Effects of missense R84Q mutation on human Pyrroline-5-carboxylate synthase enzyme properties, an in-silico analysis

Document Type : Original Article


1 Department of Biology, Payame Noor University, Avaj, Iran

2 Department of Biology, Faculty of Science, Lorestan University, Khoramabad, Iran

3 Industrial and Environmental Biotechnology Department, National Institute of Genetic Engineering & Biotechnology (NIGEB), Tehran, Iran

4 Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran

5 Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran


Mammalian ∆-(1)-Pyrroline-5-carboxylate synthase (P5CS) enzyme catalyzes the coupled phosphorylation and reduction-conversion of glutamate to ∆-(1)-pyrroline-5-carboxylate (P5C), a critical step in the proline, ornithine, citrulline and arginine biosynthesis. In plants and mammals, P5CS consists of two separate enzymatic domains: N-terminal γ-glutamyl kinase (γ-GK) and C-terminal γ-glutamyl phosphate reductase (γ–GPR). Hyperammonemia has been reported as a new inborn disorder, with a range of clinical symptoms which is associated with a reduced synthesis of proline, ornithine, citruline and arginine. A missense mutation, R84Q, which alters the conserved residue in γ-GK domain, is responsible for this disorder. In this study using in-silico approaches as a new bioinformatics method, sequence analysis was performed and the tertiary structure of γ-GK domain of human P5CS, which includes the R84Q missense mutation, was predicted and the mutation effects on structural and functional features of P5CS enzyme were analyzed. Our analysis showed that this substitution has an affect on the molecular surface accessibility and total energy of the modeled structure. We conclude that this mutation results in a reduced activity of P5CS enzyme and an impaired synthesis of these amino acids.


