A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases

Abstract
Data availability
Article and author information
Metrics

Abstract

PP2C phosphatases control biological processes including stress responses, development, and cell division in all kingdoms of life. Diverse regulatory domains adapt PP2C phosphatases to specific functions, but how these domains control phosphatase activity was unknown. We present structures representing active and inactive states of the PP2C phosphatase SpoIIE from Bacillus subtilis. Based on structural analyses and genetic and biochemical experiments, we identify an α-helical switch that shifts a carbonyl oxygen into the active site to coordinate a metal cofactor. Our analysis indicates that this switch is widely conserved among PP2C family members, serving as a platform to control phosphatase activity in response to diverse inputs. Remarkably, the switch is shared with proteasomal proteases, which we identify as evolutionary and structural relatives of PP2C phosphatases. Although these proteases use an unrelated catalytic mechanism, rotation of equivalent helices controls protease activity by movement of the equivalent carbonyl oxygen into the active site.

Data availability

The following data sets were generated

(2016) Structure of the PP2C Phosphatase Domain and a Fragment of the Regulatory Domain of the Cell Fate Determinant SpoIIE from Bacillus Subtilis
Publicly available at the RCSB Protein Data Bank (accession no: 5UCG).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5UCG
(2016) Structure of the Phosphatase Domain of the Cell Fate Determinant SpoIIE from Bacillus subtilis in a crystal form without domain swapping
Publicly available at the RCSB Protein Data Bank (accession no: 5MQH).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5MQH

The following previously published data sets were used

(2011) Structure of the Phosphatase Domain of the Cell Fate Determinant SpoIIE from Bacillus subtilis
Publicly available at the RCSB Protein Data Bank (accession no: 3T91).

http://www.rcsb.org/pdb/explore/explore.do?structureId=3t91
1. Sousa MC
2. Trame CB
3. Tsuruta H
4. Wilbanks SM
5. Reddy VS
6. McKay DB
(2000) CRYSTAL STRUCTURE OF THE HSLUV PROTEASE-CHAPERONE COMPLEX
Publicly available at the RCSB Protein Data Bank (accession no: 1G3I).

http://www.rcsb.org/pdb/explore/explore.do?structureId=1g3i
1. Sousa MC
2. McKay DB
(2000) CRYSTAL STRUCTURE OF THE H. INFLUENZAE PROTEASE HSLV AT 1.9 A RESOLUTION
Publicly available at the RCSB Protein Data Bank (accession no: 1G3K).

http://www.rcsb.org/pdb/explore/explore.do?structureId=1g3k
1. Teh AH
2. Makino M
3. Baba S
4. Shimizu N
5. Yamamoto M
6. Kumasaka T
(2013) Crystal structure of RsbX in complex with manganese in space group P21
Publicly available at the RCSB Protein Data Bank (accession no: 3W43).

http://www.rcsb.org/pdb/explore/explore.do?structureId=3w43
(2008) Structure of Orthorhombic crystal form of Pseudomonas aeruginosa RssB
Publicly available at the RCSB Protein Data Bank (accession no: 3F7A).

http://www.rcsb.org/pdb/explore/explore.do?structureId=3f7a
1. Vassylyev DG
2. Symersky J
(2007) Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)
Publicly available at the RCSB Protein Data Bank (accession no: 2PNQ).

http://www.rcsb.org/pdb/explore/explore.do?structureId=2pnq
1. Feng Y
2. Zhang Y
3. Ge J
4. Yang M
(2013) Structure of a C.elegans sex determining protein
Publicly available at the RCSB Protein Data Bank (accession no: 4JND).

http://www.rcsb.org/pdb/explore/explore.do?structureId=4jnd
1. Zhou XE
2. Soon
3. F-F
4. Ng L-M
5. Kovach A
6. Tan MHE
7. Suino-Powell KM
8. He Y
9. Xu Y
10. Brunzelle JS
11. Li J
12. Melcher K
13. Xu HE
(2011) Crystal structure of SnRK2.6 in complex with HAB1
Publicly available at the RCSB Protein Data Bank (accession no: 3UJG).

http://www.rcsb.org/pdb/explore/explore.do?structureId=3ujg

Article and author information

Author details

Niels Bradshaw

Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-6845-4717
Vladimir M Levdikov

Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Christina M Zimanyi

New York Structural Biology Center, New York, United States

Competing interests
The authors declare that no competing interests exist.
Rachelle Gaudet

Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-9177-054X
Anthony J Wilkinson

Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Richard Losick

Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States

For correspondence
losick@mcb.harvard.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-5130-6582

Funding

National Institutes of Health (GM18568)

Richard Losick

Wellcome (82829)

Anthony J Wilkinson

Damon Runyon Cancer Research Foundation (DRG 2051-10)

Niels Bradshaw

Jane Coffin Childs Memorial Fund for Medical Research

Christina M Zimanyi

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.