Structure and catalytic mechanism of the cytosolic D-ribulose-5-phosphate 3-epimerase from rice

Journal of Molecular Biology

Volumn 326, Issue 1, 2003, Pages 127-135

  Jelakovic, Stefan ^a   Kopriva, Stanislav ^a   Süss, Karl Heinz ^b   Schulz, Georg E ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

Amphibolic enzymes; Methionine at zinc ion; Oxidative pentose phosphate pathway; X ray diffraction; Zinc binding site

Indexed keywords

DEXTRO RIBULOSE 5 PHOSPHATE 3 EPIMERASE; EDETIC ACID; ENZYME; RIBULOSE PHOSPHATE; SULFATE; UNCLASSIFIED DRUG; WATER; ZINC ION;

ARTICLE; BINDING SITE; CATALYSIS; CHLOROPLAST; CONFORMATION; CONTROLLED STUDY; CRYSTALLIZATION; CYTOSOL; ENZYME STRUCTURE; NONHUMAN; PLANT LEAF; POTATO; PRIORITY JOURNAL; PROTEIN BINDING; REACTION ANALYSIS; RICE; X RAY DIFFRACTION;

SOLANUM TUBEROSUM;

EID: 0037423701     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)01374-8     Document Type: Article

References (39)

1. Teige M., Kopriva S., Bauwe H., Süss K.-H. Chloroplast pentose-5-phosphate 3-epimerase from potato: cloning, cDNA sequence, and tissue-specific enzyme accumulation. FEBS Letters. 377:1995;349-352.
2. Nowitzki U., Wyrich R., Westhoff P., Henze K., Schnarrenberger C., Martin W. Cloning of the amphibolic Calvin cycle/OPPP enzyme D-ribulose-5-phosphate 3-epimerase (EC 5.1.3.1) from spinach chloroplasts: functional and evolutionary aspects. Plant Mol. Biol. 29:1995;1279-1291.
3. Hartman F.C., Harpel M.R. Structure, function, regulation, and assembly of D-ribulose-1,5-bisphosphate carboxylase/oxygenase. Annu. Rev. Biochem. 63:1994;197-234.
4. Sprenger G.A. Genetics of pentose-phosphate pathway enzymes of Escherichia coli K-12. Arch. Microbiol. 164:1995;324-330.
5. Eicks M., Maurino V., Knappe S., Flügge U.-I., Fischer K. The plastidic pentose phosphate translocator represents a link between the cytosolic and the plastidic pentose pathways in plants. Plant Physiol. 128:2002;512-522.
6. Schnarrenberger C., Flechner A., Martin W. Enzymatic evidence for a complete oxidative pentose phosphate pathway in chloroplasts and an incomplete pathway in the cytosol of spinach leaves. Plant Physiol. 108:1995;609-614.
7. Kopriva S., Koprivova A., Süss K.-H. Identification, cloning, and properties of cytosolic D-ribulose-5-phosphate 3-epimerase from higher plants. J. Biol. Chem. 275:2000;1294-1299.
8. Juhnke H., Krems B., Koetter P., Entian K.-D. Mutants that show increased sensitivity to hydrogen peroxide reveal an important role for the pentose phosphate pathway in protection of yeast against oxidative stress. Mol. Gen. Genet. 252:1996;456-464.
9. Slekar K.H., Kosman D.J., Culotta V.C. The yeast copper/zinc superoxide dismutase and the pentose phosphate pathway play overlapping roles in oxidative stress protection. J. Biol. Chem. 271:1996;28831-28836.
10. Kopp J., Kopriva S., Süss K.-H., Schulz G.E. Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts. J. Mol. Biol. 287:1999;761-771.
11. Williamson W.T., Wood W.A. D-Ribulose 5-phosphhate 3-epimerase. Methods Enzymol. 9:1966;605-608.
12. Karmali A., Drake A.F., Spencer N. Purification, properties and assay of D-ribulose 5-phosphate 3-epimerase from human erythrocytes. Biochem. J. 211:1983;617-623.
13. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
14. Ponder J.W., Richards F.M. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193:1987;775-791.
15. Banner D.W., Bloomer A.C., Petsko G.A., Phillips D.C., Pogson C.I., Wilson I.A., et al. Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 Å resolution using amino acid sequence data. Nature. 255:1975;609-614.
