Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase.
Adenosine Diphosphate
/ chemistry
Adenosine Triphosphate
/ chemistry
Aluminum Compounds
/ chemistry
Arginine
/ chemistry
Bacterial Proteins
/ chemistry
Catalytic Domain
Cloning, Molecular
DNA, Bacterial
/ chemistry
DnaB Helicases
/ chemistry
Escherichia coli
/ enzymology
Fluorides
/ chemistry
Gene Expression
Helicobacter pylori
/ enzymology
Hydrolysis
Lysine
/ chemistry
Models, Molecular
Nuclear Magnetic Resonance, Biomolecular
Protein Binding
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Interaction Domains and Motifs
Recombinant Proteins
/ chemistry
Substrate Specificity
Thermodynamics
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
06 09 2021
06 09 2021
Historique:
received:
24
03
2021
accepted:
20
08
2021
entrez:
7
9
2021
pubmed:
8
9
2021
medline:
6
10
2021
Statut:
epublish
Résumé
The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected
Identifiants
pubmed: 34489448
doi: 10.1038/s41467-021-25599-z
pii: 10.1038/s41467-021-25599-z
pmc: PMC8421360
doi:
Substances chimiques
Aluminum Compounds
0
Bacterial Proteins
0
DNA, Bacterial
0
Recombinant Proteins
0
Adenosine Diphosphate
61D2G4IYVH
Adenosine Triphosphate
8L70Q75FXE
Arginine
94ZLA3W45F
DnaB Helicases
EC 3.6.4.12
Lysine
K3Z4F929H6
Fluorides
Q80VPU408O
aluminum fluoride
Z77H3IKW94
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
5293Informations de copyright
© 2021. The Author(s).
Références
Biol Chem. 2017 May 1;398(5-6):523-533
pubmed: 28245182
Nature. 2020 Nov;587(7832):157-161
pubmed: 33087927
J Biomol NMR. 2001 Nov;21(3):249-61
pubmed: 11775741
Nature. 2008 May 22;453(7194):489-4
pubmed: 18497818
J Am Chem Soc. 2002 Aug 21;124(33):9704-5
pubmed: 12175218
J Am Chem Soc. 2003 Dec 24;125(51):15750-1
pubmed: 14677958
Angew Chem Int Ed Engl. 2013 Feb 18;52(8):2345-9
pubmed: 23335059
Acc Chem Res. 2013 Sep 17;46(9):2059-69
pubmed: 23470055
Proteins. 1997 Dec;29(4):401-16
pubmed: 9408938
Proteins. 2005 Jun 1;59(4):687-96
pubmed: 15815974
Chemistry. 2017 Jul 12;23(39):9425-9433
pubmed: 28426169
Nat Struct Biol. 2002 Jun;9(6):416-8
pubmed: 12032555
J Comput Chem. 2003 Jul 15;24(9):1142-56
pubmed: 12759913
Proc Natl Acad Sci U S A. 2015 May 12;112(19):6009-14
pubmed: 25918412
J Am Chem Soc. 2019 Jan 16;141(2):858-869
pubmed: 30620186
Annu Rev Biochem. 1997;66:717-49
pubmed: 9242922
J Phys Chem B. 2021 Jun 17;125(23):6222-6230
pubmed: 34097409
J Am Chem Soc. 2015 Mar 4;137(8):3031-40
pubmed: 25646698
Elife. 2018 Dec 11;7:
pubmed: 30526846
J Mol Biol. 1999 Sep 17;292(2):321-32
pubmed: 10493878
J Struct Biol. 2004 Apr-May;146(1-2):11-31
pubmed: 15037234
J Biomol NMR. 2009 Nov;45(3):319-27
pubmed: 19779834
Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):9187-92
pubmed: 27489348
Annu Rev Biochem. 2011;80:943-71
pubmed: 21675921
J Mol Biol. 2002 Mar 15;317(1):41-72
pubmed: 11916378
EMBO J. 1982;1(8):945-51
pubmed: 6329717
J Magn Reson. 2018 Sep;294:143-152
pubmed: 30053753
J Am Chem Soc. 2011 Oct 5;133(39):15514-23
pubmed: 21819147
Nucleic Acids Res. 2015 Sep 30;43(17):8564-76
pubmed: 26264665
Chemistry. 2021 May 17;27(28):7745-7755
pubmed: 33822417
Phys Rev Lett. 2003 Oct 3;91(14):146401
pubmed: 14611541
Structure. 2017 Aug 1;25(8):1264-1274.e3
pubmed: 28712805
Proc Natl Acad Sci U S A. 2011 Jun 28;108(26):10396-9
pubmed: 21670262
Adv Protein Chem. 2000;54:245-75
