Cryo-EM reconstructions of inhibitor-bound SMG1 kinase reveal an autoinhibitory state dependent on SMG8.
PIKK
human
mRNA surveillance
molecular biophysics
nonsense-mediated mRNA decay
structural biology
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
26 10 2021
26 10 2021
Historique:
received:
28
07
2021
accepted:
25
10
2021
pubmed:
27
10
2021
medline:
15
12
2021
entrez:
26
10
2021
Statut:
epublish
Résumé
The PI3K-related kinase (PIKK) SMG1 monitors the progression of metazoan nonsense-mediated mRNA decay (NMD) by phosphorylating the RNA helicase UPF1. Previous work has shown that the activity of SMG1 is impaired by small molecule inhibitors, is reduced by the SMG1 interactors SMG8 and SMG9, and is downregulated by the so-called SMG1 insertion domain. However, the molecular basis for this complex regulatory network has remained elusive. Here, we present cryo-electron microscopy reconstructions of human SMG1-9 and SMG1-8-9 complexes bound to either a SMG1 inhibitor or a non-hydrolyzable ATP analog at overall resolutions ranging from 2.8 to 3.6 Å. These structures reveal the basis with which a small molecule inhibitor preferentially targets SMG1 over other PIKKs. By comparison with our previously reported substrate-bound structure (Langer et al.,2020), we show that the SMG1 insertion domain can exert an autoinhibitory function by directly blocking the substrate-binding path as well as overall access to the SMG1 kinase active site. Together with biochemical analysis, our data indicate that SMG1 autoinhibition is stabilized by the presence of SMG8. Our results explain the specific inhibition of SMG1 by an ATP-competitive small molecule, provide insights into regulation of its kinase activity within the NMD pathway, and expand the understanding of PIKK regulatory mechanisms in general.
Identifiants
pubmed: 34698635
doi: 10.7554/eLife.72353
pii: 72353
pmc: PMC8592573
doi:
pii:
Substances chimiques
Intracellular Signaling Peptides and Proteins
0
Trans-Activators
0
Protein Serine-Threonine Kinases
EC 2.7.11.1
SMG1 protein, human
EC 2.7.11.1
RNA Helicases
EC 3.6.4.13
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2021, Langer et al.
Déclaration de conflit d'intérêts
LL, FB, YG, EC No competing interests declared
Références
Methods. 2011 Sep;55(1):94-106
pubmed: 21821126
Mol Cell Biol. 2002 Nov;22(21):7428-38
pubmed: 12370290
Genes Dev. 2009 May 1;23(9):1091-105
pubmed: 19417104
Nucleic Acids Res. 2014 Aug;42(14):9447-60
pubmed: 25013172
Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):861-877
pubmed: 31588918
Nat Protoc. 2018 Dec;13(12):2964-2990
pubmed: 30446747
Am J Hum Genet. 2016 Apr 7;98(4):643-52
pubmed: 27018474
Nat Rev Mol Cell Biol. 2019 Jul;20(7):406-420
pubmed: 30992545
Mol Cell. 2003 Nov;12(5):1187-200
pubmed: 14636577
J Struct Biol. 2012 Dec;180(3):519-30
pubmed: 23000701
J Biol Chem. 2001 Jun 22;276(25):22709-14
pubmed: 11331269
Cold Spring Harb Perspect Biol. 2019 Feb 1;11(2):
pubmed: 29891560
Nat Methods. 2017 Aug;14(8):793-796
pubmed: 28671674
Nature. 2013 May 9;497(7448):217-23
pubmed: 23636326
Bioorg Med Chem Lett. 2012 Nov 1;22(21):6636-41
pubmed: 23021994
Structure. 2014 Aug 5;22(8):1105-1119
pubmed: 25002321
Prog Biophys Mol Biol. 2021 Aug;163:120-129
pubmed: 33166573
Nucleic Acids Res. 2012 Feb;40(3):1251-66
pubmed: 21965535
Nat Methods. 2017 Mar;14(3):290-296
pubmed: 28165473
Genes Cells. 2013 Mar;18(3):161-75
pubmed: 23356578
Acta Crystallogr D Biol Crystallogr. 2009 Oct;65(Pt 10):1074-80
pubmed: 19770504
Mol Cell. 2021 Feb 18;81(4):801-810.e3
pubmed: 33385326
Nucleic Acids Res. 2014 Aug;42(14):9217-35
pubmed: 25053839
Anal Biochem. 2004 Mar 1;326(1):13-20
pubmed: 14769330
Am J Hum Genet. 2020 Dec 3;107(6):1178-1185
pubmed: 33242396
RNA. 2017 Jul;23(7):1028-1034
pubmed: 28389433
Structure. 2020 Jan 7;28(1):83-95.e5
pubmed: 31740028
Oncogene. 2004 Jul 22;23(33):5654-63
pubmed: 15133498
J Mol Biol. 2003 Oct 31;333(4):721-45
pubmed: 14568533
J Struct Biol. 2017 May;198(2):124-133
pubmed: 28344036
Genes Dev. 2011 Jan 15;25(2):153-64
pubmed: 21245168
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Cell Res. 2019 Aug;29(8):683-685
pubmed: 31320732
Nat Struct Mol Biol. 2019 Dec;26(12):1089-1093
pubmed: 31792449
Genes Dev. 2001 Sep 1;15(17):2215-28
pubmed: 11544179
Mol Cell Proteomics. 2015 Jul;14(7):2030-41
pubmed: 25887394
Curr Opin Struct Biol. 2014 Dec;29:134-42
pubmed: 25460276
Cell Res. 2019 Dec;29(12):1027-1034
pubmed: 31729466
Genes Dev. 2006 Feb 1;20(3):355-67
pubmed: 16452507
Sci Adv. 2018 Jun 20;4(6):eaat1719
pubmed: 29938225
Nucleic Acids Res. 2015 Sep 3;43(15):7600-11
pubmed: 26130714
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
pubmed: 20383002
Drug Discov Today. 2011 Apr;16(7-8):325-31
pubmed: 21333749
Nat Rev Clin Oncol. 2018 May;15(5):273-291
pubmed: 29508857
Genes Dev. 2008 Jun 1;22(11):1478-89
pubmed: 18519640
J Struct Biol. 2005 Oct;152(1):36-51
pubmed: 16182563
Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
pubmed: 15572765
Elife. 2018 Nov 09;7:
pubmed: 30412051
Curr Opin Struct Biol. 2018 Apr;49:177-189
pubmed: 29625383
Structure. 2020 Jan 7;28(1):96-104.e3
pubmed: 31740029
Science. 1995 Oct 6;270(5233):50-1
pubmed: 7569949
Protein Sci. 2018 Jan;27(1):14-25
pubmed: 28710774
Nucleic Acids Res. 2019 Sep 19;47(16):8838-8859
pubmed: 31329944
Elife. 2020 May 29;9:
pubmed: 32469312