Butryn A, Schuller JM, Stoehr G, Runge-Wollmann P, Förster F, Auble DT, Hopfner KP. Structural basis for recognition and remodeling of the TBP:DNA:NC2 complex by Mot1.
eLife 2015;
4. [PMID:
26258880 PMCID:
PMC4565979 DOI:
10.7554/elife.07432]
[Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 08/08/2015] [Indexed: 12/28/2022] Open
Abstract
Swi2/Snf2 ATPases remodel substrates such as nucleosomes and transcription complexes to control a wide range of DNA-associated processes, but detailed structural information on the ATP-dependent remodeling reactions is largely absent. The single subunit remodeler Mot1 (modifier of transcription 1) dissociates TATA box-binding protein (TBP):DNA complexes, offering a useful system to address the structural mechanisms of Swi2/Snf2 ATPases. Here, we report the crystal structure of the N-terminal domain of Mot1 in complex with TBP, DNA, and the transcription regulator negative cofactor 2 (NC2). Our data show that Mot1 reduces DNA:NC2 interactions and unbends DNA as compared to the TBP:DNA:NC2 state, suggesting that Mot1 primes TBP:NC2 displacement in an ATP-independent manner. Electron microscopy and cross-linking data suggest that the Swi2/Snf2 domain of Mot1 associates with the upstream DNA and the histone fold of NC2, thereby revealing parallels to some nucleosome remodelers. This study provides a structural framework for how a Swi2/Snf2 ATPase interacts with its substrate DNA:protein complex.
DOI:http://dx.doi.org/10.7554/eLife.07432.001
An organism’s DNA contains thousands of genes, not all of which are active at the same time. Cells use a number of methods to carefully control when particular genes are switched on or off. For example, proteins called transcription factors can activate a gene by binding to particular regions of DNA called promoters. One such transcription factor is called the TATA-binding protein (TBP for short). Mot1 is a remodeling enzyme that can form a “complex” with TBP by binding to it, and in doing so remove TBP from DNA. This silences the genes at those sites. The freed TBP can then bind to other promoters that lack Mot1 and activate the genes found there.
In 2011, researchers revealed the structure of the complex formed between TBP and Mot1 after TBP has been detached from DNA. However, the structure of the complex that forms while TBP is still bound to the DNA molecule was not known. Butryn et al. – including several of the researchers involved in the 2011 work – have now described the structure of this complex using X-ray crystallography and electron microscopy. Another protein called negative cofactor 2 is also part of the complex, and helps to stabilize it.
Butryn et al. found that Mot1 reduces the strength of the interactions between DNA and both TBP and negative cofactor 2. Binding to TBP and negative cofactor 2 causes the DNA molecule to bend; however, if Mot1 is also in the complex, the DNA becomes less bent. By making these changes, Mot1 is likely to prime TBP to detach from the DNA. Since the current structures do not yet reveal the atomic structure of Mot1’s ATP dependent DNA motor domain, the next challenge is to visualize the entire complex at atomic resolution.
DOI:http://dx.doi.org/10.7554/eLife.07432.002
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