Structure and Assembly of the PI3K-like Protein Kinases (PIKKs) Revealed by Electron Microscopy

Angel Rivera-Calzada; Andrés López-Perrote; Roberto Melero; Jasminka Boskovic; Hugo Muñoz-Hernández; Fabrizio Martino; Oscar Llorca; Angel Rivera-Calzada; Andrés López-Perrote; Roberto Melero; Jasminka Boskovic; Hugo Muñoz-Hernández; Fabrizio Martino; Oscar Llorca

doi:10.3934/biophy.2015.2.36

AIMS Biophysics

2015, Volume 2, Issue 2: 36-57. doi: 10.3934/biophy.2015.2.36

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Structure and Assembly of the PI3K-like Protein Kinases (PIKKs) Revealed by Electron Microscopy

1.
Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas (Spanish National Research Council), (CSIC); Ramiro de Maeztu 9, 28040 Madrid, Spain;
2.
Electron Microscopy Unit. Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fdez. Almagro, 3, Madrid 28029, Spain

Received: 02 January 2015 Accepted: 19 March 2015 Published: 29 March 2015

The phosphatidylinositol 3-kinase-like kinases (PIKKs) are large serine-threonine protein kinases with a catalytic domain homologous to the phosphatidylinositol 3-kinase (PI3K). All PIKK family members share a general organization comprising a conserved C-terminus that contains the PI3K domain, which is preceded by a large N-terminal region made of helical HEAT repeats. In humans, the PIKK family includes six members, which play essential roles in various processes including DNA repair and DNA damage signalling (ATM, ATR, DNA-PKcs), control of cell growth (mTOR), nonsense-mediated mRNA decay (SMG1) and transcriptional regulation (TRRAP). High-resolution structural information is limited due to the large size (approx. 280-470 kDa) and structural complexity of these kinases. Adding further complexity, PIKKs work as part of larger assemblies with accessory subunits. These complexes are dynamic in composition and protein-protein and protein-DNA interactions regulate the kinase activity and functions of PIKKs. Moreover, recent findings have shown that the maturation and correct assembly of the PIKKs require a large chaperon machinery, containing RuvBL1 and RuvBL2 ATPases and the HSP90 chaperon. Single-particle electron microscopy (EM) is making key contributions to our understanding of the architecture of PIKKs and their complex regulation. This review summarizes the findings on the structure of these kinases, focusing mainly on medium-low resolution structures of several PIKKs obtained using EM, combined with X-ray crystallography of DNA-PKcs and mTOR. In addition, EM studies on higher-order complexes have revealed some of the mechanisms regulating the PIKKs, which will also be addressed. The model that emerges is that PIKKs, through their extensive interacting surfaces, integrate the information provided by multiple accessory subunits and nucleic acids to regulate their kinase activity in response to diverse stimuli.
- ATM,
- ATR,
- DNA-PKcs,
- mTOR,
- SMG1,
- TRRAP,
- PIKK,
- RuvBL1,
- RuvBL2,
- R2TP,
- 3D-electron microscopy
Citation: Angel Rivera-Calzada, Andrés López-Perrote, Roberto Melero, Jasminka Boskovic, Hugo Muñoz-Hernández, Fabrizio Martino, Oscar Llorca. Structure and Assembly of the PI3K-like Protein Kinases (PIKKs) Revealed by Electron Microscopy[J]. AIMS Biophysics, 2015, 2(2): 36-57. doi: 10.3934/biophy.2015.2.36

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Abstract

The phosphatidylinositol 3-kinase-like kinases (PIKKs) are large serine-threonine protein kinases with a catalytic domain homologous to the phosphatidylinositol 3-kinase (PI3K). All PIKK family members share a general organization comprising a conserved C-terminus that contains the PI3K domain, which is preceded by a large N-terminal region made of helical HEAT repeats. In humans, the PIKK family includes six members, which play essential roles in various processes including DNA repair and DNA damage signalling (ATM, ATR, DNA-PKcs), control of cell growth (mTOR), nonsense-mediated mRNA decay (SMG1) and transcriptional regulation (TRRAP). High-resolution structural information is limited due to the large size (approx. 280-470 kDa) and structural complexity of these kinases. Adding further complexity, PIKKs work as part of larger assemblies with accessory subunits. These complexes are dynamic in composition and protein-protein and protein-DNA interactions regulate the kinase activity and functions of PIKKs. Moreover, recent findings have shown that the maturation and correct assembly of the PIKKs require a large chaperon machinery, containing RuvBL1 and RuvBL2 ATPases and the HSP90 chaperon. Single-particle electron microscopy (EM) is making key contributions to our understanding of the architecture of PIKKs and their complex regulation. This review summarizes the findings on the structure of these kinases, focusing mainly on medium-low resolution structures of several PIKKs obtained using EM, combined with X-ray crystallography of DNA-PKcs and mTOR. In addition, EM studies on higher-order complexes have revealed some of the mechanisms regulating the PIKKs, which will also be addressed. The model that emerges is that PIKKs, through their extensive interacting surfaces, integrate the information provided by multiple accessory subunits and nucleic acids to regulate their kinase activity in response to diverse stimuli.

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