Structure of a reaction intermediate mimic in t6A biosynthesis bound in the active site of the TsaBD heterodimer from Escherichia coli.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
26 02 2021
26 02 2021
Historique:
accepted:
15
01
2021
revised:
21
12
2020
received:
25
09
2020
pubmed:
2
2
2021
medline:
10
3
2021
entrez:
1
2
2021
Statut:
ppublish
Résumé
The tRNA modification N6-threonylcarbamoyladenosine (t6A) is universally conserved in all organisms. In bacteria, the biosynthesis of t6A requires four proteins (TsaBCDE) that catalyze the formation of t6A via the unstable intermediate l-threonylcarbamoyl-adenylate (TC-AMP). While the formation and stability of this intermediate has been studied in detail, the mechanism of its transfer to A37 in tRNA is poorly understood. To investigate this step, the structure of the TsaBD heterodimer from Escherichia coli has been solved bound to a stable phosphonate isosteric mimic of TC-AMP. The phosphonate inhibits t6A synthesis in vitro with an IC50 value of 1.3 μM in the presence of millimolar ATP and L-threonine. The inhibitor binds to TsaBD by coordination to the active site Zn atom via an oxygen atom from both the phosphonate and the carboxylate moieties. The bound conformation of the inhibitor suggests that the catalysis exploits a putative oxyanion hole created by a conserved active site loop of TsaD and that the metal essentially serves as a binding scaffold for the intermediate. The phosphonate bound crystal structure should be useful for the rational design of potent, drug-like small molecule inhibitors as mechanistic probes or potentially novel antibiotics.
Identifiants
pubmed: 33524148
pii: 6125664
doi: 10.1093/nar/gkab026
pmc: PMC7913687
doi:
Substances chimiques
Escherichia coli Proteins
0
Organophosphonates
0
N(6)-(N-threonylcarbonyl)adenosine
24719-82-2
RNA, Transfer
9014-25-9
Adenosine
K72T3FS567
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2141-2160Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Biochim Biophys Acta. 1969;185(2):269-86
pubmed: 4980133
Mol Microbiol. 2015 Dec;98(6):1199-221
pubmed: 26337258
Nat Chem Biol. 2016 Jul;12(7):482-9
pubmed: 27159581
RNA. 2018 Jul;24(7):926-938
pubmed: 29650678
J Bacteriol. 2009 Aug;191(15):4732-49
pubmed: 19376873
J Biol Chem. 1972 Oct 25;247(20):6394-401
pubmed: 4561935
J Chromatogr. 1982 Jul 9;230(2):297-308
pubmed: 7050138
Nat Commun. 2018 May 14;9(1):1875
pubmed: 29760464
Curr Opin Microbiol. 2008 Apr;11(2):134-40
pubmed: 18378185
RNA. 2020 Sep;26(9):1094-1103
pubmed: 32385138
Nucleic Acids Res. 2018 Feb 16;46(3):1395-1411
pubmed: 29309633
Nat Chem Biol. 2013 Feb;9(2):105-11
pubmed: 23242255
Nucleic Acids Res. 2009 May;37(9):2894-909
pubmed: 19287007
Nucleic Acids Res. 2019 Sep 26;47(17):9464-9465
pubmed: 31428791
Nucleic Acids Res. 2011 Aug;39(14):6148-60
pubmed: 21459853
EMBO J. 2011 Mar 2;30(5):873-81
pubmed: 21183954
Sci Rep. 2014 Oct 06;4:6522
pubmed: 25283467
Biochem J. 2004 Dec 15;384(Pt 3):577-84
