Structure-based mechanism for early PLP-mediated steps of rabbit cytosolic serine hydroxymethyltransferase reaction

BioMed Research International

Volumn 2013, Issue , 2013, Pages

  Di Salvo, Martino L ^a   Scarsdale, J Neel ^b   Kazanina, Galina ^b   Contestabile, Roberto ^a   Schirch, Verne ^c   Wright, H Tonie ^c  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b Center for the Study of Biological Complexity   (United States)

^c VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIAMINE; GLYCINE; GLYCINE HYDROXYMETHYLTRANSFERASE; LYSINE; MUTANT PROTEIN; PYRIDOXAL 5 PHOSPHATE; SERINE; THREONINE;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; CYTOSOL; ENZYME KINETICS; ENZYME MECHANISM; ENZYME STABILITY; ENZYME SUBSTRATE; HYDROGEN BOND; NONHUMAN; RABBIT; WILD TYPE; AMINO ACID SEQUENCE; ANIMAL; BINDING SITE; CATALYSIS; CHEMISTRY; ENZYME ACTIVE SITE; GENE EXPRESSION; GENETICS; KINETICS; METABOLISM; MUTATION; SITE DIRECTED MUTAGENESIS; STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CATALYSIS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; GENE EXPRESSION; GLYCINE HYDROXYMETHYLTRANSFERASE; HYDROGEN BONDING; KINETICS; MUTAGENESIS, SITE-DIRECTED; MUTATION; PYRIDOXAL PHOSPHATE; RABBITS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84881525954     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2013/458571     Document Type: Article

References (32)

