Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation

Abstract
Data availability
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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.

The following data sets were generated

1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, IMP, NAD+ assembly interface cryo-EM map
Electron Microscopy Data Bank, 20687.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20687
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, IMP, NAD+ assembly interface atomic model
Protein Data Bank, 6U8E.

https://www.ebi.ac.uk/pdbe/entry/pdb/6u8e
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, IMP, NAD+ fully extended cryo-EM map
Electron Microscopy Data Bank, 20688.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20688
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, IMP, NAD+ fully extended atomic model
Protein Data Bank, 6U8N.

https://www.ebi.ac.uk/pdbe/entry/pdb/6u8n
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, IMP, NAD+ Bent (1:3) cryo-EM map
Electron Microscopy Data Bank, 20690.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20690
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, IMP, NAD+ Bent (1:3) atomic model
Protein Data Bank, 6U8R.

https://www.ebi.ac.uk/pdbe/entry/pdb/6u8r
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, NAD+ assembly interface cryo-EM map
Electron Microscopy Data Bank, 20718.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20718
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, NAD+ fully extended cryo-EM map
Electron Microscopy Data Bank, 20716.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20716
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, NAD+ fully compressed cryo-EM map
Electron Microscopy Data Bank, 20709.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20709
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, IMP assembly interface cryo-EM map
Electron Microscopy Data Bank, 20723.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20723
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, IMP fully extended cryo-EM map
Electron Microscopy Data Bank, 20722.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20722
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, IMP fully compressed cryo-EM map
Electron Microscopy Data Bank, 20720.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20720
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP free octamer
Electron Microscopy Data Bank, 20725.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20725
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP free octamer
Protein Data Bank, 6UC2.

https://www.ebi.ac.uk/pdbe/entry/pdb/6uc2
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP assembly interface
Electron Microscopy Data Bank, 20742.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20742
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP assembly interface
Protein Data Bank, 6UDP.

https://www.ebi.ac.uk/pdbe/entry/pdb/6udp
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP fully compressed
Electron Microscopy Data Bank, 20741.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20741
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP fully compressed
Protein Data Bank, 6UDO.

https://www.ebi.ac.uk/pdbe/entry/pdb/6udo
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP fully compressed end
Electron Microscopy Data Bank, 20743.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20743
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP fully compressed end
Protein Data Bank, 6UDQ.

https://www.ebi.ac.uk/pdbe/entry/pdb/6udq
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP, NAD+ assembly interface cryo-EM map
Electron Microscopy Data Bank, 20691.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20691
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP, NAD+ assembly interface atomic model
Protein Data Bank, 6U8S.

https://www.ebi.ac.uk/pdbe/entry/pdb/6u8s
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP, NAD+ bent (2:2) cryo-EM map
Electron Microscopy Data Bank, 20704.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20704
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP, NAD+ bent (2:2) atomic model
Protein Data Bank, 6UA2.

https://www.ebi.ac.uk/pdbe/entry/pdb/6ua2
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP, NAD+ bent (3:1) cryo-EM map
Electron Microscopy Data Bank, 20705.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20705
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP, NAD+ bent (3:1) atomic model
Protein Data Bank, 6UA4.

https://www.ebi.ac.uk/pdbe/entry/pdb/6ua4
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP, NAD+ fully compressed cryo-EM map
Electron Microscopy Data Bank, 20701.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20701
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP, NAD+ fully compressed atomic model
Protein Data Bank, 6U9O.

https://www.ebi.ac.uk/pdbe/entry/pdb/6u9O
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP, NAD+ free octamer cryo-EM map
Electron Microscopy Data Bank, 20707.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20707
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP, NAD+ free octamer atomic model
Protein Data Bank, 6UAJ.

https://www.ebi.ac.uk/pdbe/entry/pdb/6uaj
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP, NAD+ free interfacial octamer cryo-EM map
Electron Microscopy Data Bank, 20706.

https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-20706
1. Johnson MC
2. Kollman JM
(2019) IMPDH2 ATP, GTP, IMP, NAD+ free interfacial octamer atomic model
Protein Data Bank, 6UA5.

https://www.ebi.ac.uk/pdbe/entry/pdb/6ua5

Article and author information

Author details

Matthew C Johnson

Department of Biochemistry, University of Washington, Seattle, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1477-7801
Justin M Kollman

Department of Biochemistry, University of Washington, Seattle, United States

For correspondence
jkoll@uw.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-0350-5827

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.

Copyright

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.