Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme: A new class of oxidative decarboxylases

Structure

Volumn 7, Issue 8, 1999, Pages 877-889

  Xu, Yingwu ^a   Bhargava, Girija ^a   Wu, Hao ^b   Loeber, Gerhard ^c   Tong, Liang ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c BOEHRINGER INGELHEIM RCV GMBH AND CO KG   (Austria)

Author keywords

Allosteric interactions; Cofactor specificity; Glutamine metabolism; Protein folds

Indexed keywords

ASPARTIC ACID; CARBON DIOXIDE; DIMER; DIVALENT CATION; GLUTAMIC ACID; GLUTAMINE; ISOENZYME; MALATE DEHYDROGENASE (NADP); MALIC ACID; MONOMER; ORGANOSELENIUM DERIVATIVE; PYRUVIC ACID; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; TETRAMER;

AMINO ACID METABOLISM; ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; HUMAN; PRIORITY JOURNAL; PROTEIN FOLDING;

EID: 0033566912     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(99)80115-4     Document Type: Article

References (66)

1. Hsu, R.Y. (1982). Pigeon liver malic enzyme. Mol. Cell. Biochem. 43, 3-26.
2. + malic enzyme of tumor mitochondria. J. Biol. Chem. 259, 6222-6227.
3. +-dependent mitochondrial malic enzyme. J. Biol. Chem. 266, 3016-3021.
4. Tipton, P.A., Quinn, T.P., Peisach, J. & Cook, P.F. (1996). Role of the divalent metal ion in the NAD:malic enzyme reaction: An ESEEM determination of the ground state conformation of malate in the E:Mn:malate complex. Protein Sci. 5, 1648-1654.
5. Urbauer, J.L., Bradshaw, D.E. & Cleland, W.W. (1998). Determination of the kinetic and chemical mechanism of malic enzyme using (2R,3R)-erythro-fluoromalate as a slow alternative substrate. Biochemistry 37, 18026-18031.
6. Ochoa, S., Mehler, A. & Kornberg, A. (1947). Reversible oxidative decarboxylation of malic acid. J. Biol. Chem. 167, 871-872.
7. +-dependent malic enzyme. Biochem. J. 304, 687-692.
8. Stryer, L. Biochemistry. (1995). WH Freeman & Company, New York, NY.
9. Moore, P.D. (1982). Evolution of photosynthetic pathways in flowering plants. Nature 295, 647-648.
10. Borsch, D. & Westhoff, P. (1990). Primary structure of NADP-dependent malic enzyme in the dicotyledonous C4 plant Flaveria trinervia. FEBS Lett. 273, 111-115.
11. Wynn, J.P., Kendrick, A., Hamid, A.A. & Ratledge, C. (1997). Malic enzyme: A lipogenic enzyme in fungi. Biochem. Soc. Trans. 25, S669.
12. Goodridge, A.G., et al., & Roncero, C. (1996). Nutritional and hormonal regulation of expression of the gene for malic enzyme. Prog. Nucl. Acid Res. Mol. Biol. 52, 89-122.
13. Sanz, N., Diez-Fernandez, C., Valverde, A.M., Lorenzo, M., Benito, M. & Cascales, M. (1997). Malic enzyme and glucose 6-phosphate dehydrogenase gene expression increases in rat liver cirrhogenesis. Br. J. Cancer 75, 487-492.
14. Baggetto, L.G. (1992). Deviant energetic metabolism of glycolytic cancer cells. Biochimie 74, 959-974.
15. McKeehan, W.L. (1982). Glycolysis, glutaminolysis and cell proliferation. Cell Biol. Int. Rep. 6, 635-650.
16. Reitzer, L.J., Wice, B.M. & Kennell, D. (1979). Evidence that glutamine, not sugar, is the major energy source for cultured HeLa cells. J. Biol. Chem. 254, 2669-2676.
17. +-dependent malic enzyme. J. Biol. Chem. 269, 4780-4786.
18. Kobayashi, K., Doi, S., Negoro, S., Urabe, I. & Okada, H. (1989). Structure and properties of malic enzyme from Bacillus stearothermophilus. J. Biol. Chem. 264, 3200-3205.