pubmed: 15324301
Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
pubmed: 12136088
EMBO J. 2009 May 20;28(10):1466-78
pubmed: 19369944
Protein Sci. 2013 May;22(5):628-40
pubmed: 23471679
J Antibiot (Tokyo). 2019 Jun;72(6):325-349
pubmed: 30982830
J Biol Chem. 1999 Mar 5;274(10):6122-9
pubmed: 10037695
J Biol Chem. 2012 Apr 20;287(17):13666-73
pubmed: 22378793
Eur J Hum Genet. 2017 May;25(5):545-551
pubmed: 28272532
EMBO J. 2006 Aug 9;25(15):3576-85
pubmed: 16874308
RNA Biol. 2014;11(12):1529-39
pubmed: 25629598
Nucleic Acids Res. 2013 Feb 1;41(3):1953-64
pubmed: 23258706
Nucleic Acids Res. 2016 Aug 19;44(14):6971-80
pubmed: 27302132
Nat Genet. 2017 Oct;49(10):1529-1538
pubmed: 28805828
Proteins. 2008 Feb 15;70(3):1108-11
pubmed: 18004774
Curr Top Med Chem. 2012;12(7):766-96
pubmed: 22283817
Nucleic Acids Res. 1976 May;3(5):1185-201
pubmed: 781621
Nucleic Acids Res. 2019 Jul 9;47(12):6551-6567
pubmed: 31114923
Nucleic Acids Res. 2015 Mar 31;43(6):3358-72
pubmed: 25735745
Nucleic Acids Res. 1987 Nov 11;15(21):8783-98
pubmed: 3684574
Protein Sci. 2000 Dec;9(12):2557-66
pubmed: 11206077
Biochemistry. 1992 Oct 27;31(42):10380-9
pubmed: 1420156
Nucleic Acids Res. 2018 Jun 20;46(11):5850-5860
pubmed: 29741707
Nucleic Acids Res. 2013 Jul;41(12):6332-46
pubmed: 23620299
J Bacteriol. 2019 Apr 9;201(9):
pubmed: 30745370
Nucleic Acids Res. 2019 Jun 20;47(11):5684-5697
pubmed: 30937455
Proteins. 2002 Aug 1;48(2):220-6
pubmed: 12112691
Biochemistry. 2012 Nov 6;51(44):8950-63
pubmed: 23072323
EMBO J. 2001 Sep 3;20(17):4863-73
pubmed: 11532950
Nucleic Acids Res. 2017 Feb 28;45(4):2137-2149
pubmed: 27913732
J Org Chem. 2002 Jan 11;67(1):146-53
pubmed: 11777452
J Bacteriol. 2008 Jan;190(2):718-26
pubmed: 17965154
J Biol Chem. 2015 Aug 14;290(33):20032-43
pubmed: 26060251
Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):16918-23
pubmed: 18971327
J Comput Aided Mol Des. 1996 Aug;10(4):293-304
pubmed: 8877701
Mol Cell Biol. 2010 Jan;30(1):354-63
pubmed: 19884342
Nat Struct Mol Biol. 2004 Dec;11(12):1186-91
pubmed: 15558052
Biochemistry. 1969 Aug;8(8):3283-9
pubmed: 4897334
Biochem Pharmacol. 1973 Dec 1;22(23):3099-108
pubmed: 4202581
EMBO J. 2011 Mar 2;30(5):882-93
pubmed: 21285948
J Chem Inf Model. 2011 Oct 24;51(10):2778-86
pubmed: 21919503
Nucleic Acids Res. 1992 Nov 11;20(21):5607-15
pubmed: 1280806
Annu Rev Genet. 2012;46:69-95
pubmed: 22905870
Microbiology (Reading). 2009 Mar;155(Pt 3):944-956
pubmed: 19246765
Eukaryot Cell. 2014 Sep;13(9):1222-31
pubmed: 25038083
Nat Commun. 2010 Oct 19;1:100
pubmed: 20981028
Angew Chem Int Ed Engl. 2012 Apr 23;51(17):4046-52
pubmed: 22383337
Methods. 2018 Aug 15;146:107-119
pubmed: 29438829
Nat Commun. 2019 Sep 3;10(1):3967
pubmed: 31481669
Nucleic Acids Res. 2015 Feb 18;43(3):1804-17
pubmed: 25578970
Methods Enzymol. 1990;193:796-824
pubmed: 1706064
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W320-4
pubmed: 24753421
Cell. 2006 Mar 24;124(6):1155-68
pubmed: 16564010