Selective Inhibition of Bacterial Tryptophanyl-tRNA Synthetases by Indolmycin Is Mechanism-based

Williams, Tishan L.; Yin, Yuhui W.; Carter, Jr., Charles W.

doi:10.1074/jbc.M115.690321

Title: Selective Inhibition of Bacterial Tryptophanyl-tRNA Synthetases by Indolmycin Is Mechanism-based

Journal Article · 08 November 2015 · Journal of Biological Chemistry

DOI: https://doi.org/10.1074/jbc.M115.690321 · OSTI ID:1234733

Williams, Tishan L. ^[1]; Yin, Yuhui W. ^[2]; Carter, Jr., Charles W. ^[1]

Univ. of North Carolina, Chapel Hill, NC (United States)
Univ. of Texas Medical Branch, Galveston, TX (United States)

Indolmycin is a natural tryptophan analog that competes with tryptophan for binding to tryptophanyl-tRNA synthetase (TrpRS) enzymes. Bacterial and eukaryotic cytosolic TrpRSs have comparable affinities for tryptophan (K_m ~ 2 μm), and yet only bacterial TrpRSs are inhibited by indolmycin. Despite the similarity between these ligands, Bacillus stearothermophilus (Bs)TrpRS preferentially binds indolmycin ~1500-fold more tightly than its tryptophan substrate. Kinetic characterization and crystallographic analysis of BsTrpRS allowed us to probe novel aspects of indolmycin inhibitory action. Previous work had revealed that long range coupling to residues within an allosteric region called the D1 switch of BsTrpRS positions the Mg²⁺ ion in a manner that allows it to assist in transition state stabilization. The Mg²⁺ ion in the inhibited complex forms significantly closer contacts with non-bridging oxygen atoms from each phosphate group of ATP and three water molecules than occur in the (presumably catalytically competent) pre-transition state (preTS) crystal structures. We propose that this altered coordination stabilizes a ground state Mg²⁺·ATP configuration, accounting for the high affinity inhibition of BsTrpRS by indolmycin. Conversely, both the ATP configuration and Mg²⁺ coordination in the human cytosolic (H_c)TrpRS preTS structure differ greatly from the BsTrpRS preTS structure. The effect of these differences is that catalysis occurs via a different transition state stabilization mechanism in HcTrpRS with a yet-to-be determined role for Mg²⁺. Furthermore, modeling indolmycin into the tryptophan binding site points to steric hindrance and an inability to retain the interactions used for tryptophan substrate recognition as causes for the 1000-fold weaker indolmycin affinity to H_cTrpRS.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Inst. of Health

OSTI ID:: 1234733

Journal Information:: Journal of Biological Chemistry, Journal Name: Journal of Biological Chemistry Journal Issue: 1 Vol. 291; ISSN 0021-9258

Publisher:: American Society for Biochemistry and Molecular BiologyCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (36)

