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Structure-Function Analysis Glyceraldehyde-3-Phosphate Dehydrogenase Homologue GapB in Staphylococcus aureus

Year 2020, Volume: 4 Issue: 2, 95 - 104, 01.12.2020

Samah Almehmadi

https://doi.org/10.47947/ijnls.817092
Cited By: 1

Abstract

Glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) is the most studied reference protein that catalysis the inter-conversion reaction of glyceraldehyde-3-phosphate into 1,3-diphosphoglycerate using NAD+ as coenzyme. GAPDH is also recognized as an important player in DNA repair mechanisms, autophagic and apoptotic cell deaths and posttranslational modifications. Staphylococcus aureus is Gram positive commensal pathogenic bacteria. In the genome of S. aureus, GapA was assumed to be a glycolytic GAPDH and GapB was assumed to be a gluconeogenic GAPDH. The crystal structure of GapA has already been in preceding studies. However, to my knowledge, no structural studies on the gapB homologue is available in the literature. The main aims of this study were to analyze physicochemical properties and generate a homology model structure of GAPDH homologue GapB in S. aureus. This was carried out by Protparam tool, Phyre2 homology modeling server and PSIPRED secondary structure analysis tool. ProtParam predicted that GapB is a stable and liposoluble protein. Homology modeling studies revealed that each subunit of GapB was made up by two domains: the NAD coenzyme binding-domain and the catalytic domain. The NAD binding domain was shown to contain a Rossman fold. On the other hand, the catalytic domain was made up by a mixture of eight strands of beta sheet and seven alfa helices. PSIPRED analysis revealed that the secondary structure of the GapB contains α-helices (29.91%), extended strands (24.63%) and random coil (45.45%).

Keywords

Glyceraldehyde‐3‐phosphate dehydrogenase Staphylococcus aureus GapB Phyre2 PSIPRED

