Helicase

Structure of E. coli helicase RuvA

Helicases are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands (i.e., DNA, RNA, or RNA-DNA hybrid) using energy derived from ATP hydrolysis.

Function

Many cellular processes (DNA replication, transcription, translation, recombination, DNA repair, ribosome biogenesis) involve the separation of nucleic acid strands. Helicases are often utilized to separate strands of a DNA double helix or a self-annealed RNA molecule using the energy from ATP hydrolysis, a process characterized by the breaking of hydrogen bonds between annealed nucleotide bases. They move incrementally along one nucleic acid strand of the duplex with a directionality and processivity specific to each particular enzyme. There are many helicases (14 confirmed in E. coli, 24 in human cells) resulting from the great variety of processes in which strand separation must be catalyzed.^{[citation needed]}

Helicases adopt different structures and oligomerization states. Whereas DnaB-like helicases unwind DNA as donut-shaped hexamers, other enzymes have been shown to be active as monomers or dimers. Studies have shown that helicases may act passively, waiting for uncatalyzed unwinding to take place and then translocating between displaced strands,^[1] or can play an active role in catalyzing strand separation using the energy generated in ATP hydrolysis.^[2] In the latter case, the helicase acts comparably to an active motor, unwinding and translocating along its substrate as a direct result of its ATPase activity.^[3] Helicases may process much faster in vivo than in vitro due to the presence of accessory proteins that aid in the destabilization of the fork junction.^[3]

Defects in the gene that codes helicase cause Werner syndrome, a disorder characterized by the appearance of premature aging.

Structural features

The common function of helicases accounts for the fact that they display a certain degree of amino acid sequence homology; they all possess common sequence motifs located in the interior of their primary sequence. These are thought to be specifically involved in ATP binding, ATP hydrolysis and translocation on the nucleic acid substrate. The variable portion of the amino acid sequence is related to the specific features of each helicase.

Based on the presence of defined helicase motifs, it is possible to attribute a putative helicase activity to a given protein, though the presence of a motif does not confirm the protein as a helicase. Conserved motifs do, however, support an evolutionary homology among enzymes. Based on the presence and the form of helicase motifs, helicases have been separated in 4 superfamilies and 2 smaller families. Some members of these families are indicated, with the organism from which they are extracted, and their function.

Superfamilies

Helicases have been classified in 6 superfamilies (SF1-SF6). All of the proteins bind ATP, and, as a consequence, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs.

• Superfamily I: UvrD (E. coli, DNA repair), Rep (E. coli, DNA replication), PcrA (Staphylococcus aureus, recombination), Dda (bacteriophage T4, replication initiation), RecD (E. coli, recombinational repair), TraI (F-plasmid, conjugative DNA transfer). This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in positive-strand single-stranded RNA viruses from superfamily 1. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.^[4]
• Superfamily II: RecQ (E. coli, DNA repair), eIF4A (Baker's Yeast, RNA translation), WRN (human, DNA repair), NS3^[5] (Hepatitis C virus, replication). TRCF (Mfd) (E. coli, transcription-repair coupling).
• Superfamily III: LTag (Simian Virus 40, replication), E1 (human papillomavirus, replication), Rep (Adeno-Associated Virus, replication, viral integration, virion packaging). Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses.^[6][7] Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori (origin of DNA replication) with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated.
• DnaB-like family: dnaB (E. coli, replication), gp41 (bacteriophage T4, DNA replication), T7gp4 (bacteriophage T7, DNA replication).
• Rho-like family: Rho (E. coli, transcription termination).

Note that these superfamilies do not subsume all possible helicases. For example, XPB and ERCC2 are helicases not included in any of the above families.

RNA Helicases

RNA Helicases and DNA Helicases can be found together in all the Helicase Super Families except for SF6.^[8] However, not all RNA Helicases exhibit helicase activity as defined by enzymatic function, i.e., proteins of the Swi/Snf family. Although these proteins carry the typical helicase motifs, hydrolize ATP in a nucleic acid-dependent manner, and are built around a helicase core, in general, no unwinding activity is observed.^[9]