The crystal structure of a post-synaptic neurotoxin from sea snake at 2.2 Å resolution Tsernoglou, Demetrius; Petsko, Gregory A. FEBS Letters, Vol. 68, Issue 1 https://doi.org/10.1016/0014-5793(76)80390-0	journal	September 1976
Inhibition of phenylalanine tRNA synthetase from Bacillus subtilis by ochratoxin A Konrad, I.; Röschenthaler, R. FEBS Letters, Vol. 83, Issue 2 https://doi.org/10.1016/0014-5793(77)81037-5	journal	November 1977
Interconversion of ATP Binding and Conformational Free Energies by Tryptophanyl-tRNA Synthetase: Structures of ATP Bound to Open and Closed, Pre-Transition-state Conformations Retailleau, Pascal; Huang, Xin; Yin, Yuhui Journal of Molecular Biology, Vol. 325, Issue 1 https://doi.org/10.1016/S0022-2836(02)01156-7	journal	January 2003
Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Adenosine-5′ Tetraphosphate: Evidence for Distributed Use of Catalytic Binding Energy in Amino Acid Activation by Class I Aminoacyl-tRNA Synthetases Retailleau, Pascal; Weinreb, Violetta; Hu, Mei Journal of Molecular Biology, Vol. 369, Issue 1 https://doi.org/10.1016/j.jmb.2007.01.091	journal	May 2007
Protein production by auto-induction in high-density shaking cultures Studier, F. William Protein Expression and Purification, Vol. 41, Issue 1, p. 207-234 https://doi.org/10.1016/j.pep.2005.01.016	journal	May 2005
Functional and Crystal Structure Analysis of Active Site Adaptations of a Potent Anti-Angiogenic Human tRNA Synthetase Yang, Xiang-Lei; Guo, Min; Kapoor, Mili Structure, Vol. 15, Issue 7 https://doi.org/10.1016/j.str.2007.05.009	journal	July 2007
Mg2+-Assisted Catalysis by B. Stearothermophilus TrpRS Is Promoted by Allosteric Effects Weinreb, Violetta; Li, Li; Campbell, Cassandra L. Structure, Vol. 17, Issue 7 https://doi.org/10.1016/j.str.2009.05.007	journal	July 2009
A Master Switch Couples Mg2+-Assisted Catalysis to Domain Motion in B. stearothermophilus Tryptophanyl-tRNA Synthetase Weinreb, Violetta; Li, Li; Carter, Charles W. Structure, Vol. 20, Issue 1 https://doi.org/10.1016/j.str.2011.10.020	journal	January 2012
Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases Francklyn, Christopher S.; First, Eric A.; Perona, John J. Methods, Vol. 44, Issue 2 https://doi.org/10.1016/j.ymeth.2007.09.007	journal	February 2008
Active site titration and aminoacyl adenylate binding stoichiometry of aminoacyl-tRNA synthetases Fersht, Alan R.; Ashford, Jeremy S.; Bruton, Christopher J. Biochemistry, Vol. 14, Issue 1 https://doi.org/10.1021/bi00672a001	journal	January 1975
Thermodynamic Stability of Carbonic Anhydrase: Measurements of Binding Affinity and Stoichiometry Using ThermoFluor Matulis, Daumantas; Kranz, James K.; Salemme, F. Raymond Biochemistry, Vol. 44, Issue 13 https://doi.org/10.1021/bi048135v	journal	April 2005
Crystallographic and thermodynamic comparison of natural and synthetic ligands bound to streptavidin Weber, P. C.; Wendoloski, J. J.; Pantoliano, M. W. Journal of the American Chemical Society, Vol. 114, Issue 9 https://doi.org/10.1021/ja00035a004	journal	April 1992
Effect of Deuterium on the Strength of Hydrogen Bonds ¹ Calvin, Melvin; Hermans, Jan; Scheraga, Harold A. Journal of the American Chemical Society, Vol. 81, Issue 19 https://doi.org/10.1021/ja01528a009	journal	October 1959
2,4-Diamino-5-deaza-6-Substituted Pyrido[2,3- d ]pyrimidine Antifolates as Potent and Selective Nonclassical Inhibitors of Dihydrofolate Reductases ^1,2 Gangjee, Aleem; Vasudevan, Anil; Queener, Sherry F. Journal of Medicinal Chemistry, Vol. 39, Issue 7 https://doi.org/10.1021/jm950786p	journal	January 1996
Beta-Blocker Selectivity at Cloned Human Beta1- and Beta2-Adrenergic Receptors Smith, Carol; Teitler, Milt Cardiovascular Drugs and Therapy, Vol. 13, Issue 2, p. 123-126 https://doi.org/10.1023/A:1007784109255	journal	January 1999
NIH Image to ImageJ: 25 years of image analysis Schneider, Caroline A.; Rasband, Wayne S.; Eliceiri, Kevin W. Nature Methods, Vol. 9, Issue 7 https://doi.org/10.1038/nmeth.2089	journal	June 2012
The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability Niesen, Frank H.; Berglund, Helena; Vedadi, Masoud Nature Protocols, Vol. 2, Issue 9 https://doi.org/10.1038/nprot.2007.321	journal	September 2007