1. Schirch V., Mechanism of Folate-Requiring Enzymes in One-Carbon Metabolism 1998 1 San Diego, Calif, USA Academic Press
2. Florio R., Di Salvo M. L., Vivoli M., Contestabile R., Serine hydroxymethyltransferase: a model enzyme for mechanistic, structural, and evolutionary studies. Biochimica et Biophysica Acta 2011 1814 11 1489 1495 2-s2.0-80054683060 10.1016/j.bbapap.2010.10.010
3. Amadasi A., Bertoldi M., Contestabile R., Bettati S., Cellini B., Luigi di Salvo M., Borri-Voltattorni C., Bossa F., Mozzarelli A., Pyridoxal 5′-phosphate enzymes as targets for therapeutic agents. Current Medicinal Chemistry 2007 14 12 1291 1324 2-s2.0-34248582557 10.2174/092986707780597899 (Pubitemid 46746362)
4. Daidone F., Florio R., Rinaldo S., Contestabile R., Di Salvo M. L., Cutruzzol F., Bossa F., Paiardini A., In silico and in vitro validation of serine hydroxymethyltransferase as a chemotherapeutic target of the antifolate drug pemetrexed. European Journal of Medicinal Chemistry 2011 46 5 1616 1621 2-s2.0-79953228534 10.1016/j.ejmech.2011.02.009
5. di Salvo M. L., Contestabile R., Paiardini A., Maras B., Glycine consumption and mitochondrial serine hydroxymethyltransferase in cancer cells: the heme connection. Medical Hypotheses 2013 80 633 636 10.1016/j.mehy.2013.02. 008
6. Stover P., Schirch V., Enzymatic mechanism for the hydrolysis of 5,10-methenyltetrahydropteroylglutamate to 5-formyltetrahydropteroylglutamate by serine hydroxymethyltransferase. Biochemistry 1992 31 7 2155 2164 2-s2.0-0026645228 10.1021/bi00122a037
7. di Salvo M. L., Florio R., Paiardini A., Vivoli M., D'Aguanno S., Contestabile R., Alanine racemase from Tolypocladium inflatum: a key PLP-dependent enzyme in cyclosporin biosynthesis and a model of catalytic promiscuity. Archives of Biochemistry and Biophysics 2013 529 55 65 10.1016/j.abb.2012.11.011
8. Contestabile R., Paiardini A., Pascarella S., Di Salvo M. L., D'Aguanno S., Bossa F., L-Threonine aldolase, serine hydroxymethyltransferase and fungal alanine racemase: a subgroup of strictly related enzymes specialized for different functions. European Journal of Biochemistry 2001 268 24 6508 6525 2-s2.0-0035666383 10.1046/j.0014-2956.2001.02606.x (Pubitemid 34014759)
9. Schirch V., Szebenyi D. M. E., Serine hydroxymethyltransferase revisited. Current Opinion in Chemical Biology 2005 9 5 482 487 2-s2.0-25144460448 10.1016/j.cbpa.2005.08.017 (Pubitemid 41338200)
10. Giardina G., Montioli R., Gianni S., Cellini B., Paiardini A., Voltattorni C. B., Cutruzzolà F., Open conformation of human DOPA decarboxylase reveals the mechanism of PLP addition to Group II decarboxylases. Proceedings of the National Academy of Sciences of the United States of America 2011 108 51 20514 20519 2-s2.0-84855517335 10.1073/pnas.1111456108
11. Malerba F., Bellelli A., Giorgi A., Bossa F., Contestabile R., The mechanism of addition of pyridoxal 5′-phosphate to Escherichia coli apo-serine hydroxymethyltransferase. Biochemical Journal 2007 404 3 477 485 2-s2.0-34250789658 10.1042/BJ20061681 (Pubitemid 46953922)
12. Schirch L., Serine transhydroxymethylase: relaxation and transient kinetic study of the formation and interconversion of the enzyme glycine complexes. Journal of Biological Chemistry 1975 250 5 1939 1945 2-s2.0-0016661031
13. Cheng C.-F., Haslam J. L., A kinetic investigation of the interaction of serine transhydroxymethylase with glycine. Biochemistry 1972 11 19 3512 3518 2-s2.0-0015504267
14. Dunathan H. C., Conformation and reaction specificity in pyridoxal phosphate enzymes. Proceedings of the National Academy of Sciences of the United States of America 1966 55 4 712 716 2-s2.0-0013902457
15. Schirch L., Serine hydroxymethyltransferase. Advances in Enzymology and Related Areas of Molecular Biology 1982 53 83 112 2-s2.0-0020005825
16. Pascarella S., Angelaccio S., Contestabile R., Delle Fratte S., Di Salvo M., Bossa F., The structure of serine hydroxymethyltransferase as modeled by homology and validated by site-directed mutagenesis. Protein Science 1998 7 9 1976 1982 2-s2.0-0031709347 (Pubitemid 28432438)
17. Angelaccio S., Pascarella S., Fattori E., Bossa F., Strong W., Schirch V., Serine hydroxymethyltransferase: origin of substrate specificity. Biochemistry 1992 31 1 155 162 2-s2.0-0026507501
