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Title: Structure of the Dictyostelium Myosin-II Heavy Chain Kinase A (MHCK-A) α-kinase domain apoenzyme reveals a novel autoinhibited conformation

Abstract

The α-kinases are a family of a typical protein kinases present in organisms ranging from protozoa to mammals. Here we report an autoinhibited conformation for the α-kinase domain of Dictyostelium myosin-II heavy chain kinase A (MHCK-A) in which nucleotide binding to the catalytic cleft, located at the interface between an N-terminal and C-terminal lobe, is sterically blocked by the side chain of a conserved arginine residue (Arg592). Previous α-kinase structures have shown that an invariant catalytic aspartic acid residue (Asp766) is phosphorylated. Unexpectedly, in the autoinhibited conformation the phosphoryl group is transferred to the adjacent Asp663, creating an interaction network that stabilizes the autoinhibited state. The results suggest that Asp766 phosphorylation may play both catalytic and regulatory roles. The autoinhibited structure also provides the first view of a phosphothreonine residue docked into the phospho-specific allosteric binding site (Pi-pocket) in the C-lobe of the α-kinase domain.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [1]
  1. Queen's Univ., Kingston, ON (Canada)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
Natural Science and Engineering Research Council of Canada Discovery
OSTI Identifier:
1262431
Grant/Contract Number:  
RGPIN 391522; RGPIN 203705
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Biochemistry; Structural biology

Citation Formats

Ye, Qilu, Yang, Yidai, van Staalduinen, Laura, Crawley, Scott William, Liu, Linda, Brennan, Stephanie, Côté, Graham P., and Jia, Zongchao. Structure of the Dictyostelium Myosin-II Heavy Chain Kinase A (MHCK-A) α-kinase domain apoenzyme reveals a novel autoinhibited conformation. United States: N. p., 2016. Web. doi:10.1038/srep26634.
Ye, Qilu, Yang, Yidai, van Staalduinen, Laura, Crawley, Scott William, Liu, Linda, Brennan, Stephanie, Côté, Graham P., & Jia, Zongchao. Structure of the Dictyostelium Myosin-II Heavy Chain Kinase A (MHCK-A) α-kinase domain apoenzyme reveals a novel autoinhibited conformation. United States. https://doi.org/10.1038/srep26634
Ye, Qilu, Yang, Yidai, van Staalduinen, Laura, Crawley, Scott William, Liu, Linda, Brennan, Stephanie, Côté, Graham P., and Jia, Zongchao. Mon . "Structure of the Dictyostelium Myosin-II Heavy Chain Kinase A (MHCK-A) α-kinase domain apoenzyme reveals a novel autoinhibited conformation". United States. https://doi.org/10.1038/srep26634. https://www.osti.gov/servlets/purl/1262431.
@article{osti_1262431,
title = {Structure of the Dictyostelium Myosin-II Heavy Chain Kinase A (MHCK-A) α-kinase domain apoenzyme reveals a novel autoinhibited conformation},
author = {Ye, Qilu and Yang, Yidai and van Staalduinen, Laura and Crawley, Scott William and Liu, Linda and Brennan, Stephanie and Côté, Graham P. and Jia, Zongchao},
abstractNote = {The α-kinases are a family of a typical protein kinases present in organisms ranging from protozoa to mammals. Here we report an autoinhibited conformation for the α-kinase domain of Dictyostelium myosin-II heavy chain kinase A (MHCK-A) in which nucleotide binding to the catalytic cleft, located at the interface between an N-terminal and C-terminal lobe, is sterically blocked by the side chain of a conserved arginine residue (Arg592). Previous α-kinase structures have shown that an invariant catalytic aspartic acid residue (Asp766) is phosphorylated. Unexpectedly, in the autoinhibited conformation the phosphoryl group is transferred to the adjacent Asp663, creating an interaction network that stabilizes the autoinhibited state. The results suggest that Asp766 phosphorylation may play both catalytic and regulatory roles. The autoinhibited structure also provides the first view of a phosphothreonine residue docked into the phospho-specific allosteric binding site (Pi-pocket) in the C-lobe of the α-kinase domain.},
doi = {10.1038/srep26634},
journal = {Scientific Reports},
number = 1,
volume = 6,
place = {United States},
year = {Mon May 23 00:00:00 EDT 2016},
month = {Mon May 23 00:00:00 EDT 2016}
}

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Works referenced in this record:

Replacement of threonine residues by serine and alanine in a phosphorylatable heavy chain fragment of Dictyostelium myosin II
journal, August 1990


TRPM7 Regulates Myosin IIA Filament Stability and Protein Localization by Heavy Chain Phosphorylation
journal, May 2008

  • Clark, Kristopher; Middelbeek, Jeroen; Lasonder, Edwin
  • Journal of Molecular Biology, Vol. 378, Issue 4
  • DOI: 10.1016/j.jmb.2008.02.057

Protein kinases: evolution of dynamic regulatory proteins
journal, February 2011


Dictyostelium myosin heavy chain phosphorylation sites regulate myosin filament assembly and localization in vivo
journal, October 1993


Crystal Structure of the Atypical Protein Kinase Domain of a TRP Channel with Phosphotransferase Activity
journal, May 2001


