Structural and functional studies of Bacillus stearothermophilus serine hydroxymethyltransferase: The role of Asn341, Tyr60 nd Phe351 in tetrahydrofolate binding

Biochemical Journal

Volumn 418, Issue 3, 2009, Pages 635-642

  Pai, Vinitha R ^a,c   Rajaram, V ^a   Bisht, Shveta ^a   Bhavani, B S ^b   Rao, N Appaji ^a   Murthy, M R N ^a   Savithri, H S ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b CENTRAL FOOD TECHNOLOGICAL RESEARCH INSTITUTE   (India)

^c YENEPOYA MEDICAL COLLEGE   (India)

Author keywords

5 Formyl tetrahydrofolate (FTHF); Crystal structure; Folate binding; L allo threonine; Pyridoxal 5 Phosphate; Serine hydroxymethyltransferase (SHMT); Ternary complex

Indexed keywords

5-FORMYL TETRAHYDROFOLATE (FTHF); FOLATE BINDING; L-ALLO-THREONINE; SERINE HYDROXYMETHYLTRANSFERASE (SHMT); TERNARY COMPLEX;

AMINES; AMINO ACIDS; BACTERIOLOGY; CARBOXYLATION; CATALYSIS; ORGANIC ACIDS;

CRYSTAL STRUCTURE;

ASPARAGINE; GLYCINE; GLYCINE HYDROXYMETHYLTRANSFERASE; PHENYLALANINE; SERINE; TETRAHYDROFOLIC ACID; THYRONINE; 5,6,7,8-TETRAHYDROFOLIC ACID; FOLINIC ACID; TETRAHYDROFOLIC ACID DERIVATIVE; TYROSINE;

ARTICLE; BINDING KINETICS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME STRUCTURE; ENZYME SUBUNIT; GEOBACILLUS STEAROTHERMOPHILUS; NONHUMAN; PRIORITY JOURNAL; STRUCTURE ANALYSIS; AMINO ACID SEQUENCE; CHEMISTRY; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; ULTRAVIOLET SPECTROPHOTOMETRY;

GEOBACILLUS STEAROTHERMOPHILUS;

AMINO ACID SEQUENCE; ASPARAGINE; BACILLUS STEAROTHERMOPHILUS; GLYCINE HYDROXYMETHYLTRANSFERASE; KINETICS; LEUCOVORIN; PHENYLALANINE; SPECTROPHOTOMETRY, ULTRAVIOLET; TETRAHYDROFOLATES; TYROSINE;

EID: 62149092216     PISSN: 02646021     EISSN: 14708728     Source Type: Journal    
DOI: 10.1042/BJ20081739     Document Type: Article

References (33)

