Structure determination and biochemical studies on Bacillus stearothermophilus E53Q serine hydroxymethyltransferase and its complexes provide insights on function and enzyme memory

FEBS Journal

Volumn 274, Issue 16, 2007, Pages 4148-4160

  Rajaram, V ^a   Bhavani, B S ^b   Kaul, Purnima ^b   Prakash, V ^b   Appaji Rao, N ^a   Savithri, H S ^a   Murthy, M R N ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b CENTRAL FOOD TECHNOLOGICAL RESEARCH INSTITUTE   (India)

Author keywords

Crystal structure; Enzyme memory; Pyridoxal 5 phosphate; SHMT

Indexed keywords

CARBOXYL GROUP; GLYCINE; GLYCINE HYDROXYMETHYLTRANSFERASE; LYSINE; MUTANT PROTEIN; PYRIDOXAL 5 PHOSPHATE; TETRAHYDROFOLIC ACID;

ARTICLE; CONTROLLED STUDY; CRYSTALLIZATION; ENZYME ACTIVITY; ENZYME INACTIVATION; GENE MUTATION; GEOBACILLUS STEAROTHERMOPHILUS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; WILD TYPE;

AMINO ACID SUBSTITUTION; BACILLUS STEAROTHERMOPHILUS; BACTERIAL PROTEINS; CATALYSIS; CIRCULAR DICHROISM; CRYSTALLOGRAPHY, X-RAY; FORMYLTETRAHYDROFOLATES; GLUTAMIC ACID; GLUTAMINE; GLYCINE; GLYCINE HYDROXYMETHYLTRANSFERASE; KINETICS; MODELS, MOLECULAR; PROTEIN CONFORMATION; SPECTROPHOTOMETRY; TETRAHYDROFOLATES;

GEOBACILLUS STEAROTHERMOPHILUS;

EID: 34547797393     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2007.05943.x     Document Type: Article

References (38)

