn105 is interacting with substrate as well as the cofactor. Additionally, MD simulation has shown complexes of Ld6PGDH with 6PG and NADP to be more stable than its apo form. Altogether, the present study might provide the foundation to investigate this enzyme as potential target against leishmaniasis. KEY POINTS: • Ld6PGDH enzymatic activity is competitively inhibited by gentamicin and cefuroxime. • It displays more helical contents and all structural characteristics of 6PGDH family. • Interaction studies demonstrate higher affinity of cofactor than substrate for Ld6PGDH.

Titel:	Biochemical and structural insights into 6-phosphogluconate dehydrogenase from Leishmania donovani.
Autor/in / Beteiligte Person:	Jakkula, P ; Narsimulu, B ; Qureshi, IA
Link:	Zum Volltext
Zeitschrift:	Applied microbiology and biotechnology, Jg. 105 (2021-07-01), Heft 13, S. 5471-5489
Veröffentlichung:	Berlin ; New York : Springer International, c1984-, 2021
Medientyp:	academicJournal
ISSN:	1432-0614 (electronic)
DOI:	10.1007/s00253-021-11434-4
Schlagwort:	Humans Kinetics Pentose Phosphate Pathway Protein Structure, Secondary Leishmania donovani metabolism Phosphogluconate Dehydrogenase genetics
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Publication Type: Journal Article Language: English [Appl Microbiol Biotechnol] 2021 Jul; Vol. 105 (13), pp. 5471-5489. <i>Date of Electronic Publication: </i>2021 Jul 12. MeSH Terms: Leishmania donovani* / metabolism ; Phosphogluconate Dehydrogenase* / genetics ; Humans ; Kinetics ; Pentose Phosphate Pathway ; Protein Structure, Secondary References: Adams MJ, Ellis GH, Gover S, Naylor CE, Phillips C (1994) Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism. Structure 2:651–668. https://doi.org/10.1016/s0969-2126(00)00066-6. (PMID: 10.1016/s0969-2126(00)00066-67922042) ; Adem S, Ciftci M (2016) Purification and biochemical characterization of glucose 6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase and glutathione reductase from rat lung and inhibition effects of some antibiotics. J Enzyme Inhib Med Chem 31:1342–1348. https://doi.org/10.3109/14756366.2015.1132711. (PMID: 10.3109/14756366.2015.113271126758606) ; Akyüz M, Erat M, Ciftçi M, Gümüştekin K, Bakan N (2004) Effects of some antibiotics on human erythrocyte 6-phosphogluconate dehydrogenase: an in vitro and in vivo study. J Enzyme Inhib Med Chem 19:361–365. https://doi.org/10.1080/14756360409162451. (PMID: 10.1080/1475636040916245115558954) ; Allmann S, Morand P, Ebikeme C, Gales L, Biran M, Hubert J, Brennand A, Mazet M, Franconi JM, Michels PA, Portais JC, Boshart M, Bringaud F (2013) Cytosolic NADPH homeostasis in glucose-starved procyclic Trypanosoma brucei relies on malic enzyme and the pentose phosphate pathway fed by gluconeogenic flux. J Biol Chem 288:18494–18505. https://doi.org/10.1074/jbc.M113.462978. (PMID: 10.1074/jbc.M113.462978236654703689991) ; Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM (2008) Metal ions in biological catalysis: from enzyme databases to general principles. J Biol Inorg Chem 13:1205–1218. https://doi.org/10.1007/s00775-008-0404-5. (PMID: 10.1007/s00775-008-0404-518604568) ; Are S, Gatreddi S, Jakkula P, Qureshi IA (2020) Structural attributes and substrate specificity of pyridoxal kinase from Leishmania donovani. Int J Biol Macromol 152:812–827. https://doi.org/10.1016/j.ijbiomac.2020.02.257. (PMID: 