title: Structural basis for full-spectrum inhibition of translational functions on a tRNA synthetase.
abstract: The polyketide natural product borrelidin displays antibacterial, antifungal, antimalarial, anticancer, insecticidal and herbicidal activities through the selective inhibition of threonyl-tRNA synthetase (ThrRS). How borrelidin simultaneously attenuates bacterial growth and suppresses a variety of infections in plants and animals is not known. Here we show, using X-ray crystal structures and functional analyses, that a single molecule of borrelidin simultaneously occupies four distinct subsites within the catalytic domain of bacterial and human ThrRSs. These include the three substrate-binding sites for amino acid, ATP and tRNA associated with aminoacylation, and a fourth 'orthogonal' subsite created as a consequence of binding. Thus, borrelidin competes with all three aminoacylation substrates, providing a potent and redundant mechanism to inhibit ThrRS during protein synthesis. These results highlight a surprising natural design to achieve the quadrivalent inhibition of translation through a highly conserved family of enzymes.
authors.affiliation: Department of Cancer Biology, Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Fang
authors.affiliation: Department of Cancer Biology, Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA.
authors.forename: Xue
authors.initials: X
authors.lastname: Yu
authors.affiliation: Medicinal Bioconvergence Research Center, Seoul National University, Seoul 151-742, Korea.
authors.forename: Seung Jae
authors.initials: SJ
authors.lastname: Jeong
authors.affiliation: Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, Vermont 05405, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Mirando
authors.affiliation: Department of Cancer Biology, Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA.
authors.forename: Kaige
authors.initials: K
authors.lastname: Chen
authors.affiliation: Department of Cancer Biology, Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: Medicinal Bioconvergence Research Center, Seoul National University, Seoul 151-742, Korea.
authors.forename: Sunghoon
authors.initials: S
authors.lastname: Kim
authors.affiliation: Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, Vermont 05405, USA.
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Francklyn
authors.affiliation: Department of Cancer Biology, Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, USA.
authors.forename: Min
authors.initials: M
authors.lastname: Guo
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004926:Escherichia coli; D029968:Escherichia coli Proteins / Q000037:antagonists & inhibitors / Q000378:metabolism*; D005233:Fatty Alcohols / Q000378:metabolism; D006801:Humans; D030781:Organisms, Genetically Modified; D013914:Threonine-tRNA Ligase / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D046249:Transfer RNA Aminoacylation; D015003:Yeasts / Q000235:genetics
chemical_list: D029968:Escherichia coli Proteins; D005233:Fatty Alcohols; C005066:borrelidin; D013914:Threonine-tRNA Ligase
references.citation: Cell. 1999 Apr 30;97(3):371-81
references.pmid: 10319817
references.citation: Science. 1999 Aug 13;285(5430):1074-7
references.pmid: 10446055
references.citation: Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36
references.pmid: 10704480
references.citation: Oncol Res. 1999;11(7):319-29
references.pmid: 10757446
references.citation: Nat Struct Biol. 2000 Jun;7(6):461-5
references.pmid: 10881191
references.citation: Annu Rev Biochem. 2000;69:617-50
references.pmid: 10966471
references.citation: J Antibiot (Tokyo). 2000 Dec;53(12):1346-53
references.pmid: 11217799
references.citation: Biol Blood Marrow Transplant. 2003 Jul;9(7):417-25
references.pmid: 12869955
references.citation: J Mol Biol. 2003 Aug 1;331(1):201-11
references.pmid: 12875846
references.citation: J Antibiot (Tokyo). 2003 Aug;56(8):709-15
references.pmid: 14563161
references.citation: J Antibiot (Tokyo). 2003 Aug;56(8):727-9
references.pmid: 14563165
references.citation: Genes Dev. 2004 Apr 1;18(7):731-8
references.pmid: 15082526
