Novel properties of malarial S-adenosylmethionine decarboxylase as revealed by structural modelling

Journal of Molecular Graphics and Modelling

Volumn 24, Issue 4, 2006, Pages 307-318

  Wells, Gordon A ^a   Birkholtz, Lyn Marie ^a   Joubert, Fourie ^a   Walter, Rolf D ^b   Louw, Abraham I ^a  

^a UNIVERSITY OF PRETORIA   (South Africa)

^b BERNHARD NOCHT INSTITUTE FOR TROPICAL MEDICINE   (Germany)

Author keywords

AdoMetDC; Bifunctional; Homology model; Malaria; Polyamines; Pyruvoyl

Indexed keywords

AMINES; BIOSYNTHESIS; MATHEMATICAL MODELS; MUTAGENESIS; VIRUSES; X RAY CRYSTALLOGRAPHY;

ADOMETDC; BIFUNCTIONAL; HOMOLOGY MODEL; MALARIA; POLYAMINES; PYROVOYL;

ENZYMES;

ADENOSYLMETHIONINE DECARBOXYLASE; ARGININE; LYSINE; PUTRESCINE; TROMETAMOL;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME INHIBITION; ENZYME STRUCTURE; HUMAN VERSUS NONHUMAN DATA; MALARIA; MAMMAL; MOLECULAR MODEL; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; SITE DIRECTED MUTAGENESIS; SPECIES COMPARISON; X RAY ANALYSIS;

ADENOSYLMETHIONINE DECARBOXYLASE; AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; HUMANS; LIGANDS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PLASMODIUM FALCIPARUM; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

MAMMALIA; PLASMODIUM FALCIPARUM; SOLANUM TUBEROSUM;

EID: 28944447254     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2005.09.011     Document Type: Article

References (44)