10.1016/j.ijbiomac.2020.02.25732105687) ; Barrett MP (1997) The pentose phosphate pathway and parasitic protozoa. Parasitol Today 13:11–16. https://doi.org/10.1016/s0169-4758(96)10075-2. (PMID: 10.1016/s0169-4758(96)10075-215275160) ; Bhat SY, Jagruthi P, Srinivas A, Arifuddin M, Qureshi IA (2020) Synthesis and characterization of quinoline-carbaldehyde derivatives as novel inhibitors for leishmanial methionine aminopeptidase 1. Eur J Med Chem 186:111860. https://doi.org/10.1016/j.ejmech.2019.111860. (PMID: 10.1016/j.ejmech.2019.11186031759728) ; Braus GH (1991) Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway. Microbiol Rev 55:349–370. (PMID: 10.1128/mr.55.3.349-370.1991) ; Cabral LIL, Pomel S, Cojean S, Amado PSM, Loiseau PM, Cristiano MLS (2020) Synthesis and antileishmanial activity of 1,2,4,5-Tetraoxanes against Leishmania donovani. Molecules 25:465. https://doi.org/10.3390/molecules25030465. (PMID: 10.3390/molecules250304657038143) ; 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. (PMID: 10.1107/S1744309109012767194073742675582) ; 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. (PMID: 10.1016/j.jsb.2009.08.00619686854) ; Chen H, Zhu Z, Huang R, Zhang YP (2016) Coenzyme engineering of a hyper thermophilic 6-phosphogluconate dehydrogenase from NADP + to NAD + with its application to biobatteries. Sci Rep 6:36311. https://doi.org/10.1038/srep36311. (PMID: 10.1038/srep36311278050555090862) ; Corpas FJ, García-Salguero L, Barroso JB, Aranda F, Lupiáñez JA (1995) Kinetic properties of hexose-monophosphate dehydrogenases. II. Isolation and partial purification of 6-phosphogluconate dehydrogenase from rat liver and kidney cortex. Mol Cell Biochem 144:97–104. https://doi.org/10.1007/BF00944387. (PMID: 10.1007/BF009443877623792) ; Cronín CN, Nolan DP, Voorheis HP (1989) The enzymes of the classical pentose phosphate pathway display differential activities in procyclic and bloodstream forms of Trypanosoma brucei. FEBS Lett 244:26–30. https://doi.org/10.1016/0014-5793(89)81154-8. (PMID: 10.1016/0014-5793(89)81154-82924907) ; Dyson JE, D’Orazio RE, Hanson WH (1973) Sheep liver 6-phosphogluconate dehydrogenase: isolation procedure and effect of pH, ionic strength, and metal ions on the kinetic parameters. Arch Biochem Biophys 154:623–635. https://doi.org/10.1016/0003-9861(73)90017-9. (PMID: 10.1016/0003-9861(73)90017-94691505) ; Esteve MI, Cazzulo JJ (2004) The 6-phosphogluconate dehydrogenase from Trypanosoma cruzi: the absence of two inter-subunit salt bridges as a reason for enzyme instability. Mol Biochem Parasitol 133:197–207. https://doi.org/10.1016/j.molbiopara.2003.10.007. (PMID: 10.1016/j.molbiopara.2003.10.00714698432) ; Gatreddi S, Are S, Qureshi IA (2018) Ribokinase from Leishmania donovani: purification, characterization and X-ray crystallographic analysis. Acta Crystallogr F Struct Biol Commun 74:99–104. https://doi.org/10.1107/S2053230X18000109. (PMID: 10.1107/S2053230X18000109294003195947680) ; González D, Pérez JL, Serrano ML, Igoillo-Esteve M, Cazzulo JJ, Barrett MP, Bubis J, Mendoza-León A (2010) The 6-phosphogluconate dehydrogenase of Leishmania (Leishmania) mexicana: gene characterization and protein structure prediction. J Mol Microbiol Biotechnol 19:213–223. https://doi.org/10.1159/000320697. (PMID: 10.1159/00032069721160204) ; 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. (PMID: 