Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation
- University of Washington, United States
Abstract
Inosine monophosphate dehydrogenase (IMPDH) mediates the first committed step in guanine nucleotide biosynthesis and plays important roles in cellular proliferation and the immune response. IMPDH reversibly polymerizes in cells and tissues in response to changes in metabolic demand. Self-assembly of metabolic enzymes is increasingly recognized as a general mechanism for regulating activity, typically by stabilizing specific conformations of an enzyme, but the regulatory role of IMPDH filaments has remained unclear. Here, we report a series of human IMPDH2 cryo-EM structures in both active and inactive conformations. The structures define the mechanism of filament assembly, and reveal how filament-dependent allosteric regulation of IMPDH2 makes the enzyme less sensitive to feedback inhibition, explaining why assembly occurs under physiological conditions that require expansion of guanine nucleotide pools. Tuning sensitivity to an allosteric inhibitor distinguishes IMPDH from other metabolic filaments, and highlights the diversity of regulatory outcomes that can emerge from self-assembly.
Data availability
The cryo-EM maps described here have been deposited in the Electron Microscopy Data Bank with accession numbers 20687, 20688, 20690, 20691, 20701, 20704, 20705, 20706, 20707, 20709, 20716, 20718, 20720, 20722, 20723, 20725, 20742, 20741, and 20743. The refined atomic coordinates have been deposited in the Protein Data Bank with accession numbers 6U8E, 6U8N, 6U8R, 6U8S, 6U9O, 6UA2, 6UA4, 6UA5, 6UAJ, 6UC2, 6UDP, 6UDO, and 6UDQ.
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IMPDH2 ATP, IMP, NAD+ assembly interface cryo-EM mapElectron Microscopy Data Bank, 20687.
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IMPDH2 ATP, IMP, NAD+ assembly interface atomic modelProtein Data Bank, 6U8E.
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IMPDH2 ATP, IMP, NAD+ fully extended cryo-EM mapElectron Microscopy Data Bank, 20688.
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IMPDH2 ATP, IMP, NAD+ fully extended atomic modelProtein Data Bank, 6U8N.
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IMPDH2 ATP, IMP, NAD+ Bent (1:3) cryo-EM mapElectron Microscopy Data Bank, 20690.
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IMPDH2 ATP, IMP, NAD+ Bent (1:3) atomic modelProtein Data Bank, 6U8R.
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IMPDH2 ATP, NAD+ assembly interface cryo-EM mapElectron Microscopy Data Bank, 20718.
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IMPDH2 ATP, NAD+ fully extended cryo-EM mapElectron Microscopy Data Bank, 20716.
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IMPDH2 ATP, NAD+ fully compressed cryo-EM mapElectron Microscopy Data Bank, 20709.
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IMPDH2 ATP, IMP assembly interface cryo-EM mapElectron Microscopy Data Bank, 20723.
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IMPDH2 ATP, IMP fully extended cryo-EM mapElectron Microscopy Data Bank, 20722.
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IMPDH2 ATP, IMP fully compressed cryo-EM mapElectron Microscopy Data Bank, 20720.
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IMPDH2 ATP, GTP free octamerElectron Microscopy Data Bank, 20725.
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IMPDH2 ATP, GTP, IMP assembly interfaceElectron Microscopy Data Bank, 20742.
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IMPDH2 ATP, GTP, IMP assembly interfaceProtein Data Bank, 6UDP.
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IMPDH2 ATP, GTP, IMP fully compressedElectron Microscopy Data Bank, 20741.
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IMPDH2 ATP, GTP, IMP fully compressedProtein Data Bank, 6UDO.
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IMPDH2 ATP, GTP, IMP fully compressed endElectron Microscopy Data Bank, 20743.
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IMPDH2 ATP, GTP, IMP fully compressed endProtein Data Bank, 6UDQ.
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IMPDH2 ATP, GTP, IMP, NAD+ assembly interface cryo-EM mapElectron Microscopy Data Bank, 20691.
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IMPDH2 ATP, GTP, IMP, NAD+ assembly interface atomic modelProtein Data Bank, 6U8S.
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IMPDH2 ATP, GTP, IMP, NAD+ bent (2:2) cryo-EM mapElectron Microscopy Data Bank, 20704.
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IMPDH2 ATP, GTP, IMP, NAD+ bent (2:2) atomic modelProtein Data Bank, 6UA2.
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IMPDH2 ATP, GTP, IMP, NAD+ bent (3:1) cryo-EM mapElectron Microscopy Data Bank, 20705.
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IMPDH2 ATP, GTP, IMP, NAD+ bent (3:1) atomic modelProtein Data Bank, 6UA4.
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IMPDH2 ATP, GTP, IMP, NAD+ fully compressed cryo-EM mapElectron Microscopy Data Bank, 20701.
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IMPDH2 ATP, GTP, IMP, NAD+ fully compressed atomic modelProtein Data Bank, 6U9O.
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IMPDH2 ATP, GTP, IMP, NAD+ free octamer cryo-EM mapElectron Microscopy Data Bank, 20707.
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IMPDH2 ATP, GTP, IMP, NAD+ free octamer atomic modelProtein Data Bank, 6UAJ.
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IMPDH2 ATP, GTP, IMP, NAD+ free interfacial octamer cryo-EM mapElectron Microscopy Data Bank, 20706.
Article and author information
Author details
Funding
National Institutes of Health (5R01GM118396-04)
- Justin M Kollman
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Sjors HW Scheres, MRC Laboratory of Molecular Biology, United Kingdom
Publication history
- Received: November 1, 2019
- Accepted: January 29, 2020
- Accepted Manuscript published: January 30, 2020 (version 1)
- Version of Record published: February 13, 2020 (version 2)
Copyright
© 2020, Johnson & Kollman
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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Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation
eLife 9:e53243.
https://doi.org/10.7554/eLife.53243
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