Inhibition of leucyl-transfer ribonucleic acid synthetase in Bacillus subtilis by Granaticin Ogilvie, A.; Wiebauer, K.; Kersten, W. Biochemical Journal, Vol. 152, Issue 3 https://doi.org/10.1042/bj1520511	journal	December 1975
Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations Laowanapiban, Poramaet; Kapustina, Maryna; Vonrhein, Clemens Proceedings of the National Academy of Sciences, Vol. 106, Issue 6 https://doi.org/10.1073/pnas.0812752106	journal	January 2009
Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains Yang, X. -L.; Otero, F. J.; Skene, R. J. Proceedings of the National Academy of Sciences, Vol. 100, Issue 26 https://doi.org/10.1073/pnas.2136794100	journal	December 2003
On the attribution and additivity of binding energies Jencks, W. P. Proceedings of the National Academy of Sciences, Vol. 78, Issue 7 https://doi.org/10.1073/pnas.78.7.4046	journal	July 1981
Structural Basis for the Recognition of Isoleucyl-Adenylate and an Antibiotic, Mupirocin, by Isoleucyl-tRNA Synthetase Nakama, Takashi; Nureki, Osamu; Yokoyama, Shigeyuki Journal of Biological Chemistry, Vol. 276, Issue 50 https://doi.org/10.1074/jbc.M109089200	journal	October 2001
Indolmycin Resistance of Streptomyces coelicolor A3(2) by Induced Expression of One of Its Two Tryptophanyl-tRNA Synthetases Kitabatake, Makoto; Ali, Kamilah; Demain, Arnold Journal of Biological Chemistry, Vol. 277, Issue 26 https://doi.org/10.1074/jbc.M202639200	journal	April 2002
Crystal Structure of Human Tryptophanyl-tRNA Synthetase Catalytic Fragment: INSIGHTS INTO SUBSTRATE RECOGNITION, tRNA BINDING, AND ANGIOGENESIS ACTIVITY Yu, Yadong; Liu, Yunqing; Shen, Ning Journal of Biological Chemistry, Vol. 279, Issue 9 https://doi.org/10.1074/jbc.M311284200	journal	December 2003
Anti-staphylococcal activity of indolmycin, a potential topical agent for control of staphylococcal infections Hurdle, J. G. Journal of Antimicrobial Chemotherapy, Vol. 54, Issue 2 https://doi.org/10.1093/jac/dkh352	journal	July 2004
Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states Shen, Ning; Zhou, Minyu; Yang, Bei Nucleic Acids Research, Vol. 36, Issue 4 https://doi.org/10.1093/nar/gkm1153	journal	January 2008
Crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase: new insights into the mechanism of tryptophan activation and implications for anti-fungal drug design Zhou, Minyun; Dong, Xianchi; Shen, Ning Nucleic Acids Research, Vol. 38, Issue 10 https://doi.org/10.1093/nar/gkp1254	journal	January 2010
High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5′AMP Retailleau, Pascal; Yin, Yuhui; Hu, Mei Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 11 https://doi.org/10.1107/S090744490101215X	journal	October 2001
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
2.9 Å crystal structure of ligand-free tryptophanyl-tRNA synthetase: Domain movements fragment the adenine nucleotide binding site Ilyin, Valentin A.; Temple, Brenda; Hu, Mei Protein Science, Vol. 9, Issue 2 https://doi.org/10.1110/ps.9.2.218	journal	January 2000
Indolmycin Inhibits Prokaryotic Tryptophanyl-tRNA Ligase Werner, Rolf G.; Thorpe, Lance F.; Reuter, Wolfgang European Journal of Biochemistry, Vol. 68, Issue 1 https://doi.org/10.1111/j.1432-1033.1976.tb10758.x	journal	September 1976
A Novel Tryptophanyl-tRNA Synthetase Gene Confers High-Level Resistance to Indolmycin Vecchione, J. J.; Sello, J. K. Antimicrobial Agents and Chemotherapy, Vol. 53, Issue 9 https://doi.org/10.1128/AAC.00723-09	journal	June 2009
Antibacterial activity of mupirocin (pseudomonic acid), a new antibiotic for topical use. Sutherland, R.; Boon, R. J.; Griffin, K. E. Antimicrobial Agents and Chemotherapy, Vol. 27, Issue 4 https://doi.org/10.1128/AAC.27.4.495	journal	April 1985
In Vitro and In Vivo Antibacterial Activities of TAK-083, an Agent for Treatment of Helicobacter pylori Infection Kanamaru, T.; Nakano, Y.; Toyoda, Y. Antimicrobial Agents and Chemotherapy, Vol. 45, Issue 9 https://doi.org/10.1128/AAC.45.9.2455-2459.2001	journal	September 2001

