The crystal structure of the Thermus aquaticus DnaB helicase monomer

Bailey, Scott; Eliason, William K.; Steitz, Thomas A.

doi:10.1093/nar/gkm507

Cited by 42 publications

(62 citation statements)

References 34 publications

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“…The SF4 family of helicases possesses a RecA/F1 core fold while the SF3 helicases possess an AAA core fold. The topological differences between these have been described previously [64,65]. Despite the topological differences, the structural architecture of the ATP site has common features that become apparent when viewing the ATPbound configuration ('cylinder compressed' configuration).…”

Section: Atpase Site Architecturementioning

confidence: 75%

“…A conserved lysine and arginine of T7gp4 (K220 and R522, the arginine finger) align with the piston and trigger residues (Figures 4 and 5). All three residues are highly conserved in DnaB and are consistently structured in the structures of Taq DnaB [65] and Bst DnaB [32 ]. In the SF4 helicases, the interaction of the glutamine with the left side of the site appears to be mediated through an aromatic residue and an additional residue conserved as histidine or glutamine.…”

Section: Perturbations Of the Atpase Active Site Tethermentioning

confidence: 99%

See 1 more Smart Citation

On helicases and other motor proteins

Enemark

Joshua‐Tor

2008

Current Opinion in Structural Biology

190

238

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Helicases are molecular machines that utilize energy derived from ATP hydrolysis to move along nucleic acids and to separate base-paired nucleotides. The movement of the helicase can also be described as a stationary helicase that pumps nucleic acid. Recent structural data for the hexameric E1 helicase of papillomavirus in complex with single-stranded DNA and MgADP has provided a detailed atomic and mechanistic picture of its ATP-driven DNA translocation. The structural and mechanistic features of this helicase are compared with the hexameric helicase prototypes T7gp4 and SV40 T-antigen. The ATP-binding site architectures of these proteins are structurally similar to the sites of other prototypical ATP-driven motors such as F1-ATPase, suggesting related roles for the individual site residues in the ATPase activity. IntroductionHelicases are essential enzymes that unwind duplex DNA, RNA, or DNA-RNA hybrids. This unwinding is driven by consumption of input energy that is harnessed to separate base-paired oligonucleotides and also to maintain a unidirectional advancement of the helicase upon the nucleic acid substrate. This translocation can alternatively be described as an immobile helicase pumping nucleic acid. The energy for these transformations is derived from the hydrolysis of nucleotide triphosphate (NTP). Helicases can be depicted as an internal combustion engine with each individual NTPase site serving as one cylinder. Each individual cylinder follows a defined series of events: injection (ATP binding), compression (optimally positioning the site for hydrolysis), combustion (ATP hydrolysis/work generation), and exhaust (ADP and phosphate release). In a helicase, the individual combustion cylinders coordinate these actions to carry out the repetitive mechanical operation of prying open base pairs and/or actively translocating with respect to the nucleic acid substrate. Many other molecular motors utilize similar engines to carry out multiple diverse functions such as translocation of peptides in the case of ClpX, movement along cellular structures in the case of dyenin, and rotation about an axle as in F 1 -ATPase.Based upon conserved sequence motifs, helicases have been classified into six superfamilies [1,2 ]. An extensive review of these superfamilies has been provided recently [3 ]. Superfamily 1 (SF1) and superfamily 2 (SF2) helicases are very prevalent, generally monomeric, and participate in several diverse DNA and RNA manipulations. The other helicase superfamilies form hexameric rings (reviewed in [4]), as demonstrated by biochemistry [5][6][7][8] and electron microscopy studies [9][10][11][12][13][14][15][16][17], and often participate at the replication fork. All of these helicases bind and hydrolyze NTP at the interface between two recA-like domains. The binding site consists of a Walker A (P-loop) and a Walker B motif from the first domain and other elements such as an arginine finger from the other domain. The SF1 and SF2 helicases contain two recAlike domains coupled by a short linker, and t...

