Ribosomal Protein L11 Selectively Stabilizes a Tertiary Structure of the GTPase Center rRNA Domain.
Binding Sites
GTP Phosphohydrolases
/ chemistry
Magnesium
/ metabolism
Magnetic Resonance Spectroscopy
Nucleic Acid Conformation
Potassium
/ metabolism
Protein Binding
Protein Structure, Tertiary
RNA
/ chemistry
RNA, Ribosomal
/ chemistry
RNA, Ribosomal, 23S
/ chemistry
Ribosomal Proteins
/ chemistry
Ribosomes
/ metabolism
GTPase center
L11 stalk
RNA crystal structure
RNA folding
protein:RNA complex
Journal
Journal of molecular biology
ISSN: 1089-8638
Titre abrégé: J Mol Biol
Pays: Netherlands
ID NLM: 2985088R
Informations de publication
Date de publication:
14 02 2020
14 02 2020
Historique:
received:
26
07
2019
revised:
03
12
2019
accepted:
04
12
2019
pubmed:
25
12
2019
medline:
18
8
2020
entrez:
25
12
2019
Statut:
ppublish
Résumé
The GTPase Center (GAC) RNA domain in bacterial 23S rRNA is directly bound by ribosomal protein L11, and this complex is essential to ribosome function. Previous cocrystal structures of the 58-nucleotide GAC RNA bound to L11 revealed the intricate tertiary fold of the RNA domain, with one monovalent and several divalent ions located in specific sites within the structure. Here, we report a new crystal structure of the free GAC that is essentially identical to the L11-bound structure, which retains many common sites of divalent ion occupation. This new structure demonstrates that RNA alone folds into its tertiary structure with bound divalent ions. In solution, we find that this tertiary structure is not static, but rather is best described as an ensemble of states. While L11 protein cannot bind to the GAC until the RNA has adopted its tertiary structure, new experimental data show that L11 binds to Mg
Identifiants
pubmed: 31874150
pii: S0022-2836(19)30710-7
doi: 10.1016/j.jmb.2019.12.010
pmc: PMC7325582
mid: NIHMS1598110
pii:
doi:
Substances chimiques
RNA, Ribosomal
0
RNA, Ribosomal, 23S
0
Ribosomal Proteins
0
ribosomal protein L11
0
RNA
63231-63-0
GTP Phosphohydrolases
EC 3.6.1.-
Magnesium
I38ZP9992A
Potassium
RWP5GA015D
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
991-1007Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM122514
Pays : United States
Organisme : Wellcome Trust
ID : 79242
Pays : United Kingdom
Informations de copyright
Copyright © 2019 Elsevier Ltd. All rights reserved.
Références
Biochemistry. 1996 Feb 6;35(5):1581-8
pubmed: 8634289
Anal Chem. 2012 Jun 5;84(11):5066-73
pubmed: 22530732
J Mol Biol. 1995 Jun 2;249(2):319-31
pubmed: 7783196
Nat Struct Biol. 1997 Jan;4(1):24-7
pubmed: 8989317
J Bacteriol. 2002 Feb;184(4):1200-3
pubmed: 11807083
Biochemistry. 1999 Mar 23;38(12):3633-40
pubmed: 10090750
Science. 2008 Nov 7;322(5903):953-6
pubmed: 18988853
J Mol Biol. 2010 Nov 19;404(1):138-57
pubmed: 20875423
Nucleic Acids Res. 2007;35(2):441-54
pubmed: 17169991
J Am Chem Soc. 2011 Aug 31;133(34):13397-405
pubmed: 21776997
Biochemistry. 2013 Aug 27;52(34):5723-9
pubmed: 23947609
J Mol Biol. 2000 Jan 21;295(3):569-80
pubmed: 10623547
J Mol Biol. 2016 Nov 6;428(22):4490-4502
pubmed: 27693721
Mol Cell. 2008 Apr 11;30(1):26-38
pubmed: 18406324
J Mol Biol. 2007 Apr 6;367(4):1007-22
pubmed: 17292917
J Mol Biol. 1997 Nov 14;273(5):1020-31
pubmed: 9367788
Nucleic Acids Res. 1983 Jul 25;11(14):4923-32
pubmed: 6348702
J Mol Biol. 1987 Jun 20;195(4):909-17
pubmed: 3309345
J Mol Biol. 1979 Nov 15;134(4):767-9
pubmed: 119869
Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):710-728
pubmed: 28876235
RNA. 2018 Dec;24(12):1828-1838
pubmed: 30254137
J Appl Crystallogr. 2017 Sep 05;50(Pt 5):1545-1553
pubmed: 29021737
J Mol Biol. 2004 May 21;339(1):41-51
pubmed: 15123419
Nucleic Acids Res. 2000 Apr 15;28(8):1778-84
pubmed: 10734197
J Am Chem Soc. 2011 Aug 3;133(30):11540-56
pubmed: 21688829
J Mol Biol. 1990 May 20;213(2):275-88
pubmed: 1692883
J Mol Biol. 1997 Nov 21;274(1):101-13
pubmed: 9398519
J Mol Biol. 2015 Aug 28;427(17):2799-815
pubmed: 26210661
Chem Biol. 2005 Feb;12(2):201-6
pubmed: 15734647
Nucleic Acids Res. 1987 Nov 11;15(21):8783-98
pubmed: 3684574
RNA. 2006 Jul;12(7):1240-53
pubmed: 16682558
EMBO J. 1993 Apr;12(4):1499-504
pubmed: 7682175
J Mol Biol. 1994 Apr 15;237(5):577-87
pubmed: 8158638
Annu Rev Biophys. 2011;40:225-42
pubmed: 21332357
Cell. 1999 May 14;97(4):491-502
pubmed: 10338213
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
pubmed: 15572765
J Am Chem Soc. 2005 Jun 8;127(22):8014-5
pubmed: 15926816
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
pubmed: 20124702
Biochemistry. 1989 Dec 26;28(26):9949-56
pubmed: 2620068
Science. 2009 Oct 30;326(5953):694-9
pubmed: 19833919
Magn Reson Chem. 2006 Jul;44 Spec No:S177-84
pubmed: 16823898
J Mol Biol. 2006 Oct 20;363(2):531-44
pubmed: 16963081
J Biol Chem. 1998 Nov 27;273(48):31956-61
pubmed: 9822666
Nucleic Acids Res. 1995 Sep 11;23(17):3426-33
pubmed: 7567452
Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):6308-12
pubmed: 2068110
J Mol Biol. 2002 May 10;318(4):963-73
pubmed: 12054794
J Mol Biol. 1994 Dec 16;244(5):572-85
pubmed: 7527467
Nat Commun. 2016 Jun 13;7:ncomms11768
pubmed: 27292179
Nat Struct Biol. 2003 Nov;10(11):899-906
pubmed: 14566331
EMBO J. 1998 Mar 2;17(5):1507-14
pubmed: 9482747
Nature. 1988 Jul 28;334(6180):362-4
pubmed: 2455872
Nat Struct Biol. 1997 Jan;4(1):70-7
pubmed: 8989327
Methods Enzymol. 1995;259:261-81
pubmed: 8538458
J Mol Biol. 1991 Oct 20;221(4):1257-68
pubmed: 1942050