Cited By (8)

Escapement mechanisms: Efficient free energy transduction by reciprocally‐coupled gating Carter, Charles W. Proteins: Structure, Function, and Bioinformatics, Vol. 88, Issue 5 https://doi.org/10.1002/prot.25856	journal	May 2020
Design and synthesis of novel spirooxindole–indenoquinoxaline derivatives as novel tryptophanyl-tRNA synthetase inhibitors Ren, Wen; Zhao, Qian; Yu, Meng Molecular Diversity, Vol. 24, Issue 4 https://doi.org/10.1007/s11030-019-10011-2	journal	December 2019
Convergent biosynthetic transformations to a bacterial specialized metabolite Du, Yi-Ling; Higgins, Melanie A.; Zhao, Guiyun Nature Chemical Biology, Vol. 15, Issue 11 https://doi.org/10.1038/s41589-019-0331-5	journal	August 2019
Selective inhibition of apicoplast tryptophanyl-tRNA synthetase causes delayed death in Plasmodium falciparum Pasaje, Charisse Flerida A.; Cheung, Vanessa; Kennedy, Kit Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep27531	journal	June 2016
Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights Masschelein, J.; Jenner, M.; Challis, G. L. Natural Product Reports, Vol. 34, Issue 7 https://doi.org/10.1039/c7np00010c	journal	January 2017
Antioxidant activity and antibacterial evaluation of new thiazolin-4-one derivatives as potential tryptophanyl-tRNA synthetase inhibitors Stana, Anca; Vodnar, Dan C.; Marc, Gabriel Journal of Enzyme Inhibition and Medicinal Chemistry, Vol. 34, Issue 1 https://doi.org/10.1080/14756366.2019.1596086	journal	January 2019
Antioxidant activity and antibacterial evaluation of new thiazolin-4-one derivatives as potential tryptophanyl-tRNA synthetase inhibitors Stana, Anca; Vodnar, Dan C.; Marc, Gabriel Taylor & Francis https://doi.org/10.6084/m9.figshare.7937675	text	January 2019
Antioxidant activity and antibacterial evaluation of new thiazolin-4-one derivatives as potential tryptophanyl-tRNA synthetase inhibitors Stana, Anca; Vodnar, Dan C.; Marc, Gabriel Taylor & Francis https://doi.org/10.6084/m9.figshare.7937675.v1	text	January 2019

Similar Records

Structure of a tryptophanyl-tRNA synthetase containing an iron–sulfur cluster

Journal Article · 2010 · Acta Crystallographica. Section F · OSTI ID:1625806

Han, Gye Won; Yang, Xiang-Lei; McMullan, Daniel; +41 more

Structure and Activity of an Aminoacyl-tRNA Synthetase that Charges tRNA with Nitro-Tryptophan

Journal Article · 2004 · Nature Structural and Molecular Biology · OSTI ID:959844

Buddha, M; Crane, B

Kinetic evidence for half-of-the-sites reactivity in tRNA/sup Trp/ aminoacylation by tryptophanyl-tRNA synthetase from beef pancreas

Journal Article · 1986 · Biochemistry; (United States) · OSTI ID:6439483

Trezeguet, V; Merle, M; Gandar, J C; +1 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
aminoacyl-tRNA synthetase
enzyme catalysis
enzyme inhibitor
inhibition
inhibition by ground-state stabilization
inhibition mechanism
thermofluor
x-ray crystallography

Title: Selective Inhibition of Bacterial Tryptophanyl-tRNA Synthetases by Indolmycin Is Mechanism-based

Citation Formats

References (36)

Cited By (8)

Similar Records

Related Subjects