Reaction: n ATP + n H2O + wound RNA = n ADP + n phosphate + unwound RNA
Other name(s): DEAH/RHA protein; DEAH-box protein 2; Prp22p; DHX8; DHX36; CSFV NS3 helicase; nonstructural protein 3 helicase; KOKV helicase; Kokobera virus helicase; hepatitis C virus NS3 protein; DExH protein; MTR4; SKI2; BRR2; SUV3; Rig-I; retinoic-acid-inducible gene I; DbpA
Systematic name: RNA 3'-5' helicase (ATP-hydrolysing)
Comments: RNA helicases, which participate in nearly all aspects of RNA metabolism, utilize the energy from ATP hydrolysis to unwind RNA. The engine core of helicases is usually made of a pair of RecA-like domains that form an NTP binding cleft at their interface. Changes in the chemical state of the NTP binding cleft (binding of the NTP or its hydrolysis products) alter the relative positions of the RecA-like domains and nucleic acid-binding domains, creating structural motions that disrupt the pairing of the nucleic acid, causing separation and unwinding. Most RNA helicases utilize a mechanism known as canonical duplex unwinding, in which the helicase binds to a single stranded region adjacent to the duplex and then translocates along the bound strand with defined directionality, displacing the complementary strand. Most of these helicases proceed 3' to 5' (type A polarity), but some proceed 5' to 3' (type B polarity - cf. EC 5.6.2.5, RNA 5'-3' helicase), and some are able to catalyse unwinding in either direction [1,3]. Most canonically operating helicases require substrates with single stranded regions in a defined orientation (polarity) with respect to the duplex. A different class of RNA helicases, EC 5.6.2.7, DEAD-box RNA helicase, use a different mechanism and unwind short stretches of RNA with no translocation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Rozen, F., Edery, I., Meerovitch, K., Dever, T.E., Merrick, W.C. and Sonenberg, N. Bidirectional RNA helicase activity of eucaryotic translation initiation factors 4A and 4F. Mol. Cell Biol. 10 (1990) 1134-1144. [PMID: 2304461]
2. Shuman, S. Vaccinia virus RNA helicase. Directionality and substrate specificity. J. Biol. Chem. 268 (1993) 11798-11802. [PMID: 8505308]
3. Lee, C.G. RH70, a bidirectional RNA helicase, co-purifies with U1snRNP. J. Biol. Chem. 277 (2002) 39679-39683. [PMID: 12193588]
4. Zhang, S. and Grosse, F. Multiple functions of nuclear DNA helicase II (RNA helicase A) in nucleic acid metabolism. Acta Biochim Biophys Sin (Shanghai) 36 (2004) 177-183. [PMID: 15202501]
5. Diges, C.M. and Uhlenbeck, O.C. Escherichia coli DbpA is a 3' → 5' RNA helicase. Biochemistry 44 (2005) 7903-7911. [PMID: 15910005]
6. Frick, D.N. The hepatitis C virus NS3 protein: a model RNA helicase and potential drug target. Curr. Issues Mol. Biol. 9 (2007) 1-20. [PMID: 17263143]
7. Schwer, B. A conformational rearrangement in the spliceosome sets the stage for Prp22-dependent mRNA release. Mol. Cell 30 (2008) 743-754. [PMID: 18570877]
8. Takahasi, K., Yoneyama, M., Nishihori, T., Hirai, R., Kumeta, H., Narita, R., Gale, M., Jr., Inagaki, F. and Fujita, T. Nonself RNA-sensing mechanism of RIG-I helicase and activation of antiviral immune responses. Mol. Cell 29 (2008) 428-440. [PMID: 18242112]
9. Wang, X., Jia, H., Jankowsky, E. and Anderson, J.T. Degradation of hypomodified tRNA(iMet) in vivo involves RNA-dependent ATPase activity of the DExH helicase Mtr4p. RNA 14 (2008) 107-116. [PMID: 18000032]
10. Wen, G., Xue, J., Shen, Y., Zhang, C. and Pan, Z. Characterization of classical swine fever virus (CSFV) nonstructural protein 3 (NS3) helicase activity and its modulation by CSFV RNA-dependent RNA polymerase. Virus Res. 141 (2009) 63-70. [PMID: 19185595]