10.1016/j.jmb.2018.07.03030098336) ; Hanau S, Rippa M, Bertelli M, Dallocchio F, Barrett MP (1996) 6-Phosphogluconate dehydrogenase from Trypanosoma brucei. Kinetic analysis and inhibition by trypanocidal drugs. Eur J Biochem 240:592–599. https://doi.org/10.1111/j.1432-1033.1996.0592h.x. (PMID: 10.1111/j.1432-1033.1996.0592h.x8856059) ; Hanau S, Rinaldi E, Dallocchio F, Gilbert IH, Dardonville C, Adams MJ, Gover S, Barrett MP (2004) 6-phosphogluconate dehydrogenase: a target for drugs in African trypanosomes. Curr Med Chem 11:2639–2650. https://doi.org/10.2174/0929867043364441. (PMID: 10.2174/092986704336444115544466) ; Heise N, Opperdoes FR (1999) Purification, localisation and characterisation of glucose-6-phosphate dehydrogenase of Trypanosoma brucei. Mol Biochem Parasitol 99:21–32. https://doi.org/10.1016/s0166-6851(98)00176-5. (PMID: 10.1016/s0166-6851(98)00176-510215021) ; Holzmuller P, Bras-Gonçalves R, Lemesre JL (2006) Phenotypical characteristics, biochemical pathways, molecular targets and putative role of nitric oxide-mediated programmed cell death in Leishmania. Parasitology 132(Suppl):S19–S32. https://doi.org/10.1017/S0031182006000837. (PMID: 10.1017/S003118200600083717018162) ; Hughes MB, Lucchesi JC (1977) Genetic rescue of a lethal “null” activity allele of 6-phosphogluconate dehydrogenase in Drosophila melanogaster. Science 196:1114–1115. https://doi.org/10.1126/science.404711. (PMID: 10.1126/science.404711404711) ; Jakkula P, Qureshi R, Iqbal A, Sagurthi SR, Qureshi IA (2018) Leishmania donovani PP2C: kinetics, structural attributes and in vitro immune response. Mol Biochem Parasitol 223:37–49. https://doi.org/10.1016/j.molbiopara.2018.06.005. ; Kerkhoven EJ, Achcar F, Alibu VP, Burchmore RJ, Gilbert IH, Trybiło M, Driessen NN, Gilbert D, Breitling R, Bakker BM, Barrett MP (2013) Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei. PLoS Comput Biol 9:e1003371. https://doi.org/10.1371/journal.pcbi.1003371. (PMID: 10.1371/journal.pcbi.1003371243397663854711) ; Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096. (PMID: 10.1093/molbev/msy09659675535967553) ; Kwolek-Mirek M, Maslanka R, Molon M (2018) Disorders in NADPH generation via pentose phosphate pathway influence the reproductive potential of the Saccharomyces cerevisiae yeast due to changes in redox status. J Cell Biochem 120:8521–8533. https://doi.org/10.1002/jcb.28140. (PMID: 10.1002/jcb.28140) ; Lam HM, Winkler ME (1990) Metabolic relationships between pyridoxine (vitamin B6) and serine biosynthesis in Escherichia coli K-12. J Bacteriol 172:6518–6528. https://doi.org/10.1128/jb.172.11.6518-6528.1990. (PMID: 10.1128/jb.172.11.6518-6528.19902121717526841) ; Li L, Cook PF (2006) The 2 ' -phosphate of NADP is responsible for proper orientation of the nicotinamide ring in the oxidative decarboxylation reaction catalyzed by sheep liver 6-phosphogluconate dehydrogenase. J Biol Chem 281:36803–36810. https://doi.org/10.1074/jbc.M604609200. (PMID: 10.1074/jbc.M60460920016959777) ; Lobo Z, Maitra PK (1982) Pentose phosphate pathway mutants of yeast. Mol Gen Genet 185(2):367–368. https://doi.org/10.1007/BF00330815. (PMID: 10.1007/BF003308157045591) ; Maugeri DA, Cazzulo JJ, Burchmore RJ, Barrett MP, Ogbunude PO (2003) Pentose phosphate metabolism in Leishmania mexicana. Mol Biochem Parasitol 130:117–125. https://doi.org/10.1016/s0166-6851(03)00173-7. (PMID: 