4i67 Citations

Recognition of two distinct elements in the RNA substrate by the RNA-binding domain of the T. thermophilus DEAD box helicase Hera.

OpenAccess logo Nucleic Acids Res. (2013)
Related entries: 4i69, 4i68

Cited: 9 times
EuropePMC logo PMID: 23625962

Abstract

DEAD box helicases catalyze the ATP-dependent destabilization of RNA duplexes. Whereas duplex separation is mediated by the helicase core shared by all members of the family, flanking domains often contribute to binding of the RNA substrate. The Thermus thermophilus DEAD-box helicase Hera (for "heat-resistant RNA-binding ATPase") contains a C-terminal RNA-binding domain (RBD). We have analyzed RNA binding to the Hera RBD by a combination of mutational analyses, nuclear magnetic resonance and X-ray crystallography, and identify residues on helix α1 and the C-terminus as the main determinants for high-affinity RNA binding. A crystal structure of the RBD in complex with a single-stranded RNA resolves the RNA-protein interactions in the RBD core region around helix α1. Differences in RNA binding to the Hera RBD and to the structurally similar RBD of the Bacillus subtilis DEAD box helicase YxiN illustrate the versatility of RNA recognition motifs as RNA-binding platforms. Comparison of chemical shift perturbation patterns elicited by different RNAs, and the effect of sequence changes in the RNA on binding and unwinding show that the RBD binds a single-stranded RNA region at the core and simultaneously contacts double-stranded RNA through its C-terminal tail. The helicase core then unwinds an adjacent RNA duplex. Overall, the mode of RNA binding by Hera is consistent with a possible function as a general RNA chaperone.

Articles - 4i67 mentioned but not cited (1)

  1. Evidence for cooperative tandem binding of hnRNP C RRMs in mRNA processing. Cieniková Z, Jayne S, Damberger FF, Allain FH, Maris C. RNA 21 1931-1942 (2015)


Reviews citing this publication (3)

  1. Bacterial versatility requires DEAD-box RNA helicases. Redder P, Hausmann S, Khemici V, Yasrebi H, Linder P. FEMS Microbiol. Rev. 39 392-412 (2015)
  2. Deciphering the protein-RNA recognition code: combining large-scale quantitative methods with structural biology. Hennig J, Sattler M. Bioessays 37 899-908 (2015)
  3. RNA helicase proteins as chaperones and remodelers. Jarmoskaite I, Russell R. Annu. Rev. Biochem. 83 697-725 (2014)

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  1. The DEAD-box helicase Ded1 from yeast is an mRNP cap-associated protein that shuttles between the cytoplasm and nucleus. Senissar M, Le Saux A, Belgareh-Touzé N, Adam C, Banroques J, Tanner NK. Nucleic Acids Res. 42 10005-10022 (2014)
  2. Dye label interference with RNA modification reveals 5-fluorouridine as non-covalent inhibitor. Spenkuch F, Hinze G, Kellner S, Kreutz C, Micura R, Basché T, Helm M. Nucleic Acids Res. 42 12735-12745 (2014)
  3. eIF4B stimulates eIF4A ATPase and unwinding activities by direct interaction through its 7-repeats region. Andreou AZ, Harms U, Klostermeier D. RNA Biol 14 113-123 (2017)
  4. Allosteric regulation of helicase core activities of the DEAD-box helicase YxiN by RNA binding to its RNA recognition motif. Samatanga B, Andreou AZ, Klostermeier D. Nucleic Acids Res. 45 1994-2006 (2017)
  5. Structural Insights into a Unique Dimeric DEAD-Box Helicase CshA that Promotes RNA Decay. Huen J, Lin CL, Golzarroshan B, Yi WL, Yang WZ, Yuan HS. Structure 25 469-481 (2017)