RNA Helicases that do exhibit unwinding activity have been characterized by at least two different mechanisms: canonical duplex unwinding and local strand separation. Canonical duplex unwinding is the stepwise directional separation of a duplex strand, as described above, for DNA unwinding. However, local strand separation occurs by a process wherein the helicase enzyme is loaded at any place along the duplex. This is usually aided by a single-stranded region of the RNA, and the loading of the enzyme is accompanied with ATP binding.^[10] Once the helicase and ATP are bound, local strand separation occurs, which requires binding of ATP but not the actual process of ATP hydrolysis.^[11] Presented with fewer base pairs the duplex then dissociates without further assistance from the enzyme. This mode of unwinding is used by DEAD-box helicases.^[12]

See also

• chromodomain helicase DNA binding protein: CHD1, CHD1L, CHD2, CHD3, CHD4, CHD5, CHD6, CHD7, CHD8, CHD9
• DEAD box/DEAD/DEAH box helicase: DDX3X, DDX5, DDX6, DDX10, DDX11, DDX12, DDX58, DHX8, DHX9, DHX37, DHX40, DHX58
• ASCC3, BLM, BRIP1, DNA2, FBXO18, FBXO30, HELB, HELLS, HELQ, HELZ, HFM1, HLTF, IFIH1, NAV2, PIF1, RECQL, RTEL1, SHPRH, SMARCA4, SMARCAL1, WRN, WRNIP1

References

1. ^ Lionnet T, Spiering MM, Benkovic SJ, Bensimon D, Croquette V (2007). "Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism". PNAS 104 (50): 19790–19795. doi:10.1073/pnas.0709793104. PMC 2148377. PMID 18077411. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2148377. 
2. ^ Johnson DS, Bai L, Smith BY, Patel SS, Wang MD (2007). "Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped t7 helicase". Cell 129 (7): 1299–309. doi:10.1016/j.cell.2007.04.038. PMC 2699903. PMID 17604719. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2699903. 
3. ^ ^{a b} "Researchers solve mystery of how DNA strands separate". 2007-07-03. http://www.physorg.com/news102663442.html. Retrieved 2007-07-05. 
4. ^ Garcia JA, Kaariainen L, Gomez de cedron M, Ehsani N, Mikkola ML (1999). "RNA helicase activity of Semliki Forest virus replicase protein NSP2". FEBS Lett. 448 (1): 19–22. doi:10.1016/S0014-5793(99)00321-X. PMID 10217401. 
5. ^ Dumont S, Cheng W, Serebrov V, Beran RK, Tinoco Jr I, Pylr AM, Bustamante C, "RNA Translocation and Unwinding Mechanism of HCV NS3 Helicase and its Coordination by ATP", Nature. 2006 Jan 5; 439: 105-108.
6. ^ Koonin EV, Aravind L, Iyer LM (2001). "Common origin of four diverse families of large eukaryotic DNA viruses". J. Virol. 75 (23): 11720–34. doi:10.1128/JVI.75.23.11720-11734.2001. PMC 114758. PMID 11689653. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=114758. 
7. ^ Koonin EV, Aravind L, Leipe DD, Iyer LM (2004). "Evolutionary history and higher order classification of AAA+ ATPases". J. Struct. Biol. 146 (1–2): 11–31. doi:10.1016/j.jsb.2003.10.010. PMID 15037234. 
8. ^ "RNA Helicases" Edited by Eckhard Jankowsky, RSC Publishing 2010
9. ^ Jankowsky, E (2011). "RNA helicases at work: Binding and rearranging". Trends in biochemical sciences 36 (1): 19–29. doi:10.1016/j.tibs.2010.07.008. PMC 3017212. PMID 20813532. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3017212. 
10. ^ Yang, Quansheng; Del Campo, Mark; Lambowitz, Alan M.; Jankowsky, Eckhard (2007). "DEAD-Box Proteins Unwind Duplexes by Local Strand Separation". Molecular Cell 28 (2): 253–63. doi:10.1016/j.molcel.2007.08.016. PMID 17964264. 
11. ^ Liu, F.; Putnam, A.; Jankowsky, E. (2008). "ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding". Proceedings of the National Academy of Sciences 105 (51): 20209. doi:10.1073/pnas.0811115106. 
12. ^ Jarmoskaite, Inga; Russell, Rick (2011). "DEAD-box proteins as RNA helicases and chaperones". Wiley Interdisciplinary Reviews: RNA 2: 135. doi:10.1002/wrna.50. 

External links

• MeSH DNA+Helicases
• MeSH RNA+Helicases