Supporting Institution

Umm Al-Qura University, Saudi Arabia

References

  • Aykutoglu, G., Tartik, M., Darendelioglu, E., Ayna, A., & Baydas, G. (2020). Melatonin and vitamin E alleviate homocysteine‐induced oxidative injury and apoptosis in endothelial cells. Molecular Biology Reports, 47(7), 5285–5293. https://doi:10.1007/s11033-020-05607-z
  • Ayna, A. (2016). Glyceraldehyde-3-phosphate Dehydrogenase and fructose-1, 6-bisphosphatase of the enteric pathogens C. jejuni and H. pylori. PhD. Thesis, Univeristy of Leciester, United Kingdom.
  • Ayna, A., Özbolat, S. N., & Darendelioglu, E. (2020). Quercetin, chrysin, caffeic acid and ferulic acid ameliorate cyclophosphamide-induced toxicities in SH-SY5Y cells. Molecular Biology Reports, 47, 8535–8543. https://doi:10.1007/s11033-020-05896-4
  • Bayindir, S., Temel, Y., Ayna, A., & Ciftci, M. (2018). The synthesis of N‐benzoylindoles as inhibitors of rat erythrocyte glucose‐6‐phosphate dehydrogenase and 6‐phosphogluconate dehydrogenase. Journal of Biochemical and Molecular Toxicology, 32(9), e22193. https://doi:10.1002/jbt.22193
  • Bayindir, S., Ayna, A., Temel, Y., & Ciftci, M. (2018). The synthesis of new oxindoles as analogs of natural product 3,3-bis(indolyl)oxindole and in vitro evaluation of the enzyme activity of G6PD and 6PGD. Turkish Journal of Chemistry, 42(2), 332–345. https://doi:10.3906/kim-1706-51
  • Becker, K., Schaumburg, F., Fegeler, C., Friedrich, A. W., & Kock, R. (2017). Staphylococcus aureus from the German general population is highly diverse. International Journal of Medical Microbiology, 307(1), 21–27. https://doi:10.1016/j.ijmm.2016.11.007
  • Cowan-Jacob, S. W., Kaufmann, M., Anselmo, A. N., Stark, W., & Grütter, M. G. (2003). Structure of rabbit-muscle glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallographica Section D: Biological Crystallography, 59(12), 2218–2227. https://doi:10.1107/S0907444903020493
  • Delgado, M. L., Gil, M. L., & Gozalbo, D. (2003). Candida albicans TDH3 gene promotes secretion of internal invertase when expressed in Saccharomyces cerevisiae as a glyceraldehyde-3-phosphate dehydrogenase-invertase fusion protein. Yeast, 20(8), 713–722. https://doi:10.1002/yea.993
  • Falini, G., Fermani, S., Ripamonti, A., Sabatino, P., Sparla, F., Pupillo, P., & Trost, P. (2003). Dual coenzyme specificity of photosynthetic glyceraldehyde-3-phosphate dehydrogenase interpreted by the crystal structure of A4 isoform complexed with NAD. Biochemistry, 42(16), 4631–4639. https://doi:10.1021/bi0272149
  • Fillinger, S., Boschi-Muller, S., Azza, S., Dervyn, E., Branlant, G., & Aymerich, S. (2000), Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium. Journal of Biological Chemistry, 275(19), 14031–14037. https://doi:10.1074/jbc.275.19.14031
  • Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein Identification and Analysis Tools on the Expasy Server. In the proteomics protocols handbook, Humana Press., 571–607. https://doi:10.1385/1-59259-890-0:571
  • Gimpel, M., & Brantl, S. (2016). Dual-function sRNA encoded peptide SR1P modulates moonlighting activity of B. subtilis GapA. RNA Biology, 13(9), 916–926.
  • Gopalakrishnan, K., Sowmiya, G., Sheik, S. S., & Sekar, K. (2007). Ramachandran plot on the web (2.0). Protein and Peptide Letters, 14(7), 669–671. https://doi:10.2174/092986607781483912
  • Hidalgo, E., Limon, A., & Aguilar, J. (1996), A second Escherichia coli gene with similarity to gapA. Microbiologia, 12(1), 99–106.
  • Jenkins, J. L., & Tanner, J. J. (2006). High-resolution structure of human D-glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallographica Section D: Biological Crystallography, 62(3), 290–301. https://doi:10.1107/S0907444905042289
  • Jenul, C., & Horswill, A. R. (2019). Regulation of Staphylococcus aureus virulence. Microbiol Spectrum, 6, 669–686. https://doi:10.1128/microbiolspec.GPP3-0031-2018
  • Jones, D. T. (1999). Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology, 292(2), 195–202. https://doi:10.1006/jmbi.1999.3091
  • Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols, 10(6), 845–858. https://doi:10.1038/nprot.2015.053
  • Kitatani, T., Nakamura, Y., Wada, K., Kinoshita, T., Tamoi, M., Shigeoka, S., & Tada, T. (2006). Structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942 complexed with NADP. Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 62(4), 315–319. https://doi:10.1107/S1744309106007378
