Department of Protein Synthesis Enzymology

Head Mykhailo A. Tukalo, Professor, Dr.Sci., Deputy director for scientific recearch Tel: (380-44) 526 55 89 Fax (38 - 044) 526-07-59 E.mail: mtukalo@imbg.org.ua

The fundamental research program of the Department is focused on:

Studies on the structural basis of the RNA-protein recognition and enzymatic catalysis.

Our current research and recent achievements:

The current area of focus is the specific recognition of aminoacyl-tRNA synthetases for their cognate amino acid and tRNA, mechanisms of catalysis and editing.

Using biochemical methods, site-directed mutagenesis and X-ray crystallography, work carried out on different prokaryotic (including important pathogenic bacteria Enterococcus faecalis, Mycobacterium tuberculosis and Streptococcus pneumoniae), eukaryotic and archaeal systems.

The crystal structures of six synthetases have been determined in collaboratin with Dr S.Cusack at EMBL Grenoble (seryl-, lysyl-, histidyl-, prolyl-, leucyl- and tyrosyl-tRNA synthetases) with various combinations of the substrates, including five tRNA complexes.

The structures of the complexes of SerRS, TyrRS and LeuRS with cognate tRNAs provided the first information on the structures of a tRNAs with a long variable arm and elucidated the details of how enzymes interact with cognate tRNA and discriminate uncognate one.

The aim of one project is studying the molecular mechanisms of editing during aminoacyl-tRNA synthesis for two aminoacyl-tRNA synthetases from two different classes: leucyl- (a class I) and prolyl-tRNA synthetases (a class II).

The differences between human and prokaryotic synthetases are using for development of novel classes of antibiotics against Enterococcus faecalis and Mycobacterium tuberculosis.

Selected publications:

1. Fujinada, M., Berthet-Colominas, C., Yaremchuk, A.D., Tukalo, M.A. and Cusack S. Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 Å resolution / J .Mol.Biol. (1993) 234, 222-233.
2. Biou, V., Yaremchuk, A., Tukalo, M., Cusack, S. The crystal structure of a complex between seryl-tRNA synthetase and tRNASer from Thermus thermophilus at 2.9 Å resolution. / Science (1994) 263. 1404-1410.
3. Cusack, S., Yaremchuk, A., Krikliviy, I. and Tukalo, M. tRNApro anticodon recognition by Thermus thermophilus prolyl-tRNA synthetase./ Structure (1998) 6, 101-108
4. Egorova, S.P., Yaremchuk, A.D., Kriklivyi, I.A. and Tukalo, M. A. Comparative analysis of interaction sites of Thermus thermophilus and Escherichia coli tRNATyr with homologous aminoacyl-tRNA synthetases by means of chemical modification and nuclease hydrolysis. / Bioorg . Khim. (1998) 24,593-600.
5. Kovalenko, O.P., Petrushenko, Z.M., Kriklivyi, I.A., Yaremchuk, A.D. and Tukalo, M.A. A comparative study of phosphate reactivities in tRNASer and tRNALeu from Thermus thermophilus. / Bioorg. Khim. (1999) 25, 768-773
6. Cusack, S., Yaremchuk, A. and Tukalo, M. The 2Å crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue / EMBO J. (2000) 19, 2351-2361.
7. Yaremchuk, A., Cusack, S. and Tukalo, M. The crystal structure of a eukaryote/archaeon-like prolyl-tRNA synthetase and its complex with tRNAPro(CGG). / EMBO J. (2000) -19, 4745-4758
8. Yaremchuk, A., Tukalo, M., Grotli, M. and Cusack, S. A succession of substrate induced conformational changes ensures the amino acid specificity of Thermus thermophilus prolyl-tRNA synthetase: comparison with histidyl-tRNA synthetase./ J. Mol Biol. (2001) 309, 989-1002
9. Yaremchuk, A., Kriklivyi, I., Tukalo, M. and Cusack, S. Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. / EMBO J. (2002) 15, 3829-3840.
10. Lincecum, T.L, Tukalo, M., Yaremchuk, A., Mursinna, R.S., Williams, A.M., Sproat, B.S., Van Den Eynde, W., Link, A., Van Calenbergh ,S,, Grotli, M., Martinis, S.A., and Cusack, S. Structural and Mechanistic Basis of Pre- and Posttransfer Editing by Leucyl-tRNA Synthetase. / Molecular Cell. (2003) 11, 951-963.
11. Kobayashi, T., Nureki, O., Ishitani, R., Yaremchuk, A., Tukalo, M., Cusack, S., Sakamoto, K. and Yokoyama, S. Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. / Nature Struct. Biol. (2003) 10, 425-432