Molecular characterization and homology modeling of spermidine synthase from Synechococcus sp. PCC 7942

  • Apiradee Pothipongsa
  • Saowarath Jantaro
  • Tiina A. Salminen
  • Aran IncharoensakdiEmail author
Original Paper


Spermidine synthase (Spds) catalyzes the formation of spermidine by transferring the aminopropyl group from decarboxylated S-adenosylmethionine (dcSAM) to putrescine. The Synechococcus spds gene encoding Spds was expressed in Escherichia coli. The purified recombinant enzyme had a molecular mass of 33 kDa and showed optimal activity at pH 7.5, 37 °C. The enzyme had higher affinity for dcSAM (K m, 20 µM) than for putrescine (K m, 111 µM) and was highly specific towards the diamine putrescine with no activity observed towards longer chain diamines. The three-dimensional structural model for Synechococcus Spds revealed that most of the ligand binding residues in Spds from Synechococcus sp. PCC 7942 are identical to those of human and parasite Spds. Based on the model, the highly conserved acidic residues, Asp89, Asp159 and Asp162, are involved in the binding of substrates putrescine and dcSAM and Pro166 seems to confer substrate specificity towards putrescine.


Spermidine synthase Spermidine Synechococcus sp. PCC 7942 Homology modeling 



Apiradee Pothipongsa thanks the Commission on Higher Education, Thailand under Science Achievement Scholarship, the 90th Anniversary of Chulalongkorn University (CU) Fund, the EXPERTS Erasmus Mundus scholarship for financial support. We thank Prof. Keijiro Samejima for providing dcSAM. Aran Incharoensakdi thanks CU Food and Water Cluster (CU-58-011-FW) and Thailand Research Fund (IRG5780008) for financial support. Tiina A. Salminen thanks Sigrid Juselius Foundation for financial support. Use of Biocenter Finland infrastructure at Åbo Akademi University (bioinformatics, structural biology, and translational activities) is acknowledged.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.