1. Mehta, P. K. and Christen, P. (2000) The molecular evolution of pyridoxal-5′-phosphate-dependent enzymes. Adv. Enzymol. Relat. Areas Mol. Biol. 74, 129-184
2. Matthews, R. B. and Drummond, J. T. (1990) Providing one-carbon units for biological methylations: mechanistic studies on the serine hydroxymethyltranferase, methylenetetrahydrofolate reductase and methylthetrahydrofolate-homocysteine methyltransferase. Chem. Rev. 90, 1275-1290
3. Bertino, J. R., Silber, R., Freeman, M., Alenty, A., Albrecht, M., Gabrio, B. W. and Huennekens, F. M. (1963) Studies on normal and leukemic leukocytes: tetrahydrofolate-dependent enzyme systems and dihydrofolic reductase. J. Clin. Invest. 42, 1899-1907
4. Thorndike, J., Pelliniemi, T. and Beck, W. S. (1979) Serine hydroxymethyltransferase activity and serine incorporation in leukocytes. Cancer Res. 39, 3435-3440
5. Rao, N. A., Talwar, R. and Savithri, H. S. (2000) Molecular organization, catalytic mechanism and function of serine hydroxymethyltransferase-a potential target for cancer chemotherapy. Int. J. Biochem. Cell Biol. 32, 405-416
6. Jala, V. R., Prakash, V., Rao, N. A. and Savithri, H. S. (2000) The role of Glu74 and Tyr82 in the reaction catalyzed by sheep liver cytosolic serine hydroxymethyltransferase. Eur. J. Biochem. 267, 5967-5976
7. Chen, M. S. and Schirch, L. V. (1973) Serine transhydroxymethylase. A kinetic study of the synthesis of serine in the absence of tetrahydrofolate. J. Biol. Chem. 248, 3631-3635
8. Ulevitch, R. J. and Kallen, R. G. (1977) Purification and characterization of pyridoxal 5′-phosphate dependent serine hydroxymethylase from lamb liver and its action upon β-phenylserines. Biochemistry 16, 5342-5350
9. Schirch, V. (1998) In Comprehensive Biological Catalysis: A Mechanistic Reference (Sinnott, M., ed.), pp, 211-272, Academic Press Ltd, San Diego, CA
10. Renwick, S. B., Snell, K. and Baumann, U. (1998) The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy. Structure 6, 1105-1116
11. Szebenyi, D. M., Liu, X., Kriksunov, I. A., Stover, P. J. and Thiel, D. J. (2000) Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers. Biochemistry 39, 13313-13323
12. Scarsdale, J. N., Kazanina, G., Radaev, S., Schirch, V. and Wright, H. T. (1999) Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8 A resolution: mechanistic implications. Biochemistry 38, 8347-8358
13. Scarsdale, J. N., Radaev, S., Kazanina, G., Schirch, V. and Wright, H. T. (2000) Crystal structure at 2.4 Å resolution of E. coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate. J. Mol. Biol. 296, 155-168
14. Trivedi, V., Gupta, A., Jala, V. R., Saravanan, P., Rao, G. S. J., Rao, N. A., Savithri, H. S. and Subramanya, H. S. (2002) Crystal structure of binary and ternary complexes of serine hydroxymethyltransferase from Bacillus stearothermophilus: insights into the catalytic mechanism. J. Biol. Chem. 277, 17161-17169
15. Szebenyi, D. M., Musayev, F. N., di Salvo, M. L., Safo, M. K. and Schirch, V. (2004) Serine hydroxymethyltransferase: role of Glu75 and evidence that serine is cleaved by a retroaldol mechanism. Biochemistry 43, 6865-6876
16. Bhavani, S., Trivedi, V., Jala, V. R., Subramanya, H. S., Kaul, P., Prakash, V., Rao, N. A. and Savithri, H. S. (2005) Role of Lys-226 in the catalytic mechanism of Bacillus stearothermophilus serine hydroxymethyltransferase-crystal structure and kinetic studies. Biochemistry 44, 6929-6937
17. Rajaram, V., Bhavani, B. S., Kaul, P., Prakash, V., Rao, N. A., Savithri, H. S. and Murthy, M. R. N. (2007) Structure determination and biochemical studies on Bacillus stearothermophilus E53Q serine hydroxymethyltransferase and its complexes provide insights on function and enzyme memory. FEBS J. 274, 4148-4160
18. Studier, F. W. and Moffatt, B. A. (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 189, 113-130
19. Alexander, D. C. (1987) An efficient vector-primer cDNA cloning system: large scale preparation of competent cells. Methods Enzymol. 154, 41-64
20. Sambrook, J., Fritsch, E. F. and Maniatis, T. (1989) Molecular Cloning: a Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
21. Jala, V. R., Prakash, V., Rao, N. A. and Savithri, H. S. (2002) Overexpression and characterization of dimeric and tetrameric forms of recombinant serine hydroxymethyltransferase from Bacillus stearothermophilus. J. Biosci. 27, 233-242
22. Lowry, O. H., Rosebrough, N. J., Farr, A. L. and Randall, R. J. (1951) Protein measurement with the Folin phenol reagent. J. Biol. Chem. 193, 265-275
23. Taylor, R. T. and Weissbach, H. (1965) A radioactive assay for serine hydroxymethyltransferase. Anal. Biochem. 13, 80-84
24. Otwinowsky, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326
25. Brunger, A. T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355, 472-475
26. Brunger, A. T. (1993) Assessment of phase accuracy by cross validation: the free R value. Methods and applications. Acta Crystallogr. Sect. D Biol. Crystallogr. 49, 24-36
27. Murshudov, G. N., Vagin, A. A. and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. Sect. D Biol. Crystallogr. 53, 240-255
28. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. Sect. D Biol. Crystallogr. 50, 760-763
29. Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr. Sect. D Biol. Crystallogr. 60, 2126-2132
30. Laskowski, R. A., McArthur, M. W., Moss, D. S. and Thornton, J. M. (1993) PROCHECK: a program to check the stereo-chemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291
31. Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138
32. Reference deleted
33. Schirch, L. (1984) Folates in serine and glycine metabolism. In Folates and Pterins: Chemistry and Biochemistry of Folates (Blakley, R. L. and Benkovic, S. J., eds.), pp. 399-432, Wiley Interscience, New York