Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA.
DEAD-box helicase
NMR spectroscopy
RNA
molecular mechanism
ribosome biogenesis
Journal
RNA (New York, N.Y.)
ISSN: 1469-9001
Titre abrégé: RNA
Pays: United States
ID NLM: 9509184
Informations de publication
Date de publication:
09 2023
09 2023
Historique:
received:
08
01
2023
accepted:
29
04
2023
medline:
18
8
2023
pubmed:
24
5
2023
entrez:
23
5
2023
Statut:
ppublish
Résumé
DEAD-box RNA helicases are implicated in most aspects of RNA biology, where these enzymes unwind short RNA duplexes in an ATP-dependent manner. During the central step of the unwinding cycle, the two domains of the helicase core form a distinct closed conformation that destabilizes the RNA duplex, which ultimately leads to duplex melting. Despite the importance of this step for the unwinding process no high-resolution structures of this state are available. Here, I used nuclear magnetic resonance spectroscopy and X-ray crystallography to determine structures of the DEAD-box helicase DbpA in the closed conformation, complexed with substrate duplexes and single-stranded unwinding product. These structures reveal that DbpA initiates duplex unwinding by interacting with up to three base-paired nucleotides and a 5' single-stranded RNA duplex overhang. These high-resolution snapshots, together with biochemical assays, rationalize the destabilization of the RNA duplex and are integrated into a conclusive model of the unwinding process.
Identifiants
pubmed: 37221012
pii: rna.079582.123
doi: 10.1261/rna.079582.123
pmc: PMC10573307
doi:
Substances chimiques
Adenosine Triphosphate
8L70Q75FXE
DEAD-box RNA Helicases
EC 3.6.4.13
DNA Helicases
EC 3.6.4.-
RNA
63231-63-0
dbpA protein, E coli
EC 3.6.1.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1339-1354Informations de copyright
© 2023 Wurm; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Références
Curr Opin Struct Biol. 2010 Jun;20(3):313-24
pubmed: 20456941
Cell. 2014 Jun 19;157(7):1698-711
pubmed: 24910301
Nucleic Acids Res. 2019 Apr 23;47(7):3699-3710
pubmed: 30993346
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):133-44
pubmed: 20124693
J Biomol NMR. 1995 Nov;6(3):277-93
pubmed: 8520220
Proc Natl Acad Sci U S A. 2005 Apr 26;102(17):5958-63
pubmed: 15831591
Mol Cell. 2007 Dec 14;28(5):850-9
pubmed: 18082609
J Biol Chem. 2009 Apr 17;284(16):10296-300
pubmed: 19244245
J Mol Biol. 2016 Jan 29;428(2 Pt B):492-508
pubmed: 26730886
J Biomol NMR. 2005 Dec;33(4):199-211
pubmed: 16341750
RNA. 2006 May;12(5):903-12
pubmed: 16556937
Cell Rep. 2019 Dec 17;29(12):4024-4035.e5
pubmed: 31851931
Biochemistry. 1998 Dec 1;37(48):16989-96
pubmed: 9836593
Mol Cell. 2007 Oct 26;28(2):253-63
pubmed: 17964264
J Biol Chem. 1999 Apr 30;274(18):12236-44
pubmed: 10212190
Elife. 2017 Jan 06;6:
pubmed: 28059701
Acta Crystallogr D Biol Crystallogr. 2012 Jan;68(Pt 1):42-56
pubmed: 22194332
J Mol Biol. 1997 Oct 17;273(1):283-98
pubmed: 9367762
Adv Sci (Weinh). 2020 Jun 08;7(14):2000532
pubmed: 32714761
RNA. 2006 Jun;12(6):959-67
pubmed: 16611943
Cell. 2006 Apr 21;125(2):287-300
pubmed: 16630817
Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4046-50
pubmed: 20160110
Structure. 2014 Jul 8;22(7):941-8
pubmed: 24909782
Biochemistry. 2001 Jul 31;40(30):8898-904
pubmed: 11467951
Protein Sci. 2021 Jan;30(1):70-82
pubmed: 32881101
Nucleic Acids Res. 2014;42(16):10644-54
pubmed: 25123660
Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20209-14
pubmed: 19088201
Nat Struct Mol Biol. 2005 Oct;12(10):861-9
pubmed: 16170325
J Mol Biol. 2010 Sep 17;402(2):412-27
pubmed: 20673833
Proc Natl Acad Sci U S A. 2021 Aug 31;118(35):
pubmed: 34453003
Anal Biochem. 2003 Oct 15;321(2):266-71
pubmed: 14511695
Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):548-53
pubmed: 18184816
Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67
pubmed: 22505256
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
pubmed: 15572765
EMBO J. 2001 Oct 1;20(19):5503-12
pubmed: 11574482
Nucleic Acids Res. 2019 Jun 4;47(10):5260-5275
pubmed: 30997503
RNA. 2008 Mar;14(3):465-81
pubmed: 18192612
Nucleic Acids Res. 2009 Oct;37(19):6503-14
pubmed: 19734347
Biomol NMR Assign. 2021 Apr;15(1):121-128
pubmed: 33277687
Mol Cell. 2009 Sep 11;35(5):598-609
pubmed: 19748356
Nat Rev Mol Cell Biol. 2011 Jul 22;12(8):505-16
pubmed: 21779027
Annu Rev Biochem. 2014;83:697-725
pubmed: 24635478
Curr Opin Struct Biol. 2007 Oct;17(5):603-16
pubmed: 17913493
J Biomol NMR. 2016 Dec;66(4):259-271
pubmed: 27878649
RNA Biol. 2013 Jan;10(1):44-55
pubmed: 22995827
J Synchrotron Radiat. 2017 Jan 1;24(Pt 1):323-332
pubmed: 28009574
J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
pubmed: 19461840
Biochim Biophys Acta. 2013 Aug;1829(8):884-93
pubmed: 23416748
Nature. 2011 Apr 14;472(7342):238-42
pubmed: 21441902
Nature. 2012 Oct 4;490(7418):121-5
pubmed: 22940866