19. Wierenga, R.K., Terpstra, P. & Hol, W.G.J. (1986). Prediction of the occurrence of the ADP-binding βαβ-fold in proteins, using an amino acid sequence fingerprint. J. Mol. Biol. 187, 101-107.
20. Adams, M.J., Ellis, G.H., Gover, S., Naylor, C.E. & Phillips, C. (1994). Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: Implications for NADP specificity and the enzyme mechanism. Structure 2, 651-668.
21. Hurley, J.H., Dean, A.M., Sohl, J.L., Koshland, D.E., Jr. & Stroud, R.M. (1990). Regulation of an enzyme by phosphorylation at the active site. Science 249, 1012-1016.
22. Imada, K., Sato, M., Tanaka, N., Katsube, Y., Matsuura, Y. & Oshima, T. (1991). Three-dimensional structure of a highly thermostable enzyme, 3-isopropylmalate dehydrogenase of Thermus thermophilus at 2.2 Å resolution. J. Mol. Biol. 222, 725-738.
23. Scrutton, N.S., Berry, A. & Perham, R.N. (1990). Redesign of the coenzyme specificity of a dehydrogenase by protein engineering. Nature 343, 38-43.
24. Baker, P.J., Britton, K.L., Rice, D.W., Rob, A. & Stillman, T.J. (1992). Structural consequences of sequence patterns in the fingerprint region of the nucleotide binding fold. J. Mol. Biol. 228, 662-671.
25. + specificity-reversal mutant. Biochemistry 35, 5670-5678.
26. Sauer, L.A. (1973). An NAD- and NADP-dependent malic enzyme with regulatory properties. Biochem. Biophys. Res. Commun. 50, 524-531.
27. +-dependent malic enzyme from rat liver. J. Mol. Biol. 193, 233-235.
28. Clancy, L.L., et al., & Einspahr, H.M. (1992). Crystallization of the NAD-dependent malic enzyme from the parasitic nematode Ascaris suum. J. Mol. Biol. 226, 565-569.
29. Hendrickson, W.A. (1991). Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 254, 51-58.
30. Rossmann, M.G., Moras, D. & Olsen, K.W. (1974). Chemical and biological evolution of a nucleotide binding protein. Nature 250, 194-199.
31. Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
32. Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. (1995). SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
33. max-type cooperative enzyme phosphoglycerate dehydrogenase. Nature Struct. Biol. 2, 69-76.
34. Lamzin, V.S. et al. & Wilson, K.S. (1992). Crystal structure of NAD-dependent formate dehydrogenase. Eur. J. Biochem. 206, 441-452.
35. Goldberg, J.D., Yoshida, T. & Brick, P. (1994). Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 Å resolution. J. Mol. Biol. 236, 1123-1140.
36. + and 2-oxoisocaproate at 1.9 Å resolution. J. Mol. Biol. 267, 640-660.
37. Stillman, T.J., et al., & Rice, D.W. (1999). Insights into the mechanism of domain closure and substrate specificity of glutamate dehydrogenase from Clostridium symbiosum. J. Mol. Biol. 285, 875-885.
38. Baker, P.J., Turnbull, A.P., Sedelnikova, S.E., Stillman, T.J. & Rice, D.W. (1995). A role for quaternary structure in the substrate specificity of leucine dehydrogenase. Structure 3, 693-705.
39. Abad-Zapatero, C., Griffith, J.P., Sussman, J.L. & Rossmann, M.G. (1987). Refined crystal structure of dogfish M4 apo-lactate dehydrogenase. J. Mol. Biol. 198, 445-467.
40. Viljoen, M., van der Merwe, M., Subden, R.E. & van Vuuren, H.J. (1998). Mutation of Gly-444 inactivates the S. pombe malic enzyme. FEMS Microbiol. Lett. 167, 157-162.
41. +-dependent malic enzyme. J. Struct. Biol., in press.
