Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
25 09 2020
25 09 2020
Historique:
accepted:
31
07
2020
revised:
28
07
2020
received:
07
07
2020
pubmed:
14
8
2020
medline:
11
11
2020
entrez:
14
8
2020
Statut:
ppublish
Résumé
MiaE (2-methylthio-N6-isopentenyl-adenosine37-tRNA monooxygenase) is a unique non-heme diiron enzyme that catalyzes the O2-dependent post-transcriptional allylic hydroxylation of a hypermodified nucleotide 2-methylthio-N6-isopentenyl-adenosine (ms2i6A37) at position 37 of selected tRNA molecules to produce 2-methylthio-N6-4-hydroxyisopentenyl-adenosine (ms2io6A37). Here, we report the in vivo activity, biochemical, spectroscopic characterization and X-ray crystal structure of MiaE from Pseudomonas putida. The investigation demonstrates that the putative pp-2188 gene encodes a MiaE enzyme. The structure shows that Pp-MiaE consists of a catalytic diiron(III) domain with a four alpha-helix bundle fold. A docking model of Pp-MiaE in complex with tRNA, combined with site directed mutagenesis and in vivo activity shed light on the importance of an additional linker region for substrate tRNA recognition. Finally, krypton-pressurized Pp-MiaE experiments, revealed the presence of defined O2 site along a conserved hydrophobic tunnel leading to the diiron active center.
Identifiants
pubmed: 32785618
pii: 5891576
doi: 10.1093/nar/gkaa667
pmc: PMC7515727
doi:
Substances chimiques
Bacterial Proteins
0
RNA, Transfer
9014-25-9
Mixed Function Oxygenases
EC 1.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
9918-9930Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Nucleosides Nucleotides. 1999 Jun-Jul;18(6-7):1579-81
pubmed: 10474235
Nat Struct Mol Biol. 2009 Oct;16(10):1109-15
pubmed: 19749755
Nat Struct Biol. 1994 Jul;1(7):453-60
pubmed: 7664064
Biochemistry. 2007 May 1;46(17):5140-7
pubmed: 17407324
RNA. 1999 Feb;5(2):188-94
pubmed: 10024171
Chem Rev. 2006 May;106(5):1814-35
pubmed: 16683756
Biochemistry. 2000 Nov 7;39(44):13390-5
pubmed: 11063576
Nucleic Acids Res. 2011 Jan;39(Database issue):D195-201
pubmed: 21071406
Science. 2016 Apr 15;352(6283):309-12
pubmed: 27081063
Curr Opin Struct Biol. 1995 Dec;5(6):758-66
pubmed: 8749363
J Biol Chem. 2004 Nov 12;279(46):47555-63
pubmed: 15339930
J Biol Chem. 2002 May 10;277(19):16391-5
pubmed: 11861649
J Mol Biol. 1997 Aug 15;271(2):209-21
pubmed: 9268653
FEBS Lett. 1999 Jun 4;452(1-2):47-51
pubmed: 10376676
Angew Chem Int Ed Engl. 2001 Aug 3;40(15):2782-2807
pubmed: 11500872
Nucleic Acids Res. 2005 Dec 23;33(22):6961-71
pubmed: 16377777
Biochemistry. 2009 Jun 16;48(23):5057-65
pubmed: 19435325
Mol Cell. 2006 Nov 17;24(4):535-45
pubmed: 17188032
EMBO J. 1996 Aug 15;15(16):4081-92
pubmed: 8861937
Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67
pubmed: 21460454
Nature. 1991 Feb 7;349(6309):541-4
pubmed: 1992356
J Mol Biol. 2007 Mar 30;367(3):872-81
pubmed: 17292915
J Bacteriol. 1993 Dec;175(24):7776-85
pubmed: 8253666
Curr Opin Chem Biol. 2003 Apr;7(2):183-8
pubmed: 12714050
Nat Struct Mol Biol. 2006 Feb;13(2):153-9
pubmed: 16415880
Chem Rev. 1996 Nov 7;96(7):2625-2658
pubmed: 11848839