references.citation: Mol Microbiol. 2004 Jun;52(6):1745-56
references.pmid: 15186422
references.citation: J Biol Chem. 2005 Jan 7;280(1):571-7
references.pmid: 15507440
references.citation: RNA. 2004 Dec;10(12):1845-51
references.pmid: 15525705
references.citation: Trends Biochem Sci. 1992 Apr;17(4):159-64
references.pmid: 1585461
references.citation: Science. 2005 Sep 2;309(5740):1533
references.pmid: 16141066
references.citation: Methods Biochem Anal. 2005;46:1-265
references.pmid: 16350889
references.citation: J Med Chem. 2006 Jul 27;49(15):4447-50
references.pmid: 16854048
references.citation: Science. 2007 Jun 22;316(5832):1759-61
references.pmid: 17588934
references.citation: J Biol Chem. 1991 Sep 15;266(26):17158-64
references.pmid: 1910039
references.citation: Science. 2009 Jun 5;324(5932):1334-8
references.pmid: 19498172
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):22-5
references.pmid: 20057045
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21
references.pmid: 20124702
references.citation: Chem Biol Drug Des. 2010 Jun;75(6):535-40
references.pmid: 20374252
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501
references.pmid: 20383002
references.citation: Invest New Drugs. 2012 Aug;30(4):1361-70
references.pmid: 21678129
references.citation: J Agric Food Chem. 2012 Feb 8;60(5):1251-7
references.pmid: 22242825
references.citation: Nat Chem Biol. 2012 Feb 12;8(3):311-7
references.pmid: 22327401
references.citation: ChemMedChem. 2012 May;7(5):844-9
references.pmid: 22438279
references.citation: Cell Host Microbe. 2012 Jun 14;11(6):654-63
references.pmid: 22704625
references.citation: J Agric Food Chem. 2012 Oct 3;60(39):9874-81
references.pmid: 22967236
references.citation: Expert Opin Ther Pat. 2012 Dec;22(12):1453-65
references.pmid: 23062029
references.citation: Nature. 2013 Feb 7;494(7435):121-4
references.pmid: 23263184
references.citation: J Med Chem. 2013 Feb 28;56(4):1748-60
references.pmid: 23362938
references.citation: Sci Rep. 2013;3:1317
references.pmid: 23425968
references.citation: Bioorg Med Chem Lett. 2013 Apr 15;23(8):2302-5
references.pmid: 23499502
references.citation: Int Immunopharmacol. 2013 Aug;16(4):414-23
references.pmid: 23685128
references.citation: Sci Rep. 2013;3:2475
references.pmid: 23959225
references.citation: Nat Chem Biol. 2014 Jan;10(1):29-34
references.pmid: 24212136
references.citation: Antimicrob Agents Chemother. 1989 Feb;33(2):156-63
references.pmid: 2497702
references.citation: J Nat Prod. 2014 Nov 26;77(11):2570-4
references.pmid: 25393949
references.citation: Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):E5508-17
references.pmid: 25489076
references.citation: Methods Enzymol. 1997;276:307-26
references.pmid: 27754618
references.citation: Nature. 1965 Apr 17;206(981):265-8
references.pmid: 4284424
references.citation: FEBS Lett. 1974 Feb 15;39(2):182-6
references.pmid: 4368395
references.citation: Eur J Biochem. 1973 Jun;35(2):331-7
references.pmid: 4577856
references.citation: Biochem Z. 1966 Mar 28;344(2):190-6
references.pmid: 4860826
references.citation: Arch Mikrobiol. 1968;61(2):143-53
references.pmid: 4974079
references.citation: Mol Gen Genet. 1970;108(1):28-32
references.pmid: 5472935
references.citation: Biochem J. 1980 Oct 1;191(1):209-19
references.pmid: 6258580
references.citation: Proc Natl Acad Sci U S A. 1981 Sep;78(9):5367-70
references.pmid: 6946478
references.citation: Antimicrob Agents Chemother. 1980 Dec;18(6):858-62
references.pmid: 7235673
references.citation: Mol Gen Genet. 1976 Aug 10;147(1):39-43
references.pmid: 785224
references.citation: Science. 1994 Mar 11;263(5152):1432-6
references.pmid: 8128224
references.citation: Eur J Biochem. 1976 Aug 1;67(1):247-56
references.pmid: 823012
references.citation: Annu Rev Biochem. 1993;62:715-48
references.pmid: 8352600
references.citation: RNA. 1997 Sep;3(9):954-60
references.pmid: 9292495
references.citation: J Antibiot (Tokyo). 1997 Aug;50(8):671-6
references.pmid: 9315080
references.citation: Curr Opin Struct Biol. 1997 Dec;7(6):881-9
references.pmid: 9434910
references.citation: J Biol Chem. 1998 Nov 27;273(48):31680-90
references.pmid: 9822629