1. Mehta PK Christen P (2000) The molecular evolution of pyridoxal-5′-phosphate-dependent enzymes. Adv Enzymol Relat Areas Mol Biol 74, 129 184.
2. Matthews RB Drummond JT (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. Appaji Rao N, Talwar R Savithri HS (2000) Molecular organization, catalytic mechanism and function of serine hydroxymethyltransferase - a potential target for cancer chemotherapy. Int J Biochem Cell Biol 32, 405 416.
4. Malkin LI Greenberg DM (1964) Purification and properties of threonine or allo-threonine aldolase from rat liver. Biochim Biophys Acta 85, 117 131.
5. Chen MS Schirch LV (1973) Serine transhydroxymethylase. A kinetic study of the synthesis of serine in the absence of tetrahydrofolate. J Biol Chem 248, 3631 3635.
6. Ulevitch RJ Kallen RG (1977) Purification and characterization of pyridoxal 5′-phosphate dependent serine hydroxymethylase from lamb liver and its action upon beta-phenylserines. Biochemistry 16, 5342 5350.
7. Schirch V (1998) Compherensive Biological Catalysis: A Mechanistic Reference, pp. 211 272. Academic Press Ltd, San Diego, CA.
8. Renwick SB, Snell K Baumann U (1998) The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy. Structure 6, 1105 1116.
9. Szebenyi DM, Liu X, Kriksunov IA, Stover PJ Thiel DJ (2000) Structure of a murine cytoplasmic serine hydroxymethyltransferase quinonoid ternary complex: evidence for asymmetric obligate dimers. Biochemistry 39, 13313 13323.
10. Scarsdale JN, Kazanina G, Radaev S, Schirch V Wright HT (1999) Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8 Å resolution: mechanistic implications. Biochemistry 38, 8347 8358.
11. Scarsdale JN, Radaev S, Kazanina G, Schirch V Wright HT (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.
12. Trivedi V, Gupta A, Jala VR, Saravanan P, Rao GS, Rao NA, Savithri HS Subramanya HS (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.
13. Schirch D, Delle Fratte S, Iurescia S, Angelaccio S, Contestabile R, Bossa F Schirch V (1993) Function of the active-site lysine in Escherichia coli serine hydroxymethyltransferase. J Biol Chem 268, 23132 23138.
14. Jagath JR, Sharma B, Rao NA Savithri HS (1997) The role of His-134-147, and -150 residues in subunit assembly, cofactor binding, and catalysis of sheep liver cytosolic serine hydroxymethyltransferase. J Biol Chem 272, 24355 24362.
15. Szebenyi DM, Musayev FN, di Salvo ML, Safo MK Schirch V (2004) Serine hydroxymethyltransferase: role of glu75 and evidence that serine is cleaved by a retroaldol mechanism. Biochemistry 43, 6865 6876.
16. Jala VR, Prakash V, Rao NA Savithri HS (2002) Overexpression and characterization of dimeric and tetrameric forms of recombinant serine hydroxymethyltransferase from Bacillus stearothermophilus. J Biosci 27, 233 242.
17. Schirch L Ropp M (1967) Serine transhydroxymethylase. Affinity of tetrahydrofolate compounds for the enzyme and enzyme-glycine complex. Biochemistry 6, 253 257.
18. Katz M Westley J (1979) Enzymic memory. Steady state kinetic and physical studies with ascorbate oxidase and aspartate aminotransferase. J Biol Chem 254, 9142 9147.
19. Jean B, Jacques R Jean-Claude M (1977) Enzyme memory: kinetics and thermodynamics of the slow conformation changes of wheat-germ hexokinase LI. Eur J Biochem 80, 593 601.
20. Meunier JC, Buc J Ricard J (1979) Enzyme memory. Effect of glucose 6-phosphate and temperature on the molecular transition of wheat-germ hexokinase LI. Eur J Biochem 97, 573 583.
21. Yennawar HP, Yennawar NH, Farber GK (1995) A structural explanation for enzyme memory in nonaqueous solvents. J Am Chem Soc 117, 577 585.
22. Alexander MK (1995) What is remembered and why? Nature 374, 596.
23. Studier FW Moffatt BA (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189, 113 130.
24. Sambrook J, Fritsch EF Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
25. Alexander DC (1987) An efficient vector-primer cDNA cloning system: large scale preparation of competent cells. Meth Enzymol 154, 41 64.
26. Lowry OH, Rosebrough NJ, Farr AL Randall RJ (1951) Protein measurement with the Folin phenol reagent. J Biol Chem 193, 265 275.
27. Otwinowsky ZM W (1997) Processing of X-ray diffraction data collected in oscillation mode. Meth Enzymol 276, 307 326.
28. Murshudov GN, Vagin AA Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53, 240 255.
29. Emsley P Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126 2132.
30. Laskowski RA, McArthur MW, Moss DS Thornton JM (1993) PROCHECK: a program to check the stereo-chemical quality of protein structures. J Appl Crystallogr 26, 283 291.
31. DeLano WL (2002) The PYMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA.
32. Holm L Sander C (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol 233, 123 138.
33. Hodel A, Kim S Brunger AT (1992) Model bias in macromolecular crystal structures. Acta Cryst A48, 851 858.
34. Taylor RT Weissbach H (1965) A radioactive assay for serine hydroxymethyltransferase. Anal Biochem 13, 80 84.
35. Stover P Schirch V (1991) 5-Formyltetrahydrofolate polyglutamates are slow tight binding inhibitors of serine hydroxymethyltransferase. J Biol Chem 266, 1543 1550.
36. Baskaran N, Prakash V, Appu Rao AG, Radhakrishnan AN, Savithri HS Appaji Rao N (1989) Mechanism of interaction of O-amino-D-serine with sheep liver serine hydroxymethyltransferase. Biochemistry 28, 9607 9612.
37. Acharya JK, Prakash V, Rao AG, Savithri HS Rao NA (1991) Interactions of methoxyamine with pyridoxal-5′-phosphate-Schiff's base at the active site of sheep liver serine hydroxymethyltransferase. Indian J Biochem Biophys 28, 381 388.
38. White FL Olsen KW (1987) Effects of cross linking on the thermal stability of hemoglobin. Arch Biochem Biophys 258, 51 57.