18. Vivoli M., Angelucci F., Ilari A., Morea V., Angelaccio S., Di Salvo M. L., Contestabile R., Role of a conserved active site cation- π interaction in Escherichia coli serine hydroxymethyltransferase. Biochemistry 2009 48 50 12034 12046 2-s2.0-72449130848 10.1021/bi901568b
19. Baiocco P., Gourlay L. J., Angelucci F., Fontaine J., Hervé M., Miele A. E., Trottein F., Brunori M., Bellelli A., Probing the Mechanism of GSH Activation in Schistosoma haematobium Glutathione-S-transferase by Site-directed Mutagenesis and X-ray Crystallography. Journal of Molecular Biology 2006 360 3 678 689 2-s2.0-33745637441 10.1016/j.jmb.2006.05.040 (Pubitemid 43975115)
20. Scarsdale J. N., Kazanina G., Radaev S., Schirch V., Wright H. T., Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8 Å resolution: mechanistic implications. Biochemistry 1999 38 26 8347 8358 2-s2.0-0033614832 10.1021/bi9904151 (Pubitemid 29314207)
21. Goldberg J. M., Zheng J., Deng H., Chen Y. Q., Callender R., Kirsch J. F., Structure of the complex between pyridoxal 5′-phosphate and the tyrosine 225 to phenylalanine mutant of Escherichia coli aspartate aminotransferase determined by isotope-edited classical Raman difference spectroscopy. Biochemistry 1993 32 32 8092 8097 2-s2.0-0027218352 (Pubitemid 23265795)
22. Trivedi V., Gupta A., Jala V. R., Saravanan P., Jagannatha Rao G. S., Appaji Rao N., Savithri H. S., Subramanya H. S., Crystal structure of binary and ternary complexes of serine hydroxymethyltransferase from Bacillus stearothermophilus. Insights into the catalytic mechanism. Journal of Biological Chemistry 2002 277 19 17161 17169 2-s2.0-0037053283 10.1074/jbc.M111976200 (Pubitemid 34967749)
23. Szebenyi D. M. E., Musayev F. N., Di Salvo M. L., Safo M. K., Schirch V., Serine hydroxymethyltransferase: role of Glu75 and evidence that serine is cleaved by a retroaldol mechanism. Biochemistry 2004 43 22 6865 6876 2-s2.0-2642571803 10.1021/bi049791y (Pubitemid 38720504)
24. Fu T.-F., Scarsdale J. N., Kazanina G., Schirch V., Wright H. T., Location of the pteroylpolyglutamate-binding site on rabbit cytosolic serine hydroxymethyltransferase. Journal of Biological Chemistry 2003 278 4 2645 2653 2-s2.0-0037462648 10.1074/jbc.M210649200 (Pubitemid 36801344)
25. Szebenyi D. M. E., Liu X., Kriksunov I. A., Stover P. J., Thiel D. J., Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers. Biochemistry 2000 39 44 13313 13323 2-s2.0-0034619570 10.1021/bi000635a
26. Contestabile R., Angelaccio S., Bossa F., Wright H. T., Scarsdale N., Kazanina G., Schirch V., Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase. Biochemistry 2000 39 25 7492 7500 2-s2.0-0034720768 10.1021/bi000032z (Pubitemid 30422067)
27. Bhavani B. S., Rajaram V., Bisht S., Kaul P., Prakash V., Murthy M. R. N., Appaji Rao N., Savithri H. S., Importance of tyrosine residues of Bacillus stearothermophilus serine hydroxymethyltransferase in cofactor binding and l-allo-Thr cleavage: crystal structure and biochemical studies. FEBS Journal 2008 275 18 4606 4619 2-s2.0-50849084136 10.1111/j.1742-4658.2008.06603.x
28. Di Salvo M. L., Fratte S. D., De Biase D., Bossa F., Schirch V., Purification and characterization of recombinant rabbit cytosolic serine hydroxymethyltransferase. Protein Expression and Purification 1998 13 2 177 183 2-s2.0-0032126946 10.1006/prep.1998.0890 (Pubitemid 28349023)
29. Otwinowski M., Charles W., Carter J., Processing of X-ray diffraction data collected in oscillation mode. Methods in Enzymology 1997 Elsevier 307 326 Macromolecular Crystallography Part A
30. The CCP4 suite: programs for protein crystallography. Acta Crystallographica D 1994 50 760 763 10.1107/S0907444994003112 (Pubitemid 2143461)
31. Emsley P., Cowtan K., Coot: model-building tools for molecular graphics. Acta Crystallographica D 2004 60 12 2126 2132 2-s2.0-13244281317 10.1107/S0907444904019158 (Pubitemid 41742764)
32. Brünger A. T., Adams P. D., Clore G. M., Delano W., Gros P., Grossekunstleve R. W., Jiang J.-S., Kuszewski J., Nilges M., Pannu N. S., Read R., Rice L. M., Simonson T., Warren G., Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallographica D 1998 54 5 905 921 2-s2.0-3543012707