  • Kucukler, S., Darendelioglu, E., Caglayan, C., Ayna, A., Yıldırım, S., & Kandemir, F. M. (2020). Zingerone attenuates vancomycin-induced hepatotoxicity in rats through regulation of oxidative stress, inflammation and apoptosis. Life Sciences, 259, 118382. https://doi:10.1016/j.lfs.2020.118382
  • Lee, A. S., de Lencastre, H., Garau, J., Kluytmans, J., Malhotra-Kumar, S., Peschel, A., & Harbarth, S. (2018). Methicillin-resistant Staphylococcus aureus. Nature Reviews Disease Primers, 4(1), 1–23.
  • Mukherjee, S., Dutta, D., Saha, B., & Das, A. K. (2010). Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 1 from methicillin-resistant Staphylococcus aureus MRSA252 provides novel insights into substrate binding and catalytic mechanism. Journal of Molecular Biology, 401(5), 949–968.
  • Nagarajan, R., Sankar, S., & Ponnuraj, K. (2019). Crystal structure of GAPDH of Streptococcus agalactiae and characterization of its interaction with extracellular matrix molecules. Microbial Pathogenesis, 127, 359–367.
  • Nicholls, C., Li, H., & Liu, J. P. (2012). GAPDH: a common enzyme with uncommon functions. Clinical and Experimental Pharmacology and Physiology, 39(8), 674–679.
  • Oesper, P. (1954). The mechanism of action of glyceraldehyde-3-phosphate dehydrogenase. Journal of Biological Chemistry, 207(1), 421–430.
  • Özbolat, S. N., & Ayna, A. (2020). Chrysin suppresses HT-29 cell death ınduced by diclofenac through apoptosis and oxidative damage. Nutrition and Cancer, in press. https://doi:10.1080/01635581.2020.1801775
  • Pancholi, V., & Fischetti, V. A. (1992), A major surface protein on group a streptococci is a glyceraldehyde-3-phosphate-dehydrogenase with multiple binding activity. Journal of Experimental Medicine, 176(2), 415–426. https://doi:10.1084/jem.176.2.415
  • Park, J. B., Park, H., Son, J., Ha, S. J., & Cho, H. S. (2019). Structural study of monomethyl fumarate-bound human GAPDH. Molecules and Cells, 42(8), 597–603. https://doi:10.14348/molcells.2019.0114
  • Pavão, F., Castilho, M. S., Pupo, M. T., Dias, R. L. A., Correa, A. G., Fernandes, J. B., da Silva, M. F. G. F., Mafezoli, J., Vieira, P. C., & Oliva, G. (2002). Structure of trypanosoma cruzi glycosomal glyceraldehyde‐3‐phosphate dehydrogenase complexed with chalepin, a natural product inhibitor, at 1.95 Å resolution. FEBS Letters, 520(1-3), 13–17. https://doi:10.1016/S0014-5793(02)02700-X
  • Plata, K., Rosato, A. E., & Wegrzyn, G. (2009), Staphylococcus aureus as an infectious agent: overview of biochemistry and molecular genetics of its pathogenicity. Acta Biochimica Polonica, 56(4), 597–612. https://doi:10.18388/abp.2009_2491
  • Seta, F. D., Boschi-Muller, S., Vignais, M. L., & Branlant, G. (1997), Characterization of Escherichia coli strains with gapA and gapB genes deleted. Journal of Bacteriology, 179(16), 5218–5221. https://doi:10.1128/jb.179.16.5218-5221.1997
  • Skarzyński, T., Moody, P. C. E., & Wonacott, A. J. (1987). Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 Å resolution. Journal of Molecular Biology, 193(1), 171–187. https://doi:10.1016/0022-2836(87)90635-8
  • Yusuf, T., Ayna, A., Shafeeq, İ. H., & Ciftci, M. (2020). In vitro effects of some antibiotics on glucose-6-phosphate dehydrogenase from rat (Rattus norvegicus) erythrocyte. Drug and Chemical Toxicology, 43(2), 219–223. https://doi:10.1080/01480545.2018.1481083
  • Tristan, C., Shahani, N., Sedlak, T. W., & Sawa, A. (2011). The diverse functions of GAPDH: views from different subcellular compartments. Cellular Signalling, 23(2), 317–323. https://doi:10.1016/j.cellsig.2010.08.003.
  • van der Oost, J., Schut, G., Kengen, S. M., Hagen, W. R., Thomm, M., & de Vos, W. M. (1998). The Ferredoxin-dependent conversion of glyceraldehyde-3-phosphate in the hyperthermophilic archaeon pyrococcus furiosus represents a novel site of glycolytic regulation. Journal of Biological Chemistry, 273(43), 28149–28154. https://doi:10.1074/jbc.273.43.28149
  • Zhao, G., Pease, A. J., Bharani, N., & Winkler, M. E. (1995), Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5'-phosphate biosynthesis. Journal of Bacteriology, 177(10), 2804–2812. https://doi:10.1128/jb.177.10.2804-2812.1995