pubmed: 10829230
J Cell Sci. 2001 Feb;114(Pt 3):459-60
pubmed: 11171313
Top Curr Chem (Cham). 2017 Apr;375(2):36
pubmed: 28299727
Angew Chem Int Ed Engl. 2012 Jul 27;51(31):7855-8
pubmed: 22740125
Angew Chem Int Ed Engl. 2017 Mar 13;56(12):3369-3373
pubmed: 28191714
J Am Chem Soc. 2017 Sep 20;139(37):13006-13012
pubmed: 28724288
J Biomol NMR. 1997 Jun;9(4):359-69
pubmed: 9255942
Nat Commun. 2019 Jan 10;10(1):123
pubmed: 30631074
Trends Biochem Sci. 1990 Nov;15(11):430-4
pubmed: 2126155
Chem Commun (Camb). 2019 Jul 14;55(55):7899-7902
pubmed: 31199417
Front Mol Biosci. 2020 Sep 30;7:582033
pubmed: 33195425
Cell. 2012 Oct 12;151(2):267-77
pubmed: 23022319
Nucleic Acids Res. 2003 Dec 1;31(23):6828-40
pubmed: 14627816
Nat Commun. 2017 Dec 12;8(1):2073
pubmed: 29233991
Solid State Nucl Magn Reson. 2017 Oct;87:117-125
pubmed: 28732673
Solid State Nucl Magn Reson. 2017 Oct;87:126-136
pubmed: 28802890
Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15152-6
pubmed: 21825153
J Am Chem Soc. 2016 Dec 21;138(50):16345-16354
pubmed: 27936674
Genome Res. 2000 Jan;10(1):5-16
pubmed: 10645945
J Magn Reson. 2017 Jul;280:63-78
pubmed: 28579103
Chembiochem. 2020 Feb 3;21(3):324-330
pubmed: 31310428
J Am Chem Soc. 2014 Aug 6;136(31):11002-10
pubmed: 24988008
Mol Cell. 2013 Dec 26;52(6):844-54
pubmed: 24373746
Inorg Chem. 2015 Nov 2;54(21):10422-8
pubmed: 26488236
J Biomol NMR. 2016 Mar;64(3):189-95
pubmed: 26961129
Angew Chem Int Ed Engl. 2017 Aug 7;56(33):9732-9735
pubmed: 28498638
Chem Commun (Camb). 2018 Aug 21;54(65):8972-8975
pubmed: 29974085
J Magn Reson. 2002 Aug;157(2):178-80
pubmed: 12323135
PLoS Biol. 2018 May 21;16(5):e2006192
pubmed: 29782488
Prog Nucl Magn Reson Spectrosc. 2020 Apr;117:1-32
pubmed: 32471533
Angew Chem Int Ed Engl. 2016 Nov 2;55(45):14164-14168
pubmed: 27709753
J Biomol NMR. 2011 Dec;51(4):437-47
pubmed: 21953355
Solid State Nucl Magn Reson. 2014 Feb-Apr;57-58:22-8
pubmed: 24300107
J Phys Chem Lett. 2017 Jun 1;8(11):2399-2405
pubmed: 28492324
Angew Chem Int Ed Engl. 2014 Nov 3;53(45):12253-6
pubmed: 25225004
J Magn Reson. 2006 Jan;178(1):42-55
pubmed: 16188474
Structure. 2008 May;16(5):715-26
pubmed: 18462676
J Chem Phys. 2005 Jan 8;122(2):024515
pubmed: 15638606
Proc Natl Acad Sci U S A. 2012 Jul 10;109(28):11095-100
pubmed: 22723345
Molecules. 2020 Nov 12;25(22):
pubmed: 33198135
Front Mol Biosci. 2020 Feb 21;7:17
pubmed: 32154263
Phys Chem Chem Phys. 2005 Sep 21;7(18):3297-305
pubmed: 16240044
J Phys Chem B. 2020 Dec 10;124(49):11089-11097
pubmed: 33238710
Angew Chem Int Ed Engl. 2012 Dec 3;51(49):12242-5
pubmed: 23125010
J Struct Biol. 2006 Oct;156(1):2-11
pubmed: 16828312
Dev Cell. 2015 May 26;33(4):401-12
pubmed: 25936506
J Biomol NMR. 2020 May;74(4-5):247-256
pubmed: 32185644
J Am Chem Soc. 2019 Jul 17;141(28):11183-11195
pubmed: 31199882
Nat Commun. 2019 Jan 3;10(1):31
pubmed: 30604765
Curr Opin Struct Biol. 2002 Dec;12(6):746-53
pubmed: 12504679
Angew Chem Int Ed Engl. 2017 Apr 3;56(15):4110-4128
pubmed: 27862756
J Biol Chem. 1993 Apr 5;268(10):7093-100
pubmed: 8463244
J Phys Condens Matter. 2013 Nov 20;25(46):463101
pubmed: 24100357
Sci Rep. 2019 Jul 31;9(1):11082
pubmed: 31366983
J Am Chem Soc. 2010 Mar 24;132(11):3842-6
pubmed: 20184366
Nat Commun. 2018 Apr 25;9(1):1658
pubmed: 29695721
Philos Trans R Soc Lond B Biol Sci. 1990 Jan 30;326(1236):367-78
pubmed: 1970643