  1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefGoogle Scholar
  2. Amano Y, Namatame I, Tateishi Y, Honboh K, Tanabe E, Niimi T, Sakashita H (2015) Structural insights into the novel inhibition mechanism of Trypanosoma cruzi spermidine synthase. Acta Cryst D 71:1879–1889CrossRefGoogle Scholar
  3. Benkert P, Tosatto SC, Schomburg D (2008) QMEAN: a comprehensive scoring function for model quality assessment. Proteins 71:261–277CrossRefGoogle Scholar
  4. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235–242CrossRefGoogle Scholar
  5. Bouchereau A, Aziz A, Larher F, Martin-Tanguy J (1999) Polyamines and environmental challenges: recent development. Plant Sci 140:103–125CrossRefGoogle Scholar
  6. Cole C, Barber JD, Barton GJ (2008) The Jpred 3 secondary structure prediction server. Nucleic Acids Res 36:W197–W201CrossRefGoogle Scholar
  7. DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San CarlosGoogle Scholar
  8. Dufe VT, Lüersen K, Eschbach ML, Haider N, Karlberg T, Walter RD, Al-Karadaghi S (2005) Cloning, expression, characterisation and three-dimensional structure determination of Caenorhabditis elegans spermidine synthase. FEBS Lett 579:6037–6043CrossRefGoogle Scholar
  9. Dufe VT, Qiu W, Müller IB, Hui R, Walter RD, Al-Karadaghi S (2007) Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO. J Mol Biol 373:167–177CrossRefGoogle Scholar
  10. Flores HE, Galston AW (1982) Polyamines and plant stress: activation of putrescine biosynthesis by osmotic shock. Science 217:1259–1261CrossRefGoogle Scholar
  11. Haider N, Eschbach ML, de Souza Dias S, Gilberger TW, Walter RD, Lüersen K (2005) The spermidine synthase of the malaria parasite Plasmodium falciparum: molecular and biochemical characterisation of the polyamine synthesis enzyme. Mol Biochem Parasitol 142:224–236CrossRefGoogle Scholar
  12. Hashimoto T, Tamaki K, Suzuki KI, Yamada Y (1998) Molecular cloning of plant spermidine synthases. Plant Cell Physiol 39:73–79CrossRefGoogle Scholar
  13. Igarashi K, Kashiwagi K (2000) Polyamines: mysterious modulators of cellular functions. Biochem Biophys Res Commun 271:559–564CrossRefGoogle Scholar
  14. Illergård K, Ardell DH, Elofsson A (2009) Structure is three to ten times more conserved than sequence: a study of structural response in protein cores. Proteins 77:499–508CrossRefGoogle Scholar
  15. Incharoensakdi A, Jantaro S, Raksajit W, Mäenpää P (2010) Polyamines in cyanobacteria: biosynthesis, transport and abiotic stress response. In: Mendez-Vilas A (ed) Current research, technology and education topic in applied microbiology and microbial biotechnology. Formatex, Spain, pp 23–32Google Scholar
  16. Johnson MS, Lehtonen JV (2000) Comparison of protein three-dimensional structures. In: Higgins D, Taylor W (eds) Bioinformatics, sequence, structure and databanks. Oxford University Press, Oxford, pp 15–50Google Scholar
  17. Kajander EO, Kauppinen LI, Pajula RL, Karkola K, Eloranta T (1989) Purification and partial characterization of human polyamine synthases. Biochem J 259:879–886CrossRefGoogle Scholar
  18. Korolev S, Ikeguchi Y, Skarina T, Beasley S, Arrowsmith C, Edwards A, Joachimiak A, Pegg AE, Savchenko A (2002) The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor. Nat Struct Mol Biol 9:27–31CrossRefGoogle Scholar
  19. Laskowski RA, MacArthur MW, Moss DS et al (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291CrossRefGoogle Scholar
  20. Lee MJ, Huang CY, Sun YJ, Huang H (2005) Cloning and characterization of spermidine synthase and its implication in polyamine biosynthesis in Helicobacter pylori strain 26695. Protein Expr Purif 43:140–148CrossRefGoogle Scholar
  21. Lee MJ, Yang YT, Lin V, Huang H (2013) Site-directed mutations of the gatekeeping loop region affect the activity of Escherichia coli spermidine synthase. Mol Biotechnol 54:572–580CrossRefGoogle Scholar
  22. Lehtonen JV, Still DJ, Rantanen VV, Ekholm J, Björklund D, Iftikhar Z, Huhtala M, Repo S, Jussila A, Jaakkola J, Pentikäinen O, Nyrönen T, Salminen T, Gyllenberg M, Johnson MS (2004) BODIL: a molecular modelling environment for structure-function analysis and drug design. J Comput Aided Mol Des 18:401–419CrossRefGoogle Scholar
  23. Lu PK, Tsai JY, Chien HY, Huang H, Chu CH, Sun YJ (2007) Crystal structure of Helicobacter pylori spermidine synthase: a Rossmann-like fold with a distinct active site. Proteins 67:743–754CrossRefGoogle Scholar
  24. Malone T, Blumenthal RM, Cheng X (1995) Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyl-transferases, and suggests a catalytic mechanism for these enzymes. J Mol Biol 253:618–632CrossRefGoogle Scholar
  25. Pearson WR (2013) An introduction to sequence similarity (“homology”) searching. Curr Protoc Bioinform Chapter 3:Unit 3.1. doi: 10.1002/0471250953.bi0301s42 Google Scholar
  26. Pothipongsa A, Jantaro S, Incharoensakdi A (2016) Spermidine synthase is required for growth of Synechococcus sp. PCC 7942. Curr Microbiol 73:639–645CrossRefGoogle Scholar
  27. Raina A, Hyvönen T, Eloranta T, Voutilainen M, Samejima K, Yamanoha B (1984) Polyamine synthesis in mammalian tissues. Isolation and characterization of spermidine synthase from bovine brain. Biochem J 219:991–1000CrossRefGoogle Scholar
  28. Robert X, Gouet P (2014) Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res 42:W320–W324CrossRefGoogle Scholar
  29. Sali A, Blundell T (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 243:779–815CrossRefGoogle Scholar
  30. Samejima K, Yamanoha B (1982) Purification of spermidine synthase from rat ventral prostate by affinity chromatography on immobilized S-adenosyl (5′)-3-thiopropylamine. Arch Biochem Biophys 216:213–222CrossRefGoogle Scholar
  31. Sindhu RK, Cohen SS (1984) Propylamine transferases in Chinese cabbage leaves. Plant Physiol 74:645–649CrossRefGoogle Scholar
  32. Sippl MJ (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17:355–362CrossRefGoogle Scholar
  33. Sugita C, Ogata K, Shikata M, Jikuya H, Takano J, Furumichi M, Kanehisa M, Omata T, Sugiura M, Sugita M (2007) Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization. Photosynth Res 93:55–67CrossRefGoogle Scholar
  34. Tabor CW, Tabor H (1984) Polyamines. Annu Rev Biochem 53:749–790CrossRefGoogle Scholar
  35. Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:W407–W410CrossRefGoogle Scholar
  36. Wu H, Min J, Ikeguchi Y, Zeng H, Dong A, Loppnau P, Pegg AE, Plotnikov AN (2007) Structure and mechanism of spermidine synthases. Biochemistry 46:8331–8339CrossRefGoogle Scholar
  37. Yodsang P, Raksajit W, Brandt AM, Salminen T, Mäenpää P, Incharoensakdi A (2011) Recombinant polyamine-binding protein of Synechocystis sp. PCC 6803 specifically binds to and is induced by polyamines. Biochemistry (Moscow) 76:713–719CrossRefGoogle Scholar
  38. Yoon SO, Lee YS, Lee SH, Cho YD (2000) Polyamine synthesis in plants: isolation and characterization of spermidine synthase from soybean (Glycine max) axes. Biochim Biophys Acta 1475:17–26CrossRefGoogle Scholar
  39. Zhou X, Chua TK, Tkaczuk KL, Bujnicki JM, Sivaraman J (2010) The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket. J Struct Biol 169:277–285CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  • Apiradee Pothipongsa
    • 1
    • 2
  • Saowarath Jantaro
    • 1
  • Tiina A. Salminen
    • 2
  • Aran Incharoensakdi
    • 1
    Email author
  1. 1.Laboratory of Cyanobacterial Biotechnology, Department of Biochemistry, Faculty of ScienceChulalongkorn UniversityBangkokThailand
  2. 2.Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and EngineeringÅbo Akademi UniversityTurkuFinland

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