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Section: Atpase Site Architecturementioning

confidence: 75%

Section: Perturbations Of the Atpase Active Site Tethermentioning

confidence: 99%

On helicases and other motor proteins

Enemark

Joshua‐Tor

2008

Current Opinion in Structural Biology

190

238

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“…In bacteria, a single helicase-termed DnaB in E. coli-serves as the front end of the newly emerging replication fork. DnaB forms a twin-tiered, ring-shaped hexamer ( Figure 4a) (127)(128)(129), in which a conserved N-terminal domain (NTD) structurally homologous to the helicase interaction domain of the DnaG primase forms one tier and the C-terminal ATPase domain (CTD) forms the other (128,(130)(131)(132). Adjoining NTDs in the DnaB hexamer self-assemble into a trimer-of-dimers configuration (127)(128)(129)133), creating a collar that binds ssDNA (127).…”

Section: Helicase Loading and Activation Helicase Loading In Bacteriamentioning

confidence: 99%

Mechanisms for initiating cellular DNA replication

Bleichert

Botchan

Berger

2017

Science

189

172

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The initiation of DNA replication represents a committing step to cell proliferation. Appropriate replication onset depends on multiprotein complexes that help properly distinguish origin regions, generate nascent replication bubbles, and promote replisome formation. This review describes initiation systems employed by bacteria, archaea, and eukaryotes, with a focus on comparing and contrasting molecular mechanisms among organisms. Although commonalities can be found in the functional domains and strategies used to carry out and regulate initiation, many key participants have markedly different activities and appear to have evolved convergently. Despite significant advances in the field, major questions still persist in understanding how initiation programs are executed at the molecular level.

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“…A recent report on Thermus aquaticus (Taq) DnaB, another hexameric helicase, illustrates the conserved nature of the NTPbinding site in the homolog (32). Modeling of Taq helicase with non-hydrolyzable ATP in comparison with the T7 helicase structure shows that the NTP-binding pocket resembles that of T7 helicase.…”

Section: Role Of Residues In Ntp-binding Site Of T7mentioning

confidence: 99%

Molecular Basis for Recognition of Nucleoside Triphosphate by Gene 4 Helicase of Bacteriophage T7

Lee

Richardson

2010

Journal of Biological Chemistry

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The translocation of DNA helicases on single-stranded DNA and the unwinding of double-stranded DNA are fueled by the hydrolysis of nucleoside triphosphates (NTP). Although most helicases use ATP in these processes, the DNA helicase encoded by gene 4 of bacteriophage T7 uses dTTP most efficiently. To identify the structural requirements of the NTP, we determined the efficiency of DNA unwinding by T7 helicase using a variety of NTPs and their analogs. The 5-methyl group of thymine was critical for the efficient unwinding of DNA, although the presence of a 3-ribosyl hydroxyl group partially overcame this requirement. The NTP-binding pocket of the protein was examined by randomly substituting amino acids for several amino acid residues (Thr-320, Arg-504, Tyr-535, and Leu-542) that the crystal structure suggests interact with the nucleotide. Although positions 320 and 542 required aliphatic residues of the appropriate size, an aromatic side chain was necessary at position 535 to stabilize NTP for efficient unwinding. A basic side chain of residue 504 was essential to interact with the 4-carbonyl of the thymine base of dTTP. Replacement of this residue with a small aliphatic residue allowed the accommodation of other NTPs, resulting in the preferential use of dATP and the use of dCTP, a nucleotide not normally used. Results from this study suggest that the NTP must be stabilized by specific interactions within the NTP-binding site of the protein to achieve efficient hydrolysis. These interactions dictate NTP specificity.Helicases are ubiquitous enzymes that play pivotal roles in diverse cellular activities (1). Reactions mediated by helicases require their ability to bind and move along a DNA or RNA strand. Such a fundamental feature is coupled to the binding of nucleoside triphosphates (NTPs) 2 and their hydrolysis. An underlying mechanism in helicase action is a change in contact of the protein with the nucleic acid strand depending on the state of the bound NTP (1). Binding and subsequent hydrolysis of NTP induce conformational shifts in the nucleic acid-interacting part of the helicase that enable the enzyme to move unidirectionally. The unidirectional movement enables the helicase to translocate on the strand to which it is bound, and upon encountering duplex DNA, its continued movement results in unwinding of the dsDNA. Consequently, despite the divergence in their structure and mechanism of action, all helicases require the binding and hydrolysis of NTP to fulfill these multiple roles (2). Accordingly, signature structural motifs of helicase for NTP binding, for example the Walker motifs A and B, are conserved throughout the helicase family (3). These motifs interact with the phosphate moiety of NTP and influence DNA binding upon hydrolysis of NTP. In the case of hexameric helicases such as the T7 DNA helicase, complexity of helicase action is increased because the oligomerization of the subunits is a prerequisite for all the steps described above. In helicases of this family, binding and hydrolysis of NTP oc...

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The crystal structure of the Thermus aquaticus DnaB helicase monomer

Cited by 42 publications

References 34 publications

On helicases and other motor proteins

On helicases and other motor proteins

Mechanisms for initiating cellular DNA replication

Molecular Basis for Recognition of Nucleoside Triphosphate by Gene 4 Helicase of Bacteriophage T7

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