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7bbb

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Solution structure of C-terminal RecA and RRM domains of the DEAD box helicase DbpASolution structure of C-terminal RecA and RRM domains of the DEAD box helicase DbpA

Structural highlights

7bbb is a 1 chain structure with sequence from Ecoli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:dbpA, b1343, JW1337 (ECOLI)
Activity:RNA helicase, with EC number 3.6.4.13
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DBPA_ECOLI] DEAD-box RNA helicase involved in the assembly of the 50S ribosomal subunit. Has an RNA-dependent ATPase activity, which is specific for 23S rRNA, and a 3' to 5' RNA helicase activity that uses the energy of ATP hydrolysis to destabilize and unwind short rRNA duplexes. Requires a single-stranded RNA loading site on the 3' side of the substrate helix.[HAMAP-Rule:MF_00965][1] [2] [3] [4] [5] [6] [7] [8] [9]

Publication Abstract from PubMed

The adenosine triphosphate (ATP)-dependent DEAD-box RNA helicase DbpA from Escherichia coli functions in ribosome biogenesis. DbpA is targeted to the nascent 50S subunit by an ancillary, carboxyl-terminal RNA recognition motif (RRM) that specifically binds to hairpin 92 (HP92) of the 23S ribosomal RNA (rRNA). The interaction between HP92 and the RRM is required for the helicase activity of the RecA-like core domains of DbpA. Here, we elucidate the structural basis by which DbpA activity is endorsed when the enzyme interacts with the maturing ribosome. We used nuclear magnetic resonance (NMR) spectroscopy to show that the RRM and the carboxyl-terminal RecA-like domain tightly interact. This orients HP92 such that this RNA hairpin can form electrostatic interactions with a positively charged patch in the N-terminal RecA-like domain. Consequently, the enzyme can stably adopt the catalytically important, closed conformation. The substrate binding mode in this complex reveals that a region 5' to helix 90 in the maturing ribosome is specifically targeted by DbpA. Finally, our results indicate that the ribosome maturation defects induced by a dominant negative DbpA mutation are caused by a delayed dissociation of DbpA from the nascent ribosome. Taken together, our findings provide unique insights into the important regulatory mechanism that modulates the activity of DbpA.

Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome.,Wurm JP, Glowacz KA, Sprangers R Proc Natl Acad Sci U S A. 2021 Aug 31;118(35). pii: 2105961118. doi:, 10.1073/pnas.2105961118. PMID:34453003[10]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Tsu CA, Kossen K, Uhlenbeck OC. The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA. RNA. 2001 May;7(5):702-9. doi: 10.1017/s1355838201010135. PMID:11350034 doi:http://dx.doi.org/10.1017/s1355838201010135
  2. ↑ Diges CM, Uhlenbeck OC. Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. EMBO J. 2001 Oct 1;20(19):5503-12. doi: 10.1093/emboj/20.19.5503. PMID:11574482 doi:http://dx.doi.org/10.1093/emboj/20.19.5503
  3. ↑ Diges CM, Uhlenbeck OC. Escherichia coli DbpA is a 3' --> 5' RNA helicase. Biochemistry. 2005 May 31;44(21):7903-11. doi: 10.1021/bi050033x. PMID:15910005 doi:http://dx.doi.org/10.1021/bi050033x
  4. ↑ Henn A, Cao W, Hackney DD, De La Cruz EM. The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA. J Mol Biol. 2008 Mar 14;377(1):193-205. doi: 10.1016/j.jmb.2007.12.046. Epub 2007, Dec 28. PMID:18237742 doi:http://dx.doi.org/10.1016/j.jmb.2007.12.046
  5. ↑ Sharpe Elles LM, Sykes MT, Williamson JR, Uhlenbeck OC. A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. Nucleic Acids Res. 2009 Oct;37(19):6503-14. doi: 10.1093/nar/gkp711. Epub 2009, Sep 4. PMID:19734347 doi:http://dx.doi.org/10.1093/nar/gkp711
  6. ↑ Henn A, Cao W, Licciardello N, Heitkamp SE, Hackney DD, De La Cruz EM. Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA. Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4046-50. doi:, 10.1073/pnas.0913081107. Epub 2010 Feb 16. PMID:20160110 doi:http://dx.doi.org/10.1073/pnas.0913081107
  7. ↑ Fuller-Pace FV, Nicol SM, Reid AD, Lane DP. DbpA: a DEAD box protein specifically activated by 23s rRNA. EMBO J. 1993 Sep;12(9):3619-26. PMID:8253085
  8. ↑ Boddeker N, Stade K, Franceschi F. Characterization of DbpA, an Escherichia coli DEAD box protein with ATP independent RNA unwinding activity. Nucleic Acids Res. 1997 Feb 1;25(3):537-45. doi: 10.1093/nar/25.3.537. PMID:9016593 doi:http://dx.doi.org/10.1093/nar/25.3.537
  9. ↑ Tsu CA, Uhlenbeck OC. Kinetic analysis of the RNA-dependent adenosinetriphosphatase activity of DbpA, an Escherichia coli DEAD protein specific for 23S ribosomal RNA. Biochemistry. 1998 Dec 1;37(48):16989-96. doi: 10.1021/bi981837y. PMID:9836593 doi:http://dx.doi.org/10.1021/bi981837y
  10. ↑ Wurm JP, Glowacz KA, Sprangers R. Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome. Proc Natl Acad Sci U S A. 2021 Aug 31;118(35). pii: 2105961118. doi:, 10.1073/pnas.2105961118. PMID:34453003 doi:http://dx.doi.org/10.1073/pnas.2105961118
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