101
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Darst RP, Wang D, Auble DT. MOT1-catalyzed TBP-DNA disruption: uncoupling DNA conformational change and role of upstream DNA. EMBO J 2001; 20:2028-40. [PMID: 11296235 PMCID: PMC125425 DOI: 10.1093/emboj/20.8.2028] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
SNF2/SWI2-related ATPases employ ATP hydrolysis to disrupt protein-DNA interactions, but how ATP hydrolysis is coupled to disruption is not understood. Here we examine the mechanism of action of MOT1, a yeast SNF2/SWI2-related ATPase that uses ATP hydrolysis to remove TATA binding protein (TBP) from DNA. MOT1 function requires a 17 bp DNA 'handle' upstream of the TATA box, which must be double stranded. Remarkably, MOT1-catalyzed disruption of TBP-DNA does not appear to require DNA strand separation, DNA bending or twisting of the DNA helix. Thus, TBP-DNA disruption is accomplished in a reaction apparently not driven by a change in DNA structure. MOT1 action is supported by DNA templates in which the handle is connected to the TATA box via single-stranded DNA, indicating that the upstream duplex DNA can be conformationally uncoupled from the TATA box. Combining these results with proposed similarities between SNF2/SWI2 ATPases and helicases, we suggest that MOT1 uses ATP hydrolysis to translocate along the handle and thereby disrupt interactions between TBP and DNA.
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Affiliation(s)
| | | | - David T. Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health Science Center, 1300 Jefferson Park Avenue, Room 6213, Charlottesville, VA 22908-0733, USA
Corresponding author e-mail:
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102
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Bárcena M, Ruiz T, Donate LE, Brown SE, Dixon NE, Radermacher M, Carazo JM. The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel. EMBO J 2001; 20:1462-8. [PMID: 11250911 PMCID: PMC145514 DOI: 10.1093/emboj/20.6.1462] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Replicative helicases are motor proteins that unwind DNA at replication forks. Escherichia coli DnaB is the best characterized member of this family of enzymes. We present the 26 A resolution three-dimensional structure of the DnaB hexamer in complex with its loading partner, DnaC, obtained from cryo-electron microscopy. Analysis of the volume brings insight into the elaborate way the two proteins interact, and provides a structural basis for control of the symmetry state and inactivation of the helicase by DnaC. The complex is arranged on the basis of interactions among DnaC and DnaB dimers. DnaC monomers are observed for the first time to arrange as three dumb-bell-shaped dimers that interlock into one of the faces of the helicase. This could be responsible for the freezing of DnaB in a C(3) architecture by its loading partner. The central channel of the helicase is almost occluded near the end opposite to DnaC, such that even single-stranded DNA could not pass through. We propose that the DnaB N-terminal domain is located at this face.
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Affiliation(s)
| | - Teresa Ruiz
- Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain,
Max-Planck Institut für Biophysik, Heinrich Hoffmann Strasse 7, 60528 Frankfurt am Main, Germany and Research School of Chemistry, Australian National University, Canberra 0200, Australia Corresponding author e-mail:
| | | | - Susan E. Brown
- Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain,
Max-Planck Institut für Biophysik, Heinrich Hoffmann Strasse 7, 60528 Frankfurt am Main, Germany and Research School of Chemistry, Australian National University, Canberra 0200, Australia Corresponding author e-mail:
| | - Nicholas E. Dixon
- Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain,
Max-Planck Institut für Biophysik, Heinrich Hoffmann Strasse 7, 60528 Frankfurt am Main, Germany and Research School of Chemistry, Australian National University, Canberra 0200, Australia Corresponding author e-mail:
| | - Michael Radermacher
- Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain,
Max-Planck Institut für Biophysik, Heinrich Hoffmann Strasse 7, 60528 Frankfurt am Main, Germany and Research School of Chemistry, Australian National University, Canberra 0200, Australia Corresponding author e-mail:
| | - José María Carazo
- Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain,
Max-Planck Institut für Biophysik, Heinrich Hoffmann Strasse 7, 60528 Frankfurt am Main, Germany and Research School of Chemistry, Australian National University, Canberra 0200, Australia Corresponding author e-mail:
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103