16. Wilmanns M., Hyde C.C., Davies D.R., Kirschner K., Jansonius J.N. Structural conservation in parallel β/α-barrel enzymes that catalyze three sequential reactions in the pathway of tryptophan biosynthesis. Biochemistry. 30:1991;9161-9169.
17. Jones S., Thornton J.M. Principles of protein-protein interactions. Proc. Natl Acad. Sci. USA. 93:1996;13-20.
18. Wood T. Purification and properties of D-ribulose-5-phosphate 3-epimerase from calf liver. Biochim. Biophys. Acta. 570:1979;352-362.
19. Chen Y.-R., Larimer F.W., Serpersu E.H., Hartman F.C. Identification of a catalytic aspartyl residue of D-ribulose-5-phosphate 3-epimerase by site-directed mutagenesis. J. Biol. Chem. 274:1999;2132-2136.
20. Alberts I.L., Nadassy K., Wodak S.J. Analysis of zinc binding sites in protein crystal structures. Protein Sci. 7:1998;1700-1716.
21. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., et al. Crystallography & NMR System: a new software for macromolecular structure determination. Acta Crystallog. sect. D. 54:1998;905-921.
22. Bode W., Gomis-Rüth F.X., Stöckler W. Astacins, serralysins, snake venom and matrix metalloproteinases exhibit identical zinc-binding environments (HExxHxxGxxH and Met-turn) and topologies and should be grouped into a common family, the "metzincins" FEBS Letters. 331:1993;134-140.
23. 18. J. Biol. Chem. 236:1961;1220-1224.
24. Davis L., Lee N., Glaser L. On the mechanism of the pentose phosphate epimerases. J. Biol. Chem. 247:1972;5862-5866.
25. Luo Y., Samuel J., Mosimann S.C., Lee J.E., Tanner M.E., Strynadka N.C.J. The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization. Biochemistry. 40:2001;14763-14771.
26. Dreyer M.K., Schulz G.E. Catalytic mechanism of the metal-dependent fuculose aldolase from Escherichia coli as derived from the structure. J. Mol. Biol. 259:1996;458-466.
27. Johnson A.E., Tanner M.E. Epimerization via carbon-carbon bond cleavage. L-Ribulose-5-phosphate 4-epimerase as a masked class II aldolase. Biochemistry. 37:1998;5746-5754.
28. Joerger A.C., Gosse C., Fessner W.-D., Schulz G.E. Catalytic action of fuculose 1-phosphate aldolase (class II) as derived from structure-directed mutagenesis. Biochemistry. 39:2000;6033-6041.
29. Samuel J., Luo Y., Morgan P.M., Strynadka N.C.J., Tanner M.E. Catalysis and binding in L-ribulose-5-phosphate 4-epimerase: a comparison with L-fuculose-1-phosphate aldolase. Biochemistry. 40:2001;14772-14780.
30. Tanner M.E. Understanding nature's strategies for enzyme-catalyzed racemization and epimerization. Acc. Chem. Res. 35:2002;237-246.
31. Leslie A.G.W. Molecular data processing. Moras D., Podjarny A.D., Thierry J.C. Crystallographic Computing. 1990;50-61 Oxford University Press, Oxford, UK.
32. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D. 50:1994;760-763.
33. Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallog. sect. A. 50:1994;157-163.
34. Brünger A.T. X-PLOR Version 3.1. A system for X-ray crystallography and NMR. 1:1992;Yale Univ. Press, New Haven.
35. Cowtan K.D. DM: an automated procedure for phase improvement by density modification. Joint CCP4 ESF-EACBM Newsletter Protein Crystallog. 31:1994;24-28.
36. Jiang J.-S., Brünger A.T. Protein hydration observed by X-ray diffraction: solvation properties of penicillopepsin and neuraminidase crystal structures. J. Mol. Biol. 243:1994;100-115.
37. Kabsch W., Sander C. Dictionary of protein secondary structures: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637.
38. Frishman D., Argos P. Knowledge-based protein secondary structure assignment. Proteins: Struct. Funct. Genet. 23:1995;566-579.
39. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402.