An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering
- University of California, San Francisco, United States
- Diamond Light Source, United Kingdom
- University of Utrecht, Netherlands
Abstract
Allostery is an inherent feature of proteins, but it remains challenging to reveal the mechanisms by which allosteric signals propagate. A clearer understanding of this intrinsic circuitry would afford new opportunities to modulate protein function. Here we have identified allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal 'hidden' low-occupancy conformational states for protein and ligands. Our results converge on allosteric sites that are conformationally coupled to the active-site WPD loop and are hotspots for fragment binding. Targeting one of these sites with covalently tethered molecules or mutations allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure, revealed here by multitemperature crystallography, can elucidate allosteric mechanisms and open new doors for long-range control of protein function.
Data availability
Data have been deposited in PDB under the accession codes: 6B90, 6B8E, 6B8T, 6B8X, 6B8Z, 6BAI, 6B95, 5QDE, 5QDF, 5QDG, 5QDH, 5QDI, 5QDJ, 5QDK, 5QDL, 5QDM, 5QDN, 5QDO, 5QDP, 5QDQ, 5QDR, 5QDS, 5QDT, 5QDU, 5QDV, 5QDW, 5QDX, 5QDY, 5QDZ, 5QE0, 5QE1, 5QE2, 5QE3, 5QE4, 5QE5, 5QE6, 5QE7, 5QE8, 5QE9, 5QEA, 5QEB, 5QEC, 5QED, 5QEE, 5QEF, 5QEG, 5QEH, 5QEI, 5QEJ, 5QEK, 5QEL, 5QEM, 5QEN, 5QEO, 5QEP, 5QEQ, 5QER, 5QES, 5QET, 5QEU, 5QEV, 5QEW, 5QEX, 5QEY, 5QEZ, 5QF0, 5QF1, 5QF2, 5QF3, 5QF4, 5QF5, 5QF6, 5QF7, 5QF8, 5QF9, 5QFA, 5QFB, 5QFC, 5QFD, 5QFE, 5QFF, 5QFG, 5QFH, 5QFI, 5QFJ, 5QFK, 5QFL, 5QFM, 5QFN, 5QFO, 5QFP, 5QFQ, 5QFR, 5QFS, 5QFT, 5QFU, 5QFV, 5QFW, 5QFX, 5QFY, 5QFZ, 5QG0, 5QG1, 5QG2, 5QG3, 5QG4, 5QG5, 5QG6, 5QG7, 5QG8, 5QG9, 5QGA, 5QGB, 5QGC, 5QGD, 5QGE, 5QGF and further data available at https://zenodo.org/record/1044103
Article and author information
Author details
Funding
Kinship Foundation
- James S Fraser
National Cancer Institute (CA191018)
- James A Wells
National Cancer Institute ((F31 CA180378)
- T Justin Rettenmaier
National Institute of General Medical Sciences (GM123159)
- James S Fraser
National Institute of General Medical Sciences (GM124169)
- James S Fraser
National Institute of General Medical Sciences (GM124149)
- James S Fraser
Pew Charitable Trusts
- James S Fraser
David and Lucile Packard Foundation
- James S Fraser
National Institute of General Medical Sciences (GM110580)
- James S Fraser
National Science Foundation (STC-1231306)
- James S Fraser
University of California (LFR-17-476732)
- James S Fraser
Helen Hay Whitney Foundation
- Zachary B Hill
National Cancer Institute (K99CA203002)
- Zachary B Hill
A.P. Giannini Foundation (Postdoctoral Fellowship)
- Daniel A Keedy
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Yibing Shan, DE Shaw Research, United States
Version history
- Received: March 1, 2018
- Accepted: June 4, 2018
- Accepted Manuscript published: June 7, 2018 (version 1)
- Version of Record published: July 10, 2018 (version 2)
Copyright
© 2018, Keedy et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering
eLife 7:e36307.
https://doi.org/10.7554/eLife.36307
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