  1. Hu, C.A. Lin, W.W. Obie, C., Valle, D., Molecular enzymology of mammalian Delta1-pyrroline-5-carboxylate synthase. Alternative splice donor utilization generates isoforms with different sensitivity to ornithine inhibition.J Biol Chem, 1999,  vol. 274,  pp. 6754-62.
  2. Yoshiba, Y. Kiyosue, T. Katagiri, T. Ueda, H. Mizoguchi, T. Yamaguchi-Shinozaki, K. Wada, K. Harada, Y., Shinozaki, K., Correlation between the induction of a gene for delta 1-pyrroline-5-carboxylate synthetase and the accumulation of proline in Arabidopsis thaliana under osmotic stress.Plant J, 1995,  vol. 7,  pp. 751-60.
  3. Sekine, T. Kawaguchi, A. Hamano, Y., Takagi, H., Desensitization of feedback inhibition of the Saccharomyces cerevisiae gamma-glutamyl kinase enhances proline accumulation and freezing tolerance.Appl. Environ. Microbiol., 2007,  vol. 73,  pp. 4011-9.
  4. Phang, J.M., Yeh, G.C, and Scriver, C.R, Disorders of proline and hydroxyproline metabolism.in Scriver, C.R.,  Beaudet, A.L., sly, W.S. and Valle, D. (eds),The metabolic and molecular bases of inherited disease. McGraw Hill, New York, NY. pp 1125-1146. 1995.
  5. Wang, S.S. Brandriss, M.C., Proline utilization in Saccharomyces cerevisiae: analysis of the cloned PUT1 gene.Mol. Cell. Biol., 1986,  vol. 6,  pp. 2638-45.
  6. Hu, C.A. Delauney, A.J., Verma, D.P., A bifunctional enzyme (delta 1-pyrroline-5-carboxylate synthetase) catalyzes the first two steps in proline biosynthesis in plants.Proc. Natl. Acad. Sci. U. S. A., 1992,  vol. 89,  pp. 9354-8.
  7. Fujita, T. Maggio, A. Garcia-Rios, M. Stauffacher, C. Bressan, R.A., Csonka, L.N., Identification of regions of the tomato gamma-glutamyl kinase that are involved in allosteric regulation by proline.J Biol Chem, 2003,  vol. 278,  pp. 14203-10.
  8. Hong, Z. Lakkineni, K. Zhang, Z., Verma, D.P., Removal of feedback inhibition of delta(1)-pyrroline-5-carboxylate synthetase results in increased proline accumulation and protection of plants from osmotic stress.Plant Physiol, 2000,  vol. 122,  pp. 1129-36.
  9. Baumgartner, M.R. Hu, C.A. Almashanu, S. Steel, G. Obie, C. Aral, B. Rabier, D. Kamoun, P. Saudubray, J.M., Valle, D., Hyperammonemia with reduced ornithine, citrulline, arginine and proline: a new inborn error caused by a mutation in the gene encoding delta(1)-pyrroline-5-carboxylate synthase.Hum Mol Genet, 2000,  vol. 9,  pp. 2853-8.
  10. Kamoun, P. Aral, B., Saudubray, J.M., [A new inherited metabolic disease: delta1-pyrroline 5-carboxylate synthetase deficiency].Bull. Acad. Natl. Med., 1998,  vol. 182,  pp. 131-7; discussion 138-9.
  11. Lodato, R.F. Smith, R.J. Valle, D. Phang, J.M., Aoki, T.T., Regulation of proline biosynthesis: the inhibition of pyrroline-5-carboxylate synthase activity by ornithine.Metabolism, 1981,  vol. 30,  pp. 908-13.
  12. Hu, C.A. Khalil, S. Zhaorigetu, S. Liu, Z. Tyler, M. Wan, G., Valle, D., Human Delta(1)-pyrroline-5-carboxylate synthase: function and regulation.Amino Acids, 2008.
  13. Nakken, S. Alseth, I., Rognes, T., Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes.Neuroscience, 2007,  vol. 145,  pp. 1273-9.
  14. Wainreb, G. Ashkenazy, H. Bromberg, Y. Starovolsky-Shitrit, A. Haliloglu, T. Ruppin, E. Avraham, K.B. Rost, B., Ben-Tal, N., MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data.Nucleic acids research,  vol. 38 Suppl,  pp. W523-8.
  15. Garnier, J. Gibrat, J.F., Robson, B., GOR method for predicting protein secondary structure from amino acid sequence.Methods Enzymol., 1996,  vol. 266,  pp. 540-53.
  16. Pollastri, G. McLysaght, A., Porter: a new, accurate server for protein secondary structure prediction.Bioinformatics, 2005,  vol. 21,  pp. 1719-20.
  17. Kneller, D.G. Cohen, F.E., Langridge, R., Improvements in protein secondary structure prediction by an enhanced neural network.J. Mol. Biol., 1990,  vol. 214,  pp. 171-82.
  18. Ludwikowski, G. Szymanski, W. Szymanski, M. Adamczak, R. Kazdepka-Zieminska, A., Pasinska, M., [Influence of cigarette smoking on some sperm parameters in males with decreased fertility].Przegl Lek, 2004,  vol. 61,  pp. 1031-2.
  19. Adamczak, R. Porollo, A., Meller, J., Combining prediction of secondary structure and solvent accessibility in proteins.Proteins, 2005,  vol. 59,  pp. 467-75.
  20. Wagner, M. Adamczak, R. Porollo, A., Meller, J., Linear regression models for solvent accessibility prediction in proteins.J. Comput. Biol., 2005,  vol. 12,  pp. 355-69.
  21. Nielsen, M. Lundegaard, C. Lund, O., Petersen, T.N., CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles.Nucleic Acids Res, 2010,  vol. 38,  pp. W576-81
  22. Berezin, C. Glaser, F. Rosenberg, J. Paz, I. Pupko, T. Fariselli, P. Casadio, R., Ben-Tal, N., ConSeq: the identification of functionally and structurally important residues in protein sequences.Bioinformatics, 2004,  vol. 20,  pp. 1322-4.
  23. Chenna, R. Sugawara, H. Koike, T. Lopez, R. Gibson, T.J. Higgins, D.G., Thompson, J.D., Multiple sequence alignment with the Clustal series of programs.Nucleic Acids Res, 2003,  vol. 31,  pp. 3497-500.
  24. Ng, P.C. Henikoff, S., Predicting deleterious amino acid substitutions.Genome Res., 2001,  vol. 11,  pp. 863-74.
  25. Ng, P.C. Henikoff, S., Accounting for human polymorphisms predicted to affect protein function.Genome Res., 2002,  vol. 12,  pp. 436-46.
  26. Ramensky, V. Bork, P., Sunyaev, S., Human non-synonymous SNPs: server and survey.Nucleic Acids Res, 2002,  vol. 30,  pp. 3894-900.
  27. Marchler-Bauer, A. Bryant, S.H., CD-Search: protein domain annotations on the fly.Nucleic Acids Res, 2004,  vol. 32,  pp. W327-31.
  28. Savas, S. Kim, D.Y. Ahmad, M.F. Shariff, M., Ozcelik, H., Identifying functional genetic variants in DNA repair pathway using protein conservation analysis.Cancer Epidemiol. Biomarkers Prev., 2004,  vol. 13,  pp. 801-7.
  29. Zhu, Y. Spitz, M.R. Amos, C.I. Lin, J. Schabath, M.B., Wu, X., An evolutionary perspective on single-nucleotide polymorphism screening in molecular cancer epidemiology.Cancer Res., 2004,  vol. 64,  pp. 2251-7.
  30. Xi, T. Jones, I.M., Mohrenweiser, H.W., Many amino acid substitution variants identified in DNA repair genes during human population screenings are predicted to impact protein function.Genomics, 2004,  vol. 83,  pp. 970-9.
  31. Rudd, M.F. Williams, R.D. Webb, E.L. Schmidt, S. Sellick, G.S., Houlston, R.S., The predicted impact of coding single nucleotide polymorphisms database.Cancer Epidemiol. Biomarkers Prev., 2005,  vol. 14,  pp. 2598-604.
  32. Pietrokovski, S. Henikoff, J.G., Henikoff, S., The Blocks database--a system for protein classification.Nucleic Acids Res, 1996,  vol. 24,  pp. 197-200.
  33. Omori, K. Imai, Y. Suzuki, S., Komatsubara, S., Nucleotide sequence of the Serratia marcescens threonine operon and analysis of the threonine operon mutations which alter feedback inhibition of both aspartokinase I and homoserine dehydrogenase I.J. Bacteriol., 1993,  vol. 175,  pp. 785-94.
  34. Omori, K. Suzuki, S. Imai, Y., Komatsubara, S., Analysis of the Serratia marcescens proBA operon and feedback control of proline biosynthesis.J Gen Microbiol, 1991,  vol. 137,  pp. 509-17.
  35. Serina, L. Blondin, C. Krin, E. Sismeiro, O. Danchin, A. Sakamoto, H. Gilles, A.M., Barzu, O., Escherichia coli UMP-kinase, a member of the aspartokinase family, is a hexamer regulated by guanine nucleotides and UTP.Biochemistry (Mosc.), 1995,  vol. 34,  pp. 5066-74.