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Brosh RM, Majumdar A, Desai S, Hickson ID, Bohr VA, Seidman MM. Unwinding of a DNA triple helix by the Werner and Bloom syndrome helicases. J Biol Chem 2001; 276:3024-30. [PMID: 11110789 DOI: 10.1074/jbc.m006784200] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bloom syndrome and Werner syndrome are genome instability disorders, which result from mutations in two different genes encoding helicases. Both enzymes are members of the RecQ family of helicases, have a 3' --> 5' polarity, and require a 3' single strand tail. In addition to their activity in unwinding duplex substrates, recent studies show that the two enzymes are able to unwind G2 and G4 tetraplexes, prompting speculation that failure to resolve these structures in Bloom syndrome and Werner syndrome cells may contribute to genome instability. The triple helix is another alternate DNA structure that can be formed by sequences that are widely distributed throughout the human genome. Here we show that purified Bloom and Werner helicases can unwind a DNA triple helix. The reactions are dependent on nucleoside triphosphate hydrolysis and require a free 3' tail attached to the third strand. The two enzymes unwound triplexes without requirement for a duplex extension that would form a fork at the junction of the tail and the triplex. In contrast, a duplex formed by the third strand and a complement to the triplex region was a poor substrate for both enzymes. However, the same duplex was readily unwound when a noncomplementary 5' tail was added to form a forked structure. It seems likely that structural features of the triplex mimic those of a fork and thus support efficient unwinding by the two helicases.
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Affiliation(s)
- R M Brosh
- Laboratory of Molecular Genetics, NIA, National Institutes of Health, Baltimore, Maryland 21224, USA
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104
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Gomis-Rüth FX, Moncalián G, Pérez-Luque R, González A, Cabezón E, de la Cruz F, Coll M. The bacterial conjugation protein TrwB resembles ring helicases and F1-ATPase. Nature 2001; 409:637-41. [PMID: 11214325 DOI: 10.1038/35054586] [Citation(s) in RCA: 285] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The transfer of DNA across membranes and between cells is a central biological process; however, its molecular mechanism remains unknown. In prokaryotes, trans-membrane passage by bacterial conjugation, is the main route for horizontal gene transfer. It is the means for rapid acquisition of new genetic information, including antibiotic resistance by pathogens. Trans-kingdom gene transfer from bacteria to plants or fungi and even bacterial sporulation are special cases of conjugation. An integral membrane DNA-binding protein, called TrwB in the Escherichia coli R388 conjugative system, is essential for the conjugation process. This large multimeric protein is responsible for recruiting the relaxosome DNA-protein complex, and participates in the transfer of a single DNA strand during cell mating. Here we report the three-dimensional structure of a soluble variant of TrwB. The molecule consists of two domains: a nucleotide-binding domain of alpha/beta topology, reminiscent of RecA and DNA ring helicases, and an all-alpha domain. Six equivalent protein monomers associate to form an almost spherical quaternary structure that is strikingly similar to F1-ATPase. A central channel, 20 A in width, traverses the hexamer.
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Affiliation(s)
- F X Gomis-Rüth
- Institut de Biologia Molecular de Barcelona, CSIC, Spain
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105
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Organization, Replication, Transposition, and Repair of DNA. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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106
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Marians KJ. Crawling and wiggling on DNA: structural insights to the mechanism of DNA unwinding by helicases. Structure 2000; 8:R227-35. [PMID: 11188698 DOI: 10.1016/s0969-2126(00)00539-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Crystal structures have recently been solved of the monomeric DNA helicase PcrA bound to forked DNA, and of the hexameric helicase domain of the bacteriophage T7 gene 4 protein, a replication fork DNA helicase/primase. These structures have led to the elaboration of the first molecular models to describe DNA helicase action.
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Affiliation(s)
- K J Marians
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.
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