10.1016/s0166-6851(03)00173-712946848) ; Moritz B, Striegel K, De Graaf AA, Sahm H (2000) Kinetic properties of the glucose-6-phosphate and 6-phosphogluconate dehydrogenases from Corynebacterium glutamicum and their application for predicting pentose phosphate pathway flux in vivo. Eur J Biochem 267:3442–3452. https://doi.org/10.1046/j.1432-1327.2000.01354.x. (PMID: 10.1046/j.1432-1327.2000.01354.x10848959) ; Nettey H, Allotey-Babington GL, Nguessan BB, Afrane B, Tagoe M, Ababio A, Botchway P, Darko Y, Sasu C, Nyarko A (2016) Screening of anti-infectives against Leishmania donovani. Adv Microbiol 6:13–22. https://doi.org/10.4236/aim.2016.61002. (PMID: 10.4236/aim.2016.61002) ; Panigrahi GC, Qureshi R, Jakkula P, Kumar KA, Khan N, Qureshi IA (2020) Leishmanial aspartyl-tRNA synthetase: biochemical, biophysical and structural insights. Int J Biol Macromol 165:2869–2885. https://doi.org/10.1016/j.ijbiomac.2020.10.140. ; Pearse BM, Harris JJ (1973) 6-Phosphogluconate dehydrogenase from Bacillus stearothermophilus. FEBS Lett 38:49–52. https://doi.org/10.1016/0014-5793(73)80510-1. (PMID: 10.1016/0014-5793(73)80510-14772689) ; Pearse BM, Rosemeyer MA (1974) Human 6-phosphogluconate dehydrogenase. Purification of the erythrocyte enzyme and the influence of ions and NADPH on its activity. Eur J Biochem 42:213–223. https://doi.org/10.1111/j.1432-1033.1974.tb03331.x. (PMID: 10.1111/j.1432-1033.1974.tb03331.x4151477) ; Phillips C, Dohnalek J, Gover S, Barrett MP, Adams MJ (1998) A 2.8 Å resolution structure of 6-phosphogluconate dehydrogenase from the protozoan parasite Trypanosoma brucei: comparison with the sheep enzyme accounts for differences in activity with coenzyme and substrate analogues. J Mol Biol 282:667–681. https://doi.org/10.1006/jmbi.1998.2059. (PMID: 10.1006/jmbi.1998.20599737929) ; Ponte-Sucre A, Gamarro F, Dujardin JC, Barrett MP, López-Vélez R, García-Hernández R, Pountain AW, Mwenechanya R, Papadopoulou B (2017) Drug resistance and treatment failure in leishmaniasis: a 21st century challenge. PLoS Negl Trop Dis 11:e0006052. https://doi.org/10.1371/journal.pntd.0006052. (PMID: 10.1371/journal.pntd.0006052292407655730103) ; Qureshi R, Jakkula P, Sagurthi SR, Qureshi IA (2019) Protein phosphatase 1 of Leishmania donovani exhibits conserved catalytic residues and pro-inflammatory response. Biochem Biophys Res Commun 516:770–776. https://doi.org/10.1016/j.bbrc.2019.06.085. ; Rendina AR, Hermes JD, Cleland WW (1984) Use of multiple isotope effects to study the mechanism of 6-phosphogluconate dehydrogenase. Biochemistry 23:6257–6262. https://doi.org/10.1021/bi00320a056. (PMID: 10.1021/bi00320a0566395897) ; Rocco AG, Mollica L, Ricchiuto P, Baptista AM, Gianazza E, Eberini I (2008) Characterization of the protein unfolding processes induced by urea and temperature. Biophys J 94:2241–2251. https://doi.org/10.1529/biophysj.107.115535. (PMID: 10.1529/biophysj.107.11553518065481) ; Rosemeyer MA (1987) The biochemistry of glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase and glutathione reductase. Cell Biochem Funct 5:79–95. https://doi.org/10.1002/cbf.290050202. (PMID: 10.1002/cbf.2900502023581436) ; Ruda GF, Wong PE, Alibu VP, Norval S, Read KD, Barrett MP, Gilbert IH (2010) Aryl phosphoramidates of 5-phospho erythronohydroxamic acid, a new class of potent trypanocidal compounds. J Med Chem 53:6071–6078. https://doi.org/10.1021/jm1004754. (PMID: 