@article {6327,
	title = {Interplay of DNA repair with transcription: from structures to mechanisms.},
	journal = {Trends in Biochemical Sciences},
	volume = {37},
	year = {2012},
	month = {2012 Dec},
	pages = {543-52},
	abstract = {<p>Many DNA transactions are crucial for maintaining genomic integrity and faithful transfer of genetic information but remain poorly understood. An example is the interplay between nucleotide excision repair (NER) and transcription, also known as transcription-coupled DNA repair (TCR). Discovered decades ago, the mechanisms for TCR have remained elusive, not in small part due to the scarcity of structural studies of key players. Here we summarize recent structural information on NER/TCR factors, focusing on bacterial systems, and integrate it with existing genetic, biochemical, and biophysical data to delineate the mechanisms at play. We also review emerging, alternative modalities for recruitment of NER proteins to DNA lesions.</p>
},
	issn = {0968-0004},
	doi = {10.1016/j.tibs.2012.09.002},
	author = {Deaconescu, Alexandra M and Artsimovitch, Irina and Grigorieff, Nikolaus}
}
@article {6329,
	title = {Nucleotide excision repair (NER) machinery recruitment by the transcription-repair coupling factor involves unmasking of a conserved intramolecular interface.},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {109},
	year = {2012},
	month = {2012 Feb 28},
	pages = {3353-8},
	abstract = {<p>Transcription-coupled DNA repair targets DNA lesions that block progression of elongating RNA polymerases. In bacteria, the transcription-repair coupling factor (TRCF; also known as Mfd) SF2 ATPase recognizes RNA polymerase stalled at a site of DNA damage, removes the enzyme from the DNA, and recruits the Uvr(A)BC nucleotide excision repair machinery via UvrA binding. Previous studies of TRCF revealed a molecular architecture incompatible with UvrA binding, leaving its recruitment mechanism unclear. Here, we examine the UvrA recognition determinants of TRCF using X-ray crystallography of a core TRCF-UvrA complex and probe the conformational flexibility of TRCF in the absence and presence of nucleotides using small-angle X-ray scattering. We demonstrate that the C-terminal domain of TRCF is inhibitory for UvrA binding, but not RNA polymerase release, and show that nucleotide binding induces concerted multidomain motions. Our studies suggest that autoinhibition of UvrA binding in TRCF may be relieved only upon engaging the DNA damage.</p>
},
	keywords = {Adenosine Triphosphatases, Adenosine Triphosphate, Amino Acid Sequence, Bacterial, Bacterial Proteins, Crystallography, DNA, DNA Damage, DNA Helicases, DNA Repair, DNA-Binding Proteins, Escherichia coli, Escherichia coli Proteins, Hydrolysis, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Conformation, Protein Interaction Mapping, Protein Structure, RNA Polymerase I, Tertiary, Transcription Factors, X-Ray},
	issn = {1091-6490},
	doi = {10.1073/pnas.1115105109},
	author = {Deaconescu, Alexandra M and Sevostyanova, Anastasia and Artsimovitch, Irina and Grigorieff, Nikolaus}
}