42. Nevaldine, B.H., Bassel, A.R. & Hsu, R.Y. (1974). Mechanism of pigeon liver malic enzyme subunit structure. Biochim. Biophys. Acta 336, 283-293.
43. Chang, G.-G., Huang, T.-M. & Chang, T.-C. (1988). Reversible dissociation of the catalytically active subunits of pigeon liver malic enzyme. Biochem. J. 254, 123-130.
44. Lee, H.-J. & Chang, G.-G. (1990). Quarternary structure of pigeon liver malic enzyme. FEBS Lett. 277, 175-179.
45. Rothermel, B.A. & Nelson, T. (1989). Primary structure of the maize NADP-dependent malic enzyme. J. Biol. Chem. 264, 19587-19592.
46. 2+-L-malate binding and the subunit interactions of pigeon liver malic enzyme. Biochemistry 35, 9873-9879.
47. Burley, S.K. & Petsko, G.A. (1986). Amino-aromatic interactions in proteins. FEBS Lett. 203, 139-143.
48. Pry, T.A. & Hsu, R.Y. (1980). Equilibrium substrate binding studies of the malic enzyme of pigeon liver. Equivalence of nucleotide sites and anticooperativity associated with the binding of L-malate to the enzyme-manganese(II)-reduced nicotinamide adenine dinucleotide phosphate ternary complex. Biochemistry 19, 951-962.
49. 2+-ascorbate system. Biochemistry 33, 7931-7936.
50. 258 as the metal coordinate of pigeon liver malic enzyme by site-specific mutagenesis. Biochemistry 34, 7949-7954.
51. 2+-ascorbate system. J. Biol. Chem. 270, 25935-25941.
52. Satterlee, J. & Hsu, R.Y. (1991). Duck liver malic enzyme: Sequence of a tryptic peptide containing the cysteine residue labeled by the substrate analog bromopyruvate. Biochim. Biophys. Acta 1079, 247-252.
53. Chang, G.-G. & Huang, T.-M. (1980). Involvement of tyrosyl residues in the substrate binding of pigeon liver malic enzyme. Biochim. Biophys. Acta 611, 217-226.
54. Vernon, C.M. & Hsu, R.Y. (1983). Pigeon liver malic enzyme: Involvement of an arginyl residue at the binding site for malate and its analogs. Arch. Biochem. Biophys. 225, 296-305.
55. Rao, S.R., Kamath, B.G. & Bhagwat, A.S. (1991). Chemical modification of the functional arginine residue(s) of malic enzyme from Zea mays. Phytochem. 30, 431-435.
56. + complexes. Biochemistry 30, 8671-8678.
57. Sauer, L.A., Dauchy, R.T., Nagel, W.O. & Morris, H.P. (1980). Mitochondrial malic enzymes. J. Biol. Chem. 255, 3844-3848.
58. 2+. J. Biol. Chem. 251, 6574-6583.
59. Otwinowski, Z. (1993) Oscillation data reduction program. In CCP4 Study Weekend: Data Collection and Processing. (Sawyer, L., Isaacs, N. & Bailey, S., eds), pp56-62, SERC Daresbury Laboratory, Warrington, UK.
60. Turner, M.A., Yuan, C.-S., Borchardt, R.T., Hershfield, M.S., Smith, G.D. & Howell, P.L. (1998). Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength. Nat. Struct. Biol. 5, 369-376.
61. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119.
62. Brünger, A.T. (1992) The X-PLOR Manual. Yale University Press, Yale, New Haven, CT.
63. Carson, M. (1987). Ribbon models of macromolecules. J. Mol. Graph. 5, 103-106.
64. Birktoft, J.J. & Banaszak, L.J. (1983). The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenase. J. Biol. Chem. 258, 472-482.
65. Morioka, H., Magnuson, M.A., Mitsuhashi, T., Song, M.-K.H., Rall, J.E. & Nikodem, V.M. (1989). Structural characterization of the rat malic enzyme gene. Proc. Natl Acad. Sci. USA 86, 4912-4916.
66. Nicholls, A., Sharp, K.A. & Honig, B. (1991). Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.