8QA8

Crystal structure of the C-terminally truncated transcriptional repressor protein KorB from the RK2 plasmid complexed with CTP-gamma-S

Summary for 8QA8

• Entry DOI: 10.2210/pdb8qa8/pdb
• Descriptor: Transcriptional repressor protein KorB, CYTIDINE-5'-TRIPHOSPHATE, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: multi-drug resistance, parabs, clamp, ctp switch, dna segregation, gene expression regulation, dna binding protein
• Biological source: Escherichia coli
• Total number of polymer chains: 6
• Total formula weight: 162190.36

Authors

McLean, T.C.,Mundy, J.E.A.,Lawson, D.M.,Le, T.B.K. (deposition date: 2023-08-22, release date: 2024-02-21, Last modification date: 2025-03-05)

Primary citation

McLean, T.C.,Balaguer-Perez, F.,Chandanani, J.,Thomas, C.M.,Aicart-Ramos, C.,Burick, S.,Olinares, P.D.B.,Gobbato, G.,Mundy, J.E.A.,Chait, B.T.,Lawson, D.M.,Darst, S.A.,Campbell, E.A.,Moreno-Herrero, F.,Le, T.B.K.
KorB switching from DNA-sliding clamp to repressor mediates long-range gene silencing in a multi-drug resistance plasmid.
Nat Microbiol, 10:448-467, 2025

PubMed Abstract: Examples of long-range gene regulation in bacteria are rare and generally thought to involve DNA looping. Here, using a combination of biophysical approaches including X-ray crystallography and single-molecule analysis for the KorB-KorA system in Escherichia coli, we show that long-range gene silencing on the plasmid RK2, a source of multi-drug resistance across diverse Gram-negative bacteria, is achieved cooperatively by a DNA-sliding clamp, KorB, and a clamp-locking protein, KorA. We show that KorB is a CTPase clamp that can entrap and slide along DNA to reach distal target promoters up to 1.5 kb away. We resolved the tripartite crystal structure of a KorB-KorA-DNA co-complex, revealing that KorA latches KorB into a closed clamp state. DNA-bound KorA thus stimulates repression by stalling KorB sliding at target promoters to occlude RNA polymerase holoenzymes. Together, our findings explain the mechanistic basis for KorB role switching from a DNA-sliding clamp to a co-repressor and provide an alternative mechanism for long-range regulation of gene expression in bacteria.

PubMed: 39849085
DOI: 10.1038/s41564-024-01915-3

Experimental method

X-RAY DIFFRACTION (2.3 Å)