J Biol Chem. 2009 Mar 13;284(11):6600-4
pubmed: 19158097
J Chromatogr. 1989 Jun 2;471:3-36
pubmed: 2670985
J Biol Chem. 2007 Jul 6;282(27):19863-71
pubmed: 17463003
Nucleic Acids Res. 2008 Nov;36(20):6548-57
pubmed: 18927116
Nat Chem Biol. 2013 May;9(5):333-8
pubmed: 23542644
Acta Crystallogr D Biol Crystallogr. 2015 Jan 1;71(Pt 1):15-26
pubmed: 25615856
Proc Natl Acad Sci U S A. 2007 Aug 14;104(33):13295-300
pubmed: 17679698
Nature. 1990 Jun 14;345(6276):593-8
pubmed: 2190093
J Am Chem Soc. 2004 Dec 29;126(51):16930-6
pubmed: 15612731
Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2734-9
pubmed: 18258747
J Biol Chem. 2004 Jul 16;279(29):30600-10
pubmed: 15096510
J Bacteriol. 1985 May;162(2):752-5
pubmed: 3988713
Nucleic Acids Res. 2009 Jan;37(Database issue):D159-62
pubmed: 18957446
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W222-7
pubmed: 22553366
Nucleic Acids Res. 2003 Jul 1;31(13):3497-500
pubmed: 12824352
Nature. 2006 Feb 16;439(7078):879-84
pubmed: 16482161
Nature. 2002 Sep 12;419(6903):174-8
pubmed: 12226667
Proteins. 2008 Jan 1;70(1):1-18
pubmed: 17910062
Nucleic Acids Res. 1985 Aug 12;13(15):5697-706
pubmed: 3898020
Nat Struct Biol. 1996 Jun;3(6):539-46
pubmed: 8646540
Wiley Interdiscip Rev RNA. 2013 Jan-Feb;4(1):35-48
pubmed: 23139145
Science. 2010 Jul 30;329(5991):559-62
pubmed: 20671186
J Bacteriol. 1998 Jun;180(12):3144-51
pubmed: 9620964
J Mol Biol. 2016 Feb 22;428(4):720-725
pubmed: 26410586
Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
pubmed: 20383002
EMBO J. 2001 Sep 3;20(17):4863-73
pubmed: 11532950
Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10037-41
pubmed: 11517324
Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16142-7
pubmed: 18852462
Biochemistry. 1997 Jan 21;36(3):604-14
pubmed: 9012675
FEBS Lett. 1993 Jun 14;324(2):162-6
pubmed: 7685296
J Bacteriol. 1995 Apr;177(8):1967-75
pubmed: 7536729
Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):E4197-205
pubmed: 26183229
Nat Struct Mol Biol. 2010 May;17(5):555-60
pubmed: 20400952
Mol Cell. 2007 Apr 27;26(2):189-203
pubmed: 17466622
Bioinformatics. 2011 Oct 15;27(20):2915-6
pubmed: 21873642
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
pubmed: 20124702
Annu Rev Biochem. 2006;75:681-706
pubmed: 16756507
Nature. 2006 Jul 27;442(7101):419-24
pubmed: 16871210
Biophys J. 1986 Mar;49(3):619-27
pubmed: 3697474
Proteins. 1997 Oct;29(2):141-52
pubmed: 9329079
J Am Chem Soc. 2020 Jan 29;142(4):1911-1924
pubmed: 31899624
RNA Biol. 2014;11(12):1508-18
pubmed: 25629788
J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
pubmed: 19461840
Acc Chem Res. 2004 Jul;37(7):421-9
pubmed: 15260504
Nucleic Acids Res. 2014 Jul;42(12):7960-70
pubmed: 24914049
Biochemistry. 2015 Jan 20;54(2):363-76
pubmed: 25453905
J Biol Chem. 2002 Apr 19;277(16):13367-70
pubmed: 11882645
RNA. 2003 Jun;9(6):760-8
pubmed: 12756333
J Mol Biol. 2004 Apr 30;338(3):439-44
pubmed: 15081802
ACS Chem Biol. 2006 Mar 17;1(2):75-81
pubmed: 17163647
Biochemistry. 2013 Sep 10;52(36):6182-96
pubmed: 23906247
Structure. 2015 May 5;23(5):882-892
pubmed: 25865244
Nat Struct Biol. 2003 Oct;10(10):781-8
pubmed: 12949492