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Title: Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts

Authors:
; ; ; ; ORCiD logo; ; ; ; ; ; ; ;
Publication Date:
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1397811
Grant/Contract Number:
AC02-76SF00515
Resource Type:
Journal Article: Publisher's Accepted Manuscript
Journal Name:
Biochimie (Paris)
Additional Journal Information:
Journal Name: Biochimie (Paris); Journal Volume: 138; Journal Issue: C; Related Information: CHORUS Timestamp: 2017-10-04 22:20:08; Journal ID: ISSN 0300-9084
Publisher:
Elsevier
Country of Publication:
France
Language:
English

Citation Formats

Barros-Álvarez, Ximena, Kerchner, Keshia M., Koh, Cho Yeow, Turley, Stewart, Pardon, Els, Steyaert, Jan, Ranade, Ranae M., Gillespie, J. Robert, Zhang, Zhongsheng, Verlinde, Christophe L. M. J., Fan, Erkang, Buckner, Frederick S., and Hol, Wim G. J. Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts. France: N. p., 2017. Web. doi:10.1016/j.biochi.2017.04.006.
Barros-Álvarez, Ximena, Kerchner, Keshia M., Koh, Cho Yeow, Turley, Stewart, Pardon, Els, Steyaert, Jan, Ranade, Ranae M., Gillespie, J. Robert, Zhang, Zhongsheng, Verlinde, Christophe L. M. J., Fan, Erkang, Buckner, Frederick S., & Hol, Wim G. J. Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts. France. doi:10.1016/j.biochi.2017.04.006.
Barros-Álvarez, Ximena, Kerchner, Keshia M., Koh, Cho Yeow, Turley, Stewart, Pardon, Els, Steyaert, Jan, Ranade, Ranae M., Gillespie, J. Robert, Zhang, Zhongsheng, Verlinde, Christophe L. M. J., Fan, Erkang, Buckner, Frederick S., and Hol, Wim G. J. Sat . "Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts". France. doi:10.1016/j.biochi.2017.04.006.
@article{osti_1397811,
title = {Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts},
author = {Barros-Álvarez, Ximena and Kerchner, Keshia M. and Koh, Cho Yeow and Turley, Stewart and Pardon, Els and Steyaert, Jan and Ranade, Ranae M. and Gillespie, J. Robert and Zhang, Zhongsheng and Verlinde, Christophe L. M. J. and Fan, Erkang and Buckner, Frederick S. and Hol, Wim G. J.},
abstractNote = {},
doi = {10.1016/j.biochi.2017.04.006},
journal = {Biochimie (Paris)},
number = C,
volume = 138,
place = {France},
year = {Sat Jul 01 00:00:00 EDT 2017},
month = {Sat Jul 01 00:00:00 EDT 2017}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1016/j.biochi.2017.04.006

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  • Crystals of human mitochondrial tyrosyl-tRNA synthetase lacking the C-terminal S4-like domain diffract to 2.7 Å resolution and are suitable for structure determination. Human mitochondrial tyrosyl-tRNA synthetase and a truncated version with its C-terminal S4-like domain deleted were purified and crystallized. Only the truncated version, which is active in tyrosine activation and Escherichia coli tRNA{sup Tyr} charging, yielded crystals suitable for structure determination. These tetragonal crystals, belonging to space group P4{sub 3}2{sub 1}2, were obtained in the presence of PEG 4000 as a crystallizing agent and diffracted X-rays to 2.7 Å resolution. Complete data sets could be collected and led tomore » structure solution by molecular replacement.« less
  • The ability of Leishmania to survive in their insect or mammalian host is dependent upon an ability to sense and adapt to changes in the microenvironment. However, little is known about the molecular mechanisms underlying the parasite response to environmental changes, such as nutrient availability. To elucidate nutrient stress response pathways in Leishmania donovani, we have used purine starvation as the paradigm. The salvage of purines from the host milieu is obligatory for parasite replication; nevertheless, purine-starved parasites can persist in culture without supplementary purine for over 3 months, indicating that the response to purine starvation is robust and engendersmore » parasite survival under conditions of extreme scarcity. To understand metabolic reprogramming during purine starvation we have employed global approaches. Whole proteome comparisons between purine-starved and purine-replete parasites over a 6-48 h span have revealed a temporal and coordinated response to purine starvation. Purine transporters and enzymes involved in acquisition at the cell surface are upregulated within a few hours of purine removal from the media, while other key purine salvage components are upregulated later in the time-course and more modestly. After 48 h, the proteome of purine-starved parasites is extensively remodeled and adaptations to purine stress appear tailored to deal with both purine deprivation and general stress. To probe the molecular mechanisms affecting proteome remodeling in response to purine starvation, comparative RNA-seq analyses, qRT-PCR, and luciferase reporter assays were performed on purine-starved versus purine-replete parasites. While the regulation of a minority of proteins tracked with changes at the mRNA level, for many regulated proteins it appears that proteome remodeling during purine stress occurs primarily via translational and/or post-translational mechanisms.« less
  • The equilibrium constant for the formation of tyrosyl adenylate and pyrophosphate from ATP and tyrosine in solution has been measured by applying the Haldane relationship to wild-type and three mutant tyrosyl-tRNA synthetases from Bacillus stearothermophilus. The formation constant (=(Tyr-AMP)(PP/sub i/)/(ATP)(Tyr)) at pH 7.78, 25/sup 0/C, and 10 mM MgCl/sub 2/ (3.5 +/- 0.5) x 10/sup -7/. This corresponds to a free energy of hydrolysis of tyrosyl adenylate at pH 7.0 and 25/sup 0/C of -16.7 kcal mol/sup -1/. All necessary rate constants had been determined previously for the calculations apart from the dissociation constant of tyrosyl adenylate from its enzyme-boundmore » complex. This was measured by taking advantage of the 100-fold difference in hydrolysis rates of the tyrosyl adenylate when sequestered by the enzyme and when free in solution. These are technically difficult measurements because the dissociation constants are so low and the complexes unstable. The task was simplified by using mutants prepared by site-directed mutagenesis. These were designed to have different rate and equilibrium constants for dissociation of tyrosyl adenylate from the enzyme-bound complexes. The dissociation constants were in the range (3.5-38) x 10/sup -12/ M, with that for wild type at 13 x 10/sup -12/ M. The four enzymes all gave consistent data for the formation constant of tyrosyl adenylate in solution. This not only improves the reliability of the measurement but also provides confirmation of the reliability of the measured kinetic constants for the series of enzymes.« less