Ganoza

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We are currently working on three translation factors:

 
EF-P
RbbA
DEAD

EF-P
EF-P is a protein factor that stimulates the peptidyltransferase reaction for some aminoacyl combinations. In particular, it may help catalyze the first peptide bond. Crystals of EF-P have been produced. 
 
The intrinsic peptidyltransferase activity of the 50S ribosomal subunit cannot efficiently condense all aminoacyl template combinations (Symons et al., 1978). EF-P was isolated as a factor capable of enhanceing the condensation of these combinations.

EF-P is 20.6 kDa protein encoded by the efp gene (Aoki et al., 1991). The gene is essential for both cell viability and protein synthesis (Aoki et al., 1997a).

EF-P is homologous to the eukaryotic factor eIF-5A (Bartig et al., 1992; Aoki et al., 1997b). eIF-5A crystal structure has been determined (Kim et al., 1998) and EF-P has been crystallized (Aoki et al., 1997b).

References:
Aoki, H., Adams, S.-L., Chung, D.G., Yaguchi, M., Chuang, S.E., and Ganoza, M.C. (1991). Cloning, sequncing and overexpression of the gene for prokaryotic factor EF-P involved in peptide bond synthesis. Nucleic Acids  Res 19, 6215-6220.

Aoki, H., Dekany, K., Adams, S.-L., and Ganoza, M.C. (1997a). The gene encoding the elongation factor P protein is essential for viability and is required for protein synthesis. J Biol Chem 272, 32254-32259.
Online article

Aoki, H. Adams, S.-L., Turner, M.A., and Ganoza, M.C. (1997b). Molecular characterization of the prokaryotic efp gene product involved in a peptidyl- transferase reaction. Biochimie 79, 7-11.

Bartig, D., Lemkemeier, K., Frank, J., Lottspeich, F., and Klink, F. (1992). The archaebacterial hypusine-containing protein. Structural features suggest a common ancestry with the eukaryotic translation initiation factor 5A. Eur J Biochem 204, 751-758.

Kim, K.K., Hung, L.W., Yokota, H., Kim, R., kim, S.H. (1998). Crystal structures of eukaryotic initiation factor 5A from Methanococcus jannaschii at 1.8 A level resolution. PNAS 95(18), 10419-10424.
Online article

Symons, R.H., Harris, R.J., Greenwell, P., Eckerman, D.J., and Vanin, E.F. (1978). The use of puromycin analogs and related compounds to probe the active centre of peptidyl transferase on Escherichia coli ribosomes. Bioorg Chem 4, 409-439.


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RbbA
RbbA is a ribosome bound ATPase. It possesses both a ribosome-independent and ribosome-dependent ATPase activity; ribosomes increase the ATPase activity of RbbA by two-fold. RbbA stimulates the synthesis of polyphenylalanine from a poly(U) template by at least four-fold. The hydrolysis of ATP by RbbA is required for the stimulation.

RbbA was isolated as an ATPase that is predominantly bound to 70S ribosomes and 30S ribosomal subunits (Kiel et al., 1999). RbbA is a 91 kDa protein encoded by the gene yhih.

RbbA cross-reacts to antibodies against the yeast translation factor EF-3. EF-3, too, is an ATPase (Kamath and Chakraburtty, 1989). Like EF-3, RbbA has both a ribosome-independent and ribosome-dependent ATPase activity. 70S ribosomes increase the ATPase activity by two-fold.

RbbA stimulates the synthesis of poly-phenylalanine only when ATP is present. Non-hydrolyzable forms inhibit the stimulation (Kiel and Ganoza, 2000).

RbbA binds 16S ribosomal RNA, binds tightly to poly(G) and binds EF-Tu. The binding site on 16S rRNA is most likely a G-rich domain of 5-6 consecutive G residues. RbbA induces a conformational change within the 16S rRNA (Kiel and Ganoza, 2000). The conformational change involves the first defined rRNA switch (Lodmell and Dahlberg, 1997).

References:
Kamath, A. and Chakraburtty, K. (1989). Role of yeast elongation factor 3 in the elongation cycle. J Biol Chem 264, 15423-15428.

Kiel, M.C., Aoki, H., and Ganoza, M.C. (1999). Identification and characterization of an Escherichia coli ribosomal ATPase. Biochimie 81(12), 1097-1108.

Kiel, M.C. and Ganoza, M.C. (2000). Functional interactions of an Escherichia coli ribosomal ATPase. submitted.

Lodmell, J.S. and Dahlberg, A.E. (1997). A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA. Science 277,  1262-1267.
Online article


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DEAD
DEAD is an ATPase that has homology to other ATP-dependent helicases (the DEAD/H family of proteins). DEAD is required for the formation of the translation initiation complex with mRNAs that contain secondary structures around the start codon region. It is thought that DEAD is a helix destabilizer.

References:
Lu, J., Aoki, H., and Ganoza, M.C. (1999). Molecular characterization of a prokaryotic translation factor homologous to the eukaryotic initiation factor eIF-4A. Int J Biochem Cell Biol 31, 215-229.


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