RNA helicases

Eukaryotic initiation factor 4A (eIF4A) is a minimal (394 residues) DEAD-box RNA helicase. Its crystallographic structure reveals two domains which have similar core topology to the equivalent domains of DNA and viral RNA helicases.

eIF4a

In our crystals of full-length eIF4A, the molecule has a "dumbbell" conformation. We presume that it must condense into a compact structure in order to bind duplex RNA and dissociate the RNA strands. The structure provides a framework for further studies on the mechanism of RNA recognition and unwinding.

The "DbpA" family of prokaryotic RNA helicases, including the Bacillus subtilis YxiN protein, bind 23S ribosomal RNA with high affinity and specificity.  They are modular, consisting of a minimal helicase fragment plus a small carboxy-terminal extension that is responsible for specific RNA binding.  The carboxy-terminal RNA binding domain has an "RNA recognition motif" fold:

However, the domain appears to bind RNA in a manner that differs from that of eukaryotic RNA recognition motifs.

Publications

S. Wang, Y. Hu, M. T. Overgaard, F. V. Karginov, O. C. Uhlenbeck & D. B. McKay
"The domain of the Bacillus subtilis DEAD-box helicase YxiN that is responsible for specific binding of 23S rRNA has an RNA recognition motif fold"
RNA 12, 959-967 (2006). [PubMed] [Coordinates]

F. V. Karginov, J. M. Caruthers, Y. Hu, D. B. McKay & O. C. Uhlenbeck
"YxiN is a modular protein combining a DEx(D/H) core and a specific RNA-binding domain"
J. Biol. Chem. 280, 35499-35505 (2005). [PubMed]

J. M. Caruthers & D. B. McKay
"Helicase structure and mechanism"
Curr. Opin. Struc.t Biol. 12, 123-133. (2002). [PubMed]

J. M. Caruthers, E. R. Johnson & D. B. McKay (2000) "Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase"
Proc. Natl. Acad. Sci. USA 97, 13080-13085. [PubMed][C-terminal domain coordinates][eIF4A coordinates]

E. R. Johnson & D. B. McKay (1999) "Crystallographic structure of the amino terminal domain of yeast initiation factor 4A, a representative DEAD-box RNA helicase"
RNA 5, 1524-1536. [PubMed][N-terminal domain coordinates]

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