Year 2020, Volume: 4 Issue: 2, 95 - 104, 01.12.2020

Samah Almehmadi

https://doi.org/10.47947/ijnls.817092
Cited By: 1

Abstract

References

  • Aykutoglu, G., Tartik, M., Darendelioglu, E., Ayna, A., & Baydas, G. (2020). Melatonin and vitamin E alleviate homocysteine‐induced oxidative injury and apoptosis in endothelial cells. Molecular Biology Reports, 47(7), 5285–5293. https://doi:10.1007/s11033-020-05607-z
  • Ayna, A. (2016). Glyceraldehyde-3-phosphate Dehydrogenase and fructose-1, 6-bisphosphatase of the enteric pathogens C. jejuni and H. pylori. PhD. Thesis, Univeristy of Leciester, United Kingdom.
  • Ayna, A., Özbolat, S. N., & Darendelioglu, E. (2020). Quercetin, chrysin, caffeic acid and ferulic acid ameliorate cyclophosphamide-induced toxicities in SH-SY5Y cells. Molecular Biology Reports, 47, 8535–8543. https://doi:10.1007/s11033-020-05896-4
  • Bayindir, S., Temel, Y., Ayna, A., & Ciftci, M. (2018). The synthesis of N‐benzoylindoles as inhibitors of rat erythrocyte glucose‐6‐phosphate dehydrogenase and 6‐phosphogluconate dehydrogenase. Journal of Biochemical and Molecular Toxicology, 32(9), e22193. https://doi:10.1002/jbt.22193
  • Bayindir, S., Ayna, A., Temel, Y., & Ciftci, M. (2018). The synthesis of new oxindoles as analogs of natural product 3,3-bis(indolyl)oxindole and in vitro evaluation of the enzyme activity of G6PD and 6PGD. Turkish Journal of Chemistry, 42(2), 332–345. https://doi:10.3906/kim-1706-51
  • Becker, K., Schaumburg, F., Fegeler, C., Friedrich, A. W., & Kock, R. (2017). Staphylococcus aureus from the German general population is highly diverse. International Journal of Medical Microbiology, 307(1), 21–27. https://doi:10.1016/j.ijmm.2016.11.007
  • Cowan-Jacob, S. W., Kaufmann, M., Anselmo, A. N., Stark, W., & Grütter, M. G. (2003). Structure of rabbit-muscle glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallographica Section D: Biological Crystallography, 59(12), 2218–2227. https://doi:10.1107/S0907444903020493
  • Delgado, M. L., Gil, M. L., & Gozalbo, D. (2003). Candida albicans TDH3 gene promotes secretion of internal invertase when expressed in Saccharomyces cerevisiae as a glyceraldehyde-3-phosphate dehydrogenase-invertase fusion protein. Yeast, 20(8), 713–722. https://doi:10.1002/yea.993
  • Falini, G., Fermani, S., Ripamonti, A., Sabatino, P., Sparla, F., Pupillo, P., & Trost, P. (2003). Dual coenzyme specificity of photosynthetic glyceraldehyde-3-phosphate dehydrogenase interpreted by the crystal structure of A4 isoform complexed with NAD. Biochemistry, 42(16), 4631–4639. https://doi:10.1021/bi0272149
  • Fillinger, S., Boschi-Muller, S., Azza, S., Dervyn, E., Branlant, G., & Aymerich, S. (2000), Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium. Journal of Biological Chemistry, 275(19), 14031–14037. https://doi:10.1074/jbc.275.19.14031
  • Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein Identification and Analysis Tools on the Expasy Server. In the proteomics protocols handbook, Humana Press., 571–607. https://doi:10.1385/1-59259-890-0:571
  • Gimpel, M., & Brantl, S. (2016). Dual-function sRNA encoded peptide SR1P modulates moonlighting activity of B. subtilis GapA. RNA Biology, 13(9), 916–926.
  • Gopalakrishnan, K., Sowmiya, G., Sheik, S. S., & Sekar, K. (2007). Ramachandran plot on the web (2.0). Protein and Peptide Letters, 14(7), 669–671. https://doi:10.2174/092986607781483912
  • Hidalgo, E., Limon, A., & Aguilar, J. (1996), A second Escherichia coli gene with similarity to gapA. Microbiologia, 12(1), 99–106.
  • Jenkins, J. L., & Tanner, J. J. (2006). High-resolution structure of human D-glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallographica Section D: Biological Crystallography, 62(3), 290–301. https://doi:10.1107/S0907444905042289
  • Jenul, C., & Horswill, A. R. (2019). Regulation of Staphylococcus aureus virulence. Microbiol Spectrum, 6, 669–686. https://doi:10.1128/microbiolspec.GPP3-0031-2018
  • Jones, D. T. (1999). Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology, 292(2), 195–202. https://doi:10.1006/jmbi.1999.3091
  • Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols, 10(6), 845–858. https://doi:10.1038/nprot.2015.053
  • Kitatani, T., Nakamura, Y., Wada, K., Kinoshita, T., Tamoi, M., Shigeoka, S., & Tada, T. (2006). Structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from Synechococcus PCC7942 complexed with NADP. Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 62(4), 315–319. https://doi:10.1107/S1744309106007378
  • Kucukler, S., Darendelioglu, E., Caglayan, C., Ayna, A., Yıldırım, S., & Kandemir, F. M. (2020). Zingerone attenuates vancomycin-induced hepatotoxicity in rats through regulation of oxidative stress, inflammation and apoptosis. Life Sciences, 259, 118382. https://doi:10.1016/j.lfs.2020.118382
