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EcoSal Plus

Domain 4:

Synthesis and Processing of Macromolecules

DNA Helicases

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  • Author: Piero R. Bianco1
  • Editor: Susan T. Lovett2
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Center for Single Molecule Biophysics, Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY 14214; 2: Brandeis University, Waltham, MA
  • Received 08 December 2009 Accepted 22 February 2010 Published 24 September 2010
  • Address correspondence to Piero R. Bianco pbianco@buffalo.edu
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  • Abstract:

    DNA and RNA helicases are organized into six superfamilies of enzymes on the basis of sequence alignments, biochemical data, and available crystal structures. DNA helicases, members of which are found in each of the superfamilies, are an essential group of motor proteins that unwind DNA duplexes into their component single strands in a process that is coupled to the hydrolysis of nucleoside 5'-triphosphates. The purpose of this DNA unwinding is to provide nascent, single-stranded DNA (ssDNA) for the processes of DNA repair, replication, and recombination. Not surprisingly, DNA helicases share common biochemical properties that include the binding of single- and double-stranded DNA, nucleoside 5'-triphosphate binding and hydrolysis, and nucleoside 5'-triphosphate hydrolysis-coupled, polar unwinding of duplex DNA. These enzymes participate in every aspect of DNA metabolism due to the requirement for transient separation of small regions of the duplex genome into its component strands so that replication, recombination, and repair can occur. In, there are currently twelve DNA helicases that perform a variety of tasks ranging from simple strand separation at the replication fork to more sophisticated processes in DNA repair and genetic recombination. In this chapter, the superfamily classification, role(s) in DNA metabolism, effects of mutations, biochemical analysis, oligomeric nature, and interacting partner proteins of each of the twelve DNA helicases are discussed.

  • Citation: Bianco P. 2010. DNA Helicases, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.8

Key Concept Ranking

DNA Polymerase III
0.48758364
Genetic Recombination
0.44033238
Nucleotide Excision Repair
0.4346923
DNA Replication Proteins
0.42419487
0.48758364

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/content/journal/ecosalplus/10.1128/ecosalplus.4.4.8
2010-09-24
2017-10-20

Abstract:

DNA and RNA helicases are organized into six superfamilies of enzymes on the basis of sequence alignments, biochemical data, and available crystal structures. DNA helicases, members of which are found in each of the superfamilies, are an essential group of motor proteins that unwind DNA duplexes into their component single strands in a process that is coupled to the hydrolysis of nucleoside 5'-triphosphates. The purpose of this DNA unwinding is to provide nascent, single-stranded DNA (ssDNA) for the processes of DNA repair, replication, and recombination. Not surprisingly, DNA helicases share common biochemical properties that include the binding of single- and double-stranded DNA, nucleoside 5'-triphosphate binding and hydrolysis, and nucleoside 5'-triphosphate hydrolysis-coupled, polar unwinding of duplex DNA. These enzymes participate in every aspect of DNA metabolism due to the requirement for transient separation of small regions of the duplex genome into its component strands so that replication, recombination, and repair can occur. In, there are currently twelve DNA helicases that perform a variety of tasks ranging from simple strand separation at the replication fork to more sophisticated processes in DNA repair and genetic recombination. In this chapter, the superfamily classification, role(s) in DNA metabolism, effects of mutations, biochemical analysis, oligomeric nature, and interacting partner proteins of each of the twelve DNA helicases are discussed.

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Figures

Image of Figure 1
Figure 1

Schematics of two hypothetical, monomeric DNA helicases are shown. Each protein is bound to the DNA strand on which it translocates. (A) A 3′→5′ DNA helicase. (B) A 5′→3′ DNA helicase.

Citation: Bianco P. 2010. DNA Helicases, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.8
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Image of Figure 2
Figure 2

(Top) Four DNA helicases are shown. RecG (monomeric), RecB and D (heterotrimeric as RecBCD), DnaB (hexameric), and RuvAB (dodecameric as RuvAB with two diametrically opposed hexameric RuvB rings). (Middle) The partner proteins responsible for either loading the motor onto the DNA (SSB, DnaC, RuvA) or providing scaffolding and structural assistance in DNA unwinding (RecC and RuvA) are indicated. (Bottom) Biological role of each DNA helicase.

