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Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state

  1. Author:
    Lee,Hyun Kyung
    Lee,Yun-Tzai
    Fan,Lixin
    Wilt, Haley M
    Conrad, Chelsie E
    Yu,Ping
    Zhang, Jinwei
    Shi,Genbin
    Ji,Xinhua
    Wang,Yun-Xing
    Stagno,Jason

  2. Author Address

    Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA., Basic Science Program, Frederick National Laboratory for Cancer Research, Small-Angle X-Ray Scattering Core Facility of National Cancer Institute, Frederick, MD 21702, USA., Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA., Biomolecular Structure Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA., Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA. Electronic address: jason.stagno@nih.gov.,
    1. Year: 2023
    2. Date: Jul 7
    3. Epub Date: 2023 05 29
  2. Journal: Structure (London, England : 1993)
    1. 31
    2. 7
    3. Pages: 848-859.
  4. Type of Article: Article
  1. Abstract:

    The thiamine pyrophosphate (TPP)-sensing riboswitch is one of the earliest discovered and most widespread riboswitches. Numerous structural studies have been reported for this riboswitch bound with various ligands. However, the ligand-free (apo) structure remains unknown. Here, we report a 3.1 Å resolution crystal structure of Escherichia coli TPP riboswitch in the apo state, which exhibits an extended, Y-shaped conformation further supported by small-angle X-ray scattering data and driven molecular dynamics simulations. The loss of ligand interactions results in helical uncoiling of P5 and disruption of the key tertiary interaction between the sensory domains. Opening of the aptamer propagates to the gene-regulatory P1 helix and generates the key conformational flexibility needed for the switching behavior. Much of the ligand-binding site at the three-way junction is unaltered, thereby maintaining a partially preformed pocket. Together, these results paint a dynamic picture of the ligand-induced conformational changes in TPP riboswitches that confer conditional gene regulation. Copyright © 2023 Elsevier Ltd. All rights reserved.

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External Sources

  1. View Full Text
  2. DOI: 10.1016/j.str.2023.05.003
  3. PMID: 37253356
  4. PMCID: PMC10335363
  5. View record in Web of Science®
  6. WOS: 001042240500001
  7. PII : S0969-2126(23)00157-0

Library Notes

  1. Fiscal Year: FY2022-2023
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