  • Lee, A. S., de Lencastre, H., Garau, J., Kluytmans, J., Malhotra-Kumar, S., Peschel, A., & Harbarth, S. (2018). Methicillin-resistant Staphylococcus aureus. Nature Reviews Disease Primers, 4(1), 1–23.
  • Mukherjee, S., Dutta, D., Saha, B., & Das, A. K. (2010). Crystal structure of glyceraldehyde-3-phosphate dehydrogenase 1 from methicillin-resistant Staphylococcus aureus MRSA252 provides novel insights into substrate binding and catalytic mechanism. Journal of Molecular Biology, 401(5), 949–968.
  • Nagarajan, R., Sankar, S., & Ponnuraj, K. (2019). Crystal structure of GAPDH of Streptococcus agalactiae and characterization of its interaction with extracellular matrix molecules. Microbial Pathogenesis, 127, 359–367.
  • Nicholls, C., Li, H., & Liu, J. P. (2012). GAPDH: a common enzyme with uncommon functions. Clinical and Experimental Pharmacology and Physiology, 39(8), 674–679.
  • Oesper, P. (1954). The mechanism of action of glyceraldehyde-3-phosphate dehydrogenase. Journal of Biological Chemistry, 207(1), 421–430.
  • Özbolat, S. N., & Ayna, A. (2020). Chrysin suppresses HT-29 cell death ınduced by diclofenac through apoptosis and oxidative damage. Nutrition and Cancer, in press. https://doi:10.1080/01635581.2020.1801775
  • Pancholi, V., & Fischetti, V. A. (1992), A major surface protein on group a streptococci is a glyceraldehyde-3-phosphate-dehydrogenase with multiple binding activity. Journal of Experimental Medicine, 176(2), 415–426. https://doi:10.1084/jem.176.2.415
  • Park, J. B., Park, H., Son, J., Ha, S. J., & Cho, H. S. (2019). Structural study of monomethyl fumarate-bound human GAPDH. Molecules and Cells, 42(8), 597–603. https://doi:10.14348/molcells.2019.0114
  • Pavão, F., Castilho, M. S., Pupo, M. T., Dias, R. L. A., Correa, A. G., Fernandes, J. B., da Silva, M. F. G. F., Mafezoli, J., Vieira, P. C., & Oliva, G. (2002). Structure of trypanosoma cruzi glycosomal glyceraldehyde‐3‐phosphate dehydrogenase complexed with chalepin, a natural product inhibitor, at 1.95 Å resolution. FEBS Letters, 520(1-3), 13–17. https://doi:10.1016/S0014-5793(02)02700-X
  • Plata, K., Rosato, A. E., & Wegrzyn, G. (2009), Staphylococcus aureus as an infectious agent: overview of biochemistry and molecular genetics of its pathogenicity. Acta Biochimica Polonica, 56(4), 597–612. https://doi:10.18388/abp.2009_2491
  • Seta, F. D., Boschi-Muller, S., Vignais, M. L., & Branlant, G. (1997), Characterization of Escherichia coli strains with gapA and gapB genes deleted. Journal of Bacteriology, 179(16), 5218–5221. https://doi:10.1128/jb.179.16.5218-5221.1997
  • Skarzyński, T., Moody, P. C. E., & Wonacott, A. J. (1987). Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 Å resolution. Journal of Molecular Biology, 193(1), 171–187. https://doi:10.1016/0022-2836(87)90635-8
  • Yusuf, T., Ayna, A., Shafeeq, İ. H., & Ciftci, M. (2020). In vitro effects of some antibiotics on glucose-6-phosphate dehydrogenase from rat (Rattus norvegicus) erythrocyte. Drug and Chemical Toxicology, 43(2), 219–223. https://doi:10.1080/01480545.2018.1481083
  • Tristan, C., Shahani, N., Sedlak, T. W., & Sawa, A. (2011). The diverse functions of GAPDH: views from different subcellular compartments. Cellular Signalling, 23(2), 317–323. https://doi:10.1016/j.cellsig.2010.08.003.
  • van der Oost, J., Schut, G., Kengen, S. M., Hagen, W. R., Thomm, M., & de Vos, W. M. (1998). The Ferredoxin-dependent conversion of glyceraldehyde-3-phosphate in the hyperthermophilic archaeon pyrococcus furiosus represents a novel site of glycolytic regulation. Journal of Biological Chemistry, 273(43), 28149–28154. https://doi:10.1074/jbc.273.43.28149
  • Zhao, G., Pease, A. J., Bharani, N., & Winkler, M. E. (1995), Biochemical characterization of gapB-encoded erythrose 4-phosphate dehydrogenase of Escherichia coli K-12 and its possible role in pyridoxal 5'-phosphate biosynthesis. Journal of Bacteriology, 177(10), 2804–2812. https://doi:10.1128/jb.177.10.2804-2812.1995
There are 36 citations in total.

Details

Primary Language English
Subjects Structural Biology, Biochemistry and Cell Biology (Other)
Journal Section Article
Authors

Samah Almehmadi 0000-0002-6014-3148

Publication Date December 1, 2020
Submission Date October 27, 2020
Acceptance Date November 12, 2020
Published in Issue Year 2020 Volume: 4 Issue: 2

Cite

APA Almehmadi, S. (2020). Structure-Function Analysis Glyceraldehyde-3-Phosphate Dehydrogenase Homologue GapB in Staphylococcus aureus. International Journal of Nature and Life Sciences, 4(2), 95-104. https://doi.org/10.47947/ijnls.817092

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