10.1021/jm1004754206663712923871) ; Sundaramoorthy R, Iulek J, Barrett MP, Bidet O, Ruda GF, Gilbert IH, Hunter WN (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. (PMID: 10.1111/j.1742-4658.2006.05585.x172221876927799) ; Tetaud E, Hanau S, Wells JM, Le Page RW, Adams MJ, Arkison S, Barrett MP (1999) 6-Phosphogluconate dehydrogenase from Lactococcus lactis: a role for arginine residues in binding substrate and coenzyme. Biochem J 338:55–60. (PMID: 10.1042/bj3380055) ; 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. (PMID: 10.1002/jcc.21334194995763041641) ; Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718. https://doi.org/10.1002/jcc.20291. (PMID: 10.1002/jcc.20291) ; Villet RH, Dalziel K (1972) Studies of 6-phosphogluconate dehydrogenase from sheep liver. 2. Kinetics of the oxidative-decarboxylation reaction, coenzyme binding and analyses for metals. Eur J Biochem 27:251–258. https://doi.org/10.1111/j.1432-1033.1972.tb01834.x. (PMID: 10.1111/j.1432-1033.1972.tb01834.x4403245) ; Wang Y, Zhang YH (2009) Overexpression and simple purification of the Thermotoga maritima 6-phosphogluconate dehydrogenase in Escherichia coli and its application for NADPH regeneration. Microb Cell Fact 8:30. https://doi.org/10.1186/1475-2859-8-30. ; Webb B, Sali A (2017) Protein structure modeling with MODELLER. Methods Mol Biol 1654:39–54. https://doi.org/10.1007/978-1-4939-7231-9_4. (PMID: 10.1007/978-1-4939-7231-9_428986782) ; Wood T (1986) Distribution of the pentose phosphate pathway in living organisms. Cell Biochem Funct 4(4):235–240. https://doi.org/10.1002/cbf.290040402. (PMID: 10.1002/cbf.2900404023539385) ; Yang X, Peng X, Huang J (2018) Inhibiting 6-phosphogluconate dehydrogenase selectively targets breast cancer through AMPK activation. Clin Transl Oncol 20:1145–1152. https://doi.org/10.1007/s12094-018-1833-4. (PMID: 10.1007/s12094-018-1833-429340974) ; Yousuf M, Mukherjee D, Dey S, Pal C, Adhikari S (2016) Antileishmanial ferrocenylquinoline derivatives: Synthesis and biological evaluation against Leishmania donovani. Eur J Med Chem 124:468–479. https://doi.org/10.1016/j.ejmech.2016.08.049. (PMID: 10.1016/j.ejmech.2016.08.04927598235) ; Zhang R, Shang L, Jin H, Ma C, Wu Y, Liu Q, Xia Z, Wei F, Zhu XQ, Gao H (2010) In vitro and in vivo antileishmanial efficacy of nitazoxanide against Leishmania donovani. Parasitol Res 107:475–479. https://doi.org/10.1007/s00436-010-1906-y. (PMID: 10.1007/s00436-010-1906-y20495931) ; Zhao G, Winkler ME (1994) An Escherichia coli K-12 tktAtktB mutant deficient in transketolase activity requires pyridoxine (vitamin B6) as well as the aromatic amino acids and vitamins for growth. J Bacteriol 176:6134–6138. https://doi.org/10.1128/jb.176.19.6134-6138.1994. (PMID: 10.1128/jb.176.19.6134-6138.19947928977196835) Grant Information: EMR/2016/007746 Science and Engineering Research Board, India Contributed Indexing: Keywords: 6-phosphogluconate dehydrogenase; Antibiotics; Enzyme kinetics; Leishmania donovani; Pentose phosphate pathway; Structural insights Substance Nomenclature: EC 1.1.1.43 (Phosphogluconate Dehydrogenase) Entry Date(s): Date Created: 20210712 Date Completed: 20210720 Latest Revision: 20210720 Update Code: 20240513

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Biochemical and structural insights into 6-phosphogluconate dehydrogenase from Leishmania donovani.