1. J. Breman The ears of the hippopotamus: manifestations, determinants, and estimates of the malaria burden Am. J. Trop. Med. Hyg. 64 Suppl. 1/2 2001 1 11
2. K. Igarashi, I. Sakamoto, N. Goto, K. Kashiwagi, R. Honma, and S. Hirose Interaction between polyamines and nucleic acids or phospholipids Arch. Biochem. Biophys. 219 2 1982 438 443
3. C.W. Tabor, and H. Tabor Methionine adenosyltransferase (S-adenosylmethionine synthetase) and S-adenosylmethionine decarboxylase Adv. Enzymol. Relat. Areas Mol. Biol. 56 1984 251 282
4. T. Byers, B. Ganem, and A. Pegg Cytostasis induced in L1210 murine leukaemia cells by the S-adenosyl-l-methionine decarboxylase inhibitor 5'-([(Z)-4-amino-2-butenyl]methylamino)-5'-deoxyadenosine may be due to hypusine depletion Biochem. J. 287 Pt 3 1992 717 724
5. T.L. Byers, R.S. Wechter, R.H. Hu, and A.E. Pegg Effects of the S-adenosylmethionine decarboxylase inhibitor, 5'-([(Z)-4-amino-2-butenyl] methylamino)-5'-deoxyadenosine, on cell growth and polyamine metabolism and transport in chinese hamster ovary cell cultures Biochem. J. 303 Pt 1 1994 89 96
6. S. Mller, E. Liebau, R. Walter, and R. Krauth-Siegel Thiol-based redox metabolism of protozoan parasites Trends Parasitol. 19 7 2003 320 328
7. O. Heby, S. Roberts, and B. Ullman Polyamine biosynthetic enzymes as drug targets in parasitic protozoa Biochem. Soc. Trans. 31 2 2003 415 419
8. L.J. Marton, and A.E. Pegg Polyamines as targets for therapeutic intervention Annu. Rev. Pharmacol. Toxicol. 35 1995 55 91
9. J.E. Seely, H. Ps, and A.E. Pegg Measurement of the number of ornithine decarboxylase molecules in rat and mouse tissues under various physiological conditions by binding of radiolabelled alpha-difluoromethylornithine Biochem. J. 206 2 1982 311 318
10. C.C. Wang molecular mechanisms and therapeutic approaches to the treatment of African trypanosomiasis Annu. Rev. Pharmacol. Toxicol. 35 1995 93 127
11. S. Mller, G.H. Coombs, and R.D. Walter targeting polyamines of parasitic protozoa in chemotherapy Trends Parasitol. 17 5 2001 242 249
12. S. Müller, A. Da'dara, K. L'́uersen, C. Wrenger, R. Das Gupta, R. Madhubala, and R.D. Walter In the human malaria parasite emPlasmodium falciparumem, polyamines are synthesized by a bifunctional ornithine decarboxylase, S-adenosylmethionine decarboxylase J. Biol. Chem. 275 11 2000 8097 8102
13. C. Wrenger, K. Lüersen, T. Krause, S. Müller, and R.D. Walter The emPlasmodium falciparumem bifunctional ornithine decarboxylase, S-adenosyl-l-methionine decarboxylase, enables a well balanced polyamine synthesis without domain-domain interaction J. Biol. Chem. 276 32 2001 29651 29656
14. L. Birkholtz, C. Wrenger, F. Joubert, G. Wells, R. Walter, and A. Louw Parasite-specific inserts in the bifunctional S-adenosylmethionine decarboxylase/ornithine decarboxylase of Plasmodium falciparum modulate catalytic activities and domain interactions Biochem. J. 377 Pt 2 2004 439 448
15. R.R. Allen, and J.P. Klinman Stereochemistry and kinetic isotope effects in the decarboxylation of S-adenosylmethionine as catalyzed by the pyruvoyl enzyme, S-adenosylmethionine decarboxylase J. Biol. Chem. 256 7 1981 3233 3239
16. H. Xiong, B.A. Stanley, and A.E. Pegg Role of cysteine-82 in the catalytic mechanism of human S-adenosylmethionine decarboxylase Biochemistry 38 8 1999 2462 2470
17. J.L. Ekstrom, I.I. Mathews, B.A. Stanley, A.E. Pegg, and S.E. Ealick The crystal structure of human S-adenosylmethionine decarboxylase at 2.25 Åresolution reveals a novel fold Struct. Fold Des. 7 5 1999 583 595
18. J.L. Ekstrom, W.D. Tolbert, H. Xiong, A.E. Pegg, and S.E. Ealick Structure of a human S-adenosylmethionine decarboxylase self-processing ester intermediate and mechanism of putrescine stimulation of processing as revealed by the H243A mutant Biochemistry 40 32 2001 9495 9504
19. B.A. Stanley, and A.E. Pegg Amino acid residues necessary for putrescine stimulation of human S-adenosylmethionine decarboxylase proenzyme processing and catalytic activity J. Biol. Chem. 266 28 1991 18502 18506
20. M.A. Hoyt, L.J. Williams-Abbott, J.W. Pitkin, and R.H. Davis Cloning and expression of the S-adenosylmethionine decarboxylase gene of Neurospora crassa and processing of its product Mol. Gen. Genet. 263 4 2000 664 673
21. H. Xiong, B.A. Stanley, B.L. Tekwani, and A.E. Pegg Processing of mammalian and plant S-adenosylmethionine decarboxylase proenzymes J. Biol. Chem. 272 45 1997 28342 28348
22. E.M. Bennett, J.L. Ekstrom, A.E. Pegg, and S.E. Ealick Monomeric S-adenosylmethionine decarboxylase from plants provides an alternative to putrescine stimulation Biochemistry 41 49 2002 14509 14517
23. W.D. Tolbert, J.L. Ekstrom, I.I. Mathews, P. Kapoor, A.E. Pegg, and S.E. Ealick The structural basis for substrate specificity and inhibition of human S-adenosylmethionine decarboxylase Biochemistry 40 32 2001 9484 9494
24. J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins The clustalx windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 25 24 1997 4876 4882
25. T.L. Bailey, and C. Elkan Fitting a mixture model by expectation maximization to discover motifs in biopolymers Proc. Int. Conf. Intell. Syst. Mol. Biol. 2 1994 28 36
26. A. Šali, and T.L. Blundell Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234 3 1993 779 815
27. M.A. Marti-Renom, A.C. Stuart, A. Fiser, R. Sánchez, F. Melo, and A. Šali Comparative protein structure modeling of genes and genomes Annu. Rev. Biophys. Biomol. Struct. 29 2000 291 325
28. A. Fiser, R.K. Do, and A. Šali Modeling of loops in protein structures Protein Sci. 9 9 2000 1753 1773
29. G.N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan Stereochemistry of polypeptide chain configurations J. Mol. Biol. 7 1963 95 99
30. A. Morris, M. MacArthur, E. Hutchinson, and J. Thornton Stereochemical quality of protein structure coordinates Proteins 12 4 1992 345 364
31. A.C. Wallace, R.A. Laskowski, and J.M. Thornton Ligplot: a program to generate schematic diagrams of protein-ligand interactions Protein Eng. 8 2 1995 127 134
32. Accelrys Inc., Cerius2 4. 6, Accelrys, Inc., San Diego, 2001.
33. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 12 1983 2577 2637
34. L. Birkholtz, F. Joubert, A. Neitz, and A. Louw Comparative properties of a three-dimensional model of Plasmodium falciparum ornithine decarboxylase Proteins 50 3 2003 464 473
35. E. Hafner, C. Tabor, and H. Tabor Mutants of Escherichia coli that do not contain 1,4-diaminobutane (putrescine) or spermidine J. Biol. Chem. 254 24 1979 12419 12426
36. M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal. Biochem. 72 1976 248 254
37. B. Rost Twilight zone of protein sequence alignments Protein Eng. 12 2 1999 85 94
38. E. Krieger, S. Nabuurs, and G. Vriend Homology modelling Meth. Biochem. Anal. 44 2003 509 523
39. A. Pegg, and H. Williams-Ashman On the role of S-adenosylmethionine in the Biosynthesis of spermidine by rat prostate J. Biol. Chem. 244 1969 682 693
40. W.D. Tolbert, Y. Zhang, S.E. Cottet, E.M. Bennett, J.L. Ekstrom, A.E. Pegg, and S.E. Ealick Mechanism of human S-adenosylmethionine decarboxylase proenzyme processing as revealed by the structure of the S68A mutant Biochemistry 42 8 2003 2386 2395
41. M. Pankaskie, and M.M. Abdel-Monem Inhibitors of polyamine biosynthesis. 8. Irreversible inhibition of mammalian S-adenosyl-l-methionine decarboxylase by substrate analogues J. Med. Chem. 23 2 1980 121 127
42. A.E. Pegg, and G. Jacobs Comparison of inhibitors of S-adenosylmethionine decarboxylase from different species Biochem. J. 213 2 1983 495 502
43. L.N. Kinch, J.R. Scott, B. Ullman, and M.A. Phillips Cloning and kinetic characterization of the Trypanosoma cruzi Mol. Biochem. Parasitol. 101 1/2 1999 1 11
44. T. Clyne, L. Kinch, and M. Phillips Putrescine activation of Trypanosoma cruzi S-adenosylmethionine decarboxylase Biochemistry 41 44 2002 13207 13216