Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction

• Published in: Nucleic acids research Vol. 38; no. 22; pp. 8357 - 8369
• Main Authors: Westblade, Lars F, Campbell, Elizabeth A, Pukhrambam, Chirangini, Padovan, Julio C, Nickels, Bryce E, Lamour, Valerie, Darst, Seth A
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.12.2010
• Subjects: Amino Acid Sequence; Amino Acid Substitution; Bacteria; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Coupling factors; Crystal structure; Crystallography, X-Ray; DNA damage; DNA repair; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - genetics; DNA-Directed RNA Polymerases - metabolism; Homology; Ionizing radiation; Models, Molecular; Molecular Sequence Data; Mycobacterium tuberculosis; Nucleotide excision repair; Protein interaction; Protein Interaction Domains and Motifs; rRNA; Structural Biology; Transcription; Transcription Factors - chemistry; Transcription Factors - genetics; Transcription Factors - metabolism; translocase; Two-Hybrid System Techniques
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkq692

The transcription-repair coupling factor (TRCF, the product of the mfd gene) is a widely conserved bacterial protein that mediates transcription-coupled DNA repair. TRCF uses its ATP-dependent DNA translocase activity to remove transcription complexes stalled at sites of DNA damage, and stimulates repair by recruiting components of the nucleotide excision repair pathway to the site. A protein/protein interaction between TRCF and the β-subunit of RNA polymerase (RNAP) is essential for TRCF function. CarD (also called CdnL), an essential regulator of rRNA transcription in Mycobacterium tuberculosis, shares a homologous RNAP interacting domain with TRCF and also interacts with the RNAP β-subunit. We determined the 2.9-Å resolution X-ray crystal structure of the RNAP interacting domain of TRCF complexed with the RNAP-β1 domain, which harbors the TRCF interaction determinants. The structure reveals details of the TRCF/RNAP protein/protein interface, providing a basis for the design and interpretation of experiments probing TRCF, and by homology CarD, function and interactions with the RNAP.