Citation: Bianco P. 2010. DNA Helicases, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.8
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Image of Figure 3
Figure 3

Two diametrically opposed DnaB homohexamers are shown translocating and unwinding DNA. Once loaded onto the DNA at , these motor complexes move in opposite directions and are tightly coupled to the replication machinery that follows immediately behind (not shown). To unwind the DNA duplex, one strand of DNA passes through the center of the ring while the other is forced to the outside. Unwound strands of DNA can be bound by SSB protein (gray spheres).

Citation: Bianco P. 2010. DNA Helicases, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.8
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Image of Figure 4A
Figure 4A

(A) The interaction of the translocating RecBCD enzyme with chi elicits a complex set of changes in the enzyme. RecBCD binds to DNA ends with high affinity and, in the presence of ATP, translocates, unwinds, and degrades the unwound strands of DNA. Prior to chi, endonucleolytic degradation of DNA is asymmetric as indicated by the dashed lines. Upon encountering chi, the enzyme recognizes the sequence and pauses; the resulting changes include inactivation of the RecD subunit (now in black), alteration of the polarity of endonucleolytic activity, and loading of RecA onto the strand of DNA containing chi to facilitate recombination initiation (not shown).

Citation: Bianco P. 2010. DNA Helicases, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.8
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Image of Figure 4B
Figure 4B

(B) A side view of the RecBCD heterotrimer is shown bound to the DNA. Each of the subunits is shown in a different color and RecC is transparent so that the path of the DNA through the subunit is apparent. DNA that has been cleaved by the nuclease domain present in RecB is indicated by the dashed lines. This figure is adapted from references 129 , 128 , and 133 .

Citation: Bianco P. 2010. DNA Helicases, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.8
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Image of Figure 4C
Figure 4C

(Top) RecBCD is shown translocating and unwinding dsDNA. (Bottom) The RecBCD enzyme is shown in the same orientation as in panel B, except that the RecD subunit has been removed so that the path of the unwound DNA through the channels in RecC is clearly visible. To facilitate passage of DNA into and through the enzyme, the leading domain of RecB reaches ahead onto the duplex and then pulls the DNA into the enzyme. DNA strands are separated on the surface of RecC and then pass through the channels within RecC (yellow arrow).

Citation: Bianco P. 2010. DNA Helicases, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.8
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Image of Figure 5A
Figure 5A

(A) Architecture of a RecG monomer with the domains identified as follows: pink, wedge domain (AA 1–218); green, linker (AA 219–246); blue, helicase domain (AA 247–658), and orange, TRG motif ( 147 , 153 ). The color schemes in the left and right panels are the same to enable identification of domains within the structure of RecG. This figure is adapted from reference 153 .

Citation: Bianco P. 2010. DNA Helicases, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.8
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Image of Figure 5B
Figure 5B

(B) A surface representation of RecG regressing a stalled fork. Here, the RecG wedge domain is pink and helicase domain is cyan. The arms of the fork are shown in red. Following regression as indicated by the arrow (Right), the DNA at the fork resembles a “chicken foot” with the central, nascent heteroduplex region shown in green. A single SSB tetramer is indicated (it is unclear whether SSB participates in any way in fork regression). Blue spheres, SSB.

Citation: Bianco P. 2010. DNA Helicases, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.8
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Image of Figure 6
Figure 6

A schematic of the sequential assembly and resulting activity of the enzyme on a Holliday junction. (step 1) A RuvA tetramer (mauve circles) bound to a dimer of RuvB (grey ovals) assembles on a junction. Another RuvA tetramer binds to form a junction sandwich flanked by partially assembled RuvB hexamers. (step 2) Additional RuvB monomers bind leading to formation of the complete branch migration complex. (step 3) Following branch migration, the translocating complex may pause with one RuvA tetramer dissociating, followed by association of the RuvC dimer (green ovals). Cleavage by RuvC ensues, and after RuvABC dissociation and DNA ligation, resolution is completed (step 4).

Citation: Bianco P. 2010. DNA Helicases, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.8
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Tables

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Table 1

DNA helicases of

Citation: Bianco P. 2010. DNA Helicases, EcoSal Plus 2010; doi:10.1128/ecosalplus.4.4.8

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