BIOC3390 Tutorials: 16 & 18 November 1999

RNA and DNA helicases

These ATP-driven motors are responsible for unwinding double helical regions in RNA and DNA during recombination, replication, transcription and splicing. The protein family is universally distributed and numerous recognisable sequence motifs have been discovered in eukaryotic, bacterial and viral genomes. Some of the helicase enzymes share features with ATP synthase.

This is the X-ray structure of the Pcra helicase from Bacillus stearothermophilus, reported by Velankar et al in 1999. [Brookhaven code 3PJR.] These workers suggested an "inchworm" mechanism.

Switch to ribbon view and colour in the protein and the DNA strands. Click HERE for a brief reminder of the main CHIME commands, or HERE for a full tutorial. Rotate the molecule and experiment with different views to study the unwinding mechanism. There is an ATP molecule in the structure: see if you can find it.

Try to resist the temptation to talk about helicase genetics, and concentrate on the mechanics of the process. How much force is required to separate a double helix? How many hydrogen bonds might reasonably be cleaved per ATP? What is the stoichiometry of the overall process? Are all these molecular motors built fundamentally to the same design?

Allison, TJ et al (1998) Crystal structure of the RNA-binding domain from transcription termination factor rho. Nature Structural Biology 5(5), 352-356. [Write down the volume and page numbers for future reference. Click HERE for access instructions. Click HERE to gain access via the Leeds University network.]

Biswas, EE & Biswas, SB (1999) Mechanism of DnaB helicase of Escherichia coli: Structural domains involved in ATP hydrolysis, DNA binding, and oligomerization. Biochemistry 38(34), 10919-10928. [Click HERE for the HTML version, or HERE for PDF format.]

Biswas, EE & Biswas, SB (1999) Mechanism of DNA binding by the DnaB helicase of Escherichia coli: Analysis of the roles of domain gamma in DNA binding. Biochemistry 38(34), 10929-10939. [Click HERE for the HTML version, or HERE for PDF format.]

Carpousis et al (1999) mRNA degradation - a tale of poly(A) and multiprotein machines Trends in Genetics 15(1), 24-28. [No electronic copies are available.]

delaCruz et al (1999) Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families TIBS 24(5) 192-198. [No electronic copies are available.]

Davies, GP et al (1999) On the structure and operation of type I DNA restriction enzymes. J. Mol. Biol. 290(2), 565-579. [Click HERE for HTML format, or HERE for the PDF version.]

Dillingham, MS et al (1999) Site-directed mutagenesis of motif III in PcrA helicase reveals a role in coupling ATP hydrolysis to strand separation. Nucleic Acids Research 27(16), 3310-3317. [Click HERE for the HTML version.]

Egelman, EH (1998) Bacterial helicases. J. Struct. Biol. 124(2-3), 123-128. [Click HERE for the abstract, or HERE for the PDF version.]

Eisen, A & Lucchesi, JC (1998) Unraveling the role of helicases in transcription. Bioessays 20(8), 634-641. [Inter-library loan needed.]

Hall, MC et al (1998) Site-directed mutations in motif VI of Escherichia coli DNA helicase II result in multiple biochemical defects: Evidence for the involvement of motif VI in the coupling of ATPase and DNA binding activities via conformational changes J. Mol. Biol. 277(2), 257-271. [Click HERE for HTML format, or HERE for the PDF version.]

Hsieh, J et al (1999) A two-site kinetic mechanism for ATP binding and hydrolysis by E-coli Rep helicase dimer bound to a single-stranded oligodeoxynucleotide. J. Mol. Biol. 288(2), 255-274. [Click HERE for HTML format, or HERE for the PDF version.]

Kadare, G & Haenni, AL (1997) Virus-encoded RNA helicases. J. Virology 71(4), 2583-2590. [No electronic copies are available.]

Kanemaki, M et al (1999) TIP49b, a new RuvB-like DNA helicase, is included in a complex together with another RuvB-like DNA helicase, TIP49a. J. Biol. Chem. 274(32), 22437-22444. [Click HERE for the HTML version, or HERE for PDF format.]

Kodadek, T (1998) Mechanistic parallels between DNA replication, recombination and transcription TIBS 23(2), 79-83. [No electronic copies are available.]

Lohman, TM & Bjornson, KP (1996) Mechanisms of helicase-catalyzed DNA unwinding. Annual Rev. Biochem. 65, 169-214. [Click HERE for the abstract and citations. Unfortunately there is no full-text version of this paper available in PDF format.]

Lohman, TM et al (1998) Staying on track: Common features of DNA helicases and microtubule motors Cell 93(1), 9-12. [No electronic copies are available.]

Luking et al (1998) The protein family of RNA helicases. Crit. Rev. Biochem. Mol. Biol. 33(4), 259-296. [No electronic copies are available.]

Morris, PD & Raney, KD (1999) DNA helicases displace streptavidin from biotin-labeled oligonucleotides. Biochemistry 38(16), 5164-5171. [Click HERE for the HTML version, or HERE for PDF format.]

Shen, JC et al (1998) Werner syndrome protein I. DNA helicase and DNA exonuclease reside on the same polypeptide. J. Biol. Chem. 273(51), 34139-34144. [Click HERE for the HTML version, or HERE for PDF format.]

Soultanas, P et al (1999) DNA binding mediates conformational changes and metal ion coordination in the active site of PcrA helicase J. Mol. Biol. 290(1), 137-148. [Click HERE for HTML format, or HERE for the PDF version.]

Staley, JP & Guthrie, C (1998) Mechanical devices of the spliceosome: Motors, clocks, springs, and things Cell 92(3), 315-326. [No electronic copies are available.]

Stitt, BL & Xu, YM (1998) Sequential hydrolysis of ATP molecules bound in interacting catalytic sites of Escherichia coli transcription termination protein Rho. J. Biol. Chem. 273(41), 26477-26486. [Click HERE for the HTML version, or HERE for PDF format.]

Swagemakers, SMA et al (1998) The human Rad54 recombinational DNA repair protein is a double-stranded DNA-dependent ATPase J. Biol. Chem. 273(43), 28292-28297. [This paper has only a tenuous connection with helicase, but is nonetheless fascinating. Click HERE for the HTML version, or HERE for PDF format.]

Pazin, MJ & Kadonaga, JT (1997) SW12/SNF2 and related proteins: ATP-Driven motors that disrupt protein-DNA interactions? Cell 88(6), 737-740. [No electronic copies are available.]

Tuteja, N (1997) Unraveling DNA helicases from plant cells. Plant Molecular Biology 33(6), 947-952. [No electronic copies are available.]

Velankar, SS et al (1999) Crystal Structures of Complexes of Pcra DNA Helicase with a DNA Substrate Indicate an Inchworm Mechanism. Cell 97, 75. [No electronic copies are available, but the structure is in the PDB.]

Waga, S;Stillman, B (1998) The DNA replication fork in eukaryotic cells. Annual Rev. Biochem. 67, 721-751. [Click HERE for the HTML version, or HERE for PDF format.]

Wagner, JDO et al (1998) The DEAH-box protein PRP22 is an ATPase that mediates ATP- dependent mRNA release from the spliceosome and unwinds RNA duplexes EMBO J. 17(10), 2926-2937. [Click HERE for the HTML version, or HERE for PDF format.]

West, SC (1996) DNA helicases: New breeds of translocating motors and molecular pumps. Cell 86(2), 177-180. [No electronic copies are available.]

West, SC (1997) Processing of recombination intermediates by the RuvABC proteins Annual Rev. Genetics 31, 213-244. [Click HERE for the HTML version, or HERE for PDF format.]

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