Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus.Kelly, C.A., Nishiyama, M., Ohnishi, Y., Beppu, T., Birktoft, J.J.
(1993) Biochemistry 32: 3913-3922
- PubMed: 8471603
- DOI: 10.1021/bi00066a010
- Structures With Same Primary Citation
- PubMed Abstract:
- Preliminary X-Ray Diffraction Analysis of a Crystallizable Mutant of Malate Dehydrogenase from the Thermophile Thermus Flavus
Kelly, C.A., Sarfaty, S., Nishiyama, M., Beppu, T., Birktoft, J.J.
(1991) J Mol Biol 221: 383
- Role of Threonine 190 in Modulating the Catalytic Function of Malate Dehydrogenase from a Thermophile Thermus Flavus
Nishiyama, M., Shimada, K., Horinouchi, S., Beppu, T.
(1991) J Biol Chem 266: 14294
- Refined Crystal Structure of Cytoplasmic Malate Dehydrogenase at 2.5-Angstroms Resolution
Birktoft, J.J., Rhodes, G., Banaszak, L.J.
(1989) Biochemistry 28: 6065
- Nucleotide Sequence of the Malate Dehydrogenase Gene of Thermus Flavus and its Mutation Directing an Increase in Enzyme Activity
Nishiyama, M., Matsubara, N., Yamamoto, K., Iijima, S., Uozumi, T., Beppu, T.
(1986) J Biol Chem 261: 14178
- Chemistry and Solution Conformation of the Pyridine Coenzymes
(1982) The Pyridine Nucleotide Coenzymes --: 51
- Malate Dehydrogenase
Banaszak, L.J., Bradshaw, R.A.
(1975) The Enzymes,third Edition 11A: 369
A binary complex of malate dehydrogenase from the thermophilic bacterium Thermus flavus (tMDH) with NADH has been crystallized from poly(ethylene glycol) 3500, pH 8.5, yielding diffraction-quality crystals in space group P2(1)2(1)2(1). The structure ...
A binary complex of malate dehydrogenase from the thermophilic bacterium Thermus flavus (tMDH) with NADH has been crystallized from poly(ethylene glycol) 3500, pH 8.5, yielding diffraction-quality crystals in space group P2(1)2(1)2(1). The structure was solved at 1.9-A resolution using molecular replacement and refined to an R factor of 15.8% with good geometry. The primary sequence of tMDH is 55% identical to that of cytoplasmic malate dehydrogenase (cMDH) [Birktoft, J. J., Rhodes, G., & Banaszak, L. J. (1989) Biochemistry 28, 6065-6081], and overall their three-dimensional structures are very similar. Like cMDH, tMDH crystallized as a dimer with one coenzyme bound per subunit. The coenzyme binds in the extended conformation, and most of the interactions with enzyme are similar to those in cMDH. In tMDH, small local conformational changes are caused by the replacement of a glutamic acid for the aspartic acid involved in hydrogen bonding to the adenine ribose of NADH. Comparison of tMDH with cMDH reveals that both tMDH subunits more closely resemble the B subunit of cMDH which therefore is the more likely representative of the solution conformation. While cMDH is inactivated at temperatures above about 50 degrees C, tMDH is fully active at 90 degrees C. On the basis of the X-ray crystal structure, a number of factors have been identified which are likely to contribute to the relative thermostability of tMDH compared to cMDH. The most striking of the differences involves the introduction of four ion pairs per monomer. All of these ion pairs are solvent-accessible. Three of these ion pairs are located in the dimer interface, Glu27-Lys31, Glu57-Lys168, and Glu57-Arg229, and one ion pair, Glu275-Arg149, is at the domain interface within each subunit. Additionally, we observe incorporation of additional alanines into alpha-helices of tMDH and, in one instance, incorporation of an aspartate that functions as a counterchange to an alpha-helix dipole. The possible contributions of these and other factors to protein thermostability in tMDH are discussed.
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110.