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Title: Low and Room Temperature X-ray Structures of Protein Kinase A Ternary Complexes Shed New Light on Its Activity

Abstract

Posttranslational protein phosphorylation by protein kinase A (PKA) is a ubiquitous signaling mechanism which regulates many cellular processes. A low temperature X-ray structure of the PKA catalytic subunit (PKAc) ternary complex with ATP and a 20-residue peptidic inhibitor (IP20) at the physiological Mg 2+ concentration of < 0.5mM revealed a single metal ion in the active site. The lack of a second metal in the low-temperature LT-PKAc-MgATP-IP20 renders the β- and γ- phosphoryl groups of ATP to be very flexibile, with high thermal B-factors. Thus, the second metal is crucial for tight positioning of the terminal phosphoryl for transfer to a substrate, as demonstrated by comparison of the former structure with LT-PKAc- Mg 2ATP-IP20 complex. In addition to the kinase activity, PKAc is also able to slowly catalyze the hydrolysis of ATP using a water molecule as a substrate. We found that at room temperature under X-ray irradiation ATP can be readily and completely hydrolyzed into ATP and a free phosphate ion in the crystals of the ternary complex LT-PKAc- Mg 2ATP-IP20. The cleavage of ATP may be aided by X-ray-born free hydroxyl radicals, a very reactive chemical species, that move quickly through the crystal at room temperature. The phosphatemore » anion is clearly visible in the electron density maps; it remains in the active site, but slides about 2Å from its position in ATP toward Ala21 of IP20 that mimics the phosphorylation site. The phosphate, thus, pushes the peptidic inhibitor away from the product ADP, while resulting in dramatic conformational changes of IP20 terminal residues 24 and 25. X-ray structures of PKAc in complex with non-hydrolyzable ATP analog, AMPPNP, at both room and low temperatures demonstrated no temperature effects on the conformation and position of IP20.« less

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1050341
DOE Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
Acta Crystallographica. Section D: Biological Crystallography
Additional Journal Information:
Journal Volume: 68; Journal Issue: 7; Journal ID: ISSN 0907-4449
Publisher:
International Union of Crystallography
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; ANIONS; CLEAVAGE; CONFORMATIONAL CHANGES; ELECTRON DENSITY; HYDROLYSIS; HYDROXYL RADICALS; IRRADIATION; PHOSPHATES; PHOSPHORYLATION; PHOSPHOTRANSFERASES; POSITIONING; PROTEINS; RESIDUES; TEMPERATURE DEPENDENCE; WATER

Citation Formats

Kovalevsky, Andrey Y., Johnson, Hanna, Hanson, B. Leif, Waltman, Mary Jo, Fisher, S. Zoe, Taylor, Susan, and Langan, Paul. Low and Room Temperature X-ray Structures of Protein Kinase A Ternary Complexes Shed New Light on Its Activity. United States: N. p., 2012. Web. doi:10.1107/S0907444912014886.
Kovalevsky, Andrey Y., Johnson, Hanna, Hanson, B. Leif, Waltman, Mary Jo, Fisher, S. Zoe, Taylor, Susan, & Langan, Paul. Low and Room Temperature X-ray Structures of Protein Kinase A Ternary Complexes Shed New Light on Its Activity. United States. https://doi.org/10.1107/S0907444912014886
Kovalevsky, Andrey Y., Johnson, Hanna, Hanson, B. Leif, Waltman, Mary Jo, Fisher, S. Zoe, Taylor, Susan, and Langan, Paul. Fri . "Low and Room Temperature X-ray Structures of Protein Kinase A Ternary Complexes Shed New Light on Its Activity". United States. https://doi.org/10.1107/S0907444912014886.
@article{osti_1050341,
title = {Low and Room Temperature X-ray Structures of Protein Kinase A Ternary Complexes Shed New Light on Its Activity},
author = {Kovalevsky, Andrey Y. and Johnson, Hanna and Hanson, B. Leif and Waltman, Mary Jo and Fisher, S. Zoe and Taylor, Susan and Langan, Paul},
abstractNote = {Posttranslational protein phosphorylation by protein kinase A (PKA) is a ubiquitous signaling mechanism which regulates many cellular processes. A low temperature X-ray structure of the PKA catalytic subunit (PKAc) ternary complex with ATP and a 20-residue peptidic inhibitor (IP20) at the physiological Mg2+ concentration of < 0.5mM revealed a single metal ion in the active site. The lack of a second metal in the low-temperature LT-PKAc-MgATP-IP20 renders the β- and γ- phosphoryl groups of ATP to be very flexibile, with high thermal B-factors. Thus, the second metal is crucial for tight positioning of the terminal phosphoryl for transfer to a substrate, as demonstrated by comparison of the former structure with LT-PKAc- Mg2ATP-IP20 complex. In addition to the kinase activity, PKAc is also able to slowly catalyze the hydrolysis of ATP using a water molecule as a substrate. We found that at room temperature under X-ray irradiation ATP can be readily and completely hydrolyzed into ATP and a free phosphate ion in the crystals of the ternary complex LT-PKAc- Mg2ATP-IP20. The cleavage of ATP may be aided by X-ray-born free hydroxyl radicals, a very reactive chemical species, that move quickly through the crystal at room temperature. The phosphate anion is clearly visible in the electron density maps; it remains in the active site, but slides about 2Å from its position in ATP toward Ala21 of IP20 that mimics the phosphorylation site. The phosphate, thus, pushes the peptidic inhibitor away from the product ADP, while resulting in dramatic conformational changes of IP20 terminal residues 24 and 25. X-ray structures of PKAc in complex with non-hydrolyzable ATP analog, AMPPNP, at both room and low temperatures demonstrated no temperature effects on the conformation and position of IP20.},
doi = {10.1107/S0907444912014886},
url = {https://www.osti.gov/biblio/1050341}, journal = {Acta Crystallographica. Section D: Biological Crystallography},
issn = {0907-4449},
number = 7,
volume = 68,
place = {United States},
year = {2012},
month = {6}
}

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