Structural and Functional Diversity of the Microbial Kinome
journal, March 2007


ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit
journal, October 2012

  • Ferreira-Cerca, Sébastien; Sagar, Vatsala; Schäfer, Thorsten
  • Nature Structural & Molecular Biology, Vol. 19, Issue 12
  • DOI: 10.1038/nsmb.2403

TRPM7, a novel regulator of actomyosin contractility and cell adhesion
journal, January 2006

  • Clark, Kristopher; Langeslag, Michiel; van Leeuwen, Bart
  • The EMBO Journal, Vol. 25, Issue 2
  • DOI: 10.1038/sj.emboj.7600931

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
journal, September 1998

  • Brünger, A. T.; Adams, P. D.; Clore, G. M.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 5
  • DOI: 10.1107/S0907444998003254

Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444912001308

Inference of Macromolecular Assemblies from Crystalline State
journal, September 2007


WD Repeat Domains Target Dictyostelium Myosin Heavy Chain Kinases by Binding Directly to Myosin Filaments
journal, December 2000

  • Steimle, Paul A.; Naismith, Teresa; Licate, Lucila
  • Journal of Biological Chemistry, Vol. 276, Issue 9
  • DOI: 10.1074/jbc.m008992200

Signaling pathways regulating Dictyostelium myosin II
journal, January 2002

  • De La Roche, Marc A.; Smith, Janet L.; Betapudi, Venkaiah
  • Journal of Muscle Research and Cell Motility, Vol. 23, Issue 7/8, p. 703-718
  • DOI: 10.1023/A:1024467426244

The alpha-kinase family: an exceptional branch on the protein kinase tree
journal, December 2009

  • Middelbeek, Jeroen; Clark, Kristopher; Venselaar, Hanka
  • Cellular and Molecular Life Sciences, Vol. 67, Issue 6
  • DOI: 10.1007/s00018-009-0215-z

Lamellipodial localization of Dictyostelium myosin heavy chain kinase A is mediated via F-actin binding by the coiled-coil domain
journal, March 2002


Dictyostelium myosin heavy chain kinase A regulates myosin localization during growth and development.
journal, January 1996

  • Kolman, M. F.; Futey, L. M.; Egelhoff, T. T.
  • The Journal of Cell Biology, Vol. 132, Issue 1
  • DOI: 10.1083/jcb.132.1.101

Dominant Rio1 kinase/ATPase catalytic mutant induces trapping of late pre-40S biogenesis factors in 80S-like ribosomes
text, January 2014

  • Ferreira-Cerca, Sébastien; Kiburu, Irene; Thomson, Emma
  • Universität Regensburg
  • DOI: 10.5283/epub.30504

Characterization of the Catalytic and Nucleotide Binding Properties of the α-Kinase Domain of Dictyostelium Myosin-II Heavy Chain Kinase A
journal, August 2015

  • Yang, Yidai; Ye, Qilu; Jia, Zongchao
  • Journal of Biological Chemistry, Vol. 290, Issue 39
  • DOI: 10.1074/jbc.m115.672410

The alpha-kinase family: an exceptional branch on the protein kinase tree
journal, December 2009

  • Middelbeek, Jeroen; Clark, Kristopher; Venselaar, Hanka
  • Cellular and Molecular Life Sciences, Vol. 67, Issue 6
  • DOI: 10.1007/s00018-009-0215-z

The Ancient Microbial RIO Kinases
journal, February 2014


Autophosphorylation Activates Dictyostelium Myosin II Heavy Chain Kinase A by Providing a Ligand for an Allosteric Binding Site in the α-Kinase Domain
journal, November 2010

  • Crawley, Scott W.; Gharaei, Mojdeh Samimi; Ye, Qilu
  • Journal of Biological Chemistry, Vol. 286, Issue 4
  • DOI: 10.1074/jbc.m110.177014

Multiple Myosin II Heavy Chain Kinases: Roles in Filament Assembly Control and Proper Cytokinesis in Dictyostelium
journal, September 2005

  • Yumura, Shigehiko; Yoshida, Masashi; Betapudi, Venkaiah
  • Molecular Biology of the Cell, Vol. 16, Issue 9
  • DOI: 10.1091/mbc.e05-03-0219

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
journal, July 2006

  • Dundas, J.; Ouyang, Z.; Tseng, J.
  • Nucleic Acids Research, Vol. 34, Issue Web Server
  • DOI: 10.1093/nar/gkl282

Alpha-kinases: a new class of protein kinases with a novel catalytic domain
journal, January 1999


Structural Evolution of the Protein Kinase-Like Superfamily
journal, January 2005


Inference of Macromolecular Assemblies from Crystalline State
journal, September 2007


XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

Differential localization in cells of myosin II heavy chain kinases during cytokinesis and polarized migration
journal, January 2002

  • Liang, Wenchuan; Licate, Lucila S.; Warrick, Hans M.
  • BMC Cell Biology, Vol. 3, Issue 1, p. 19
  • DOI: 10.1186/1471-2121-3-19

A Conserved Loop in the Catalytic Domain of Eukaryotic Elongation Factor 2 Kinase Plays a Key Role in Its Substrate Specificity
journal, April 2014

  • Moore, C. E.; Regufe da Mota, S.; Mikolajek, H.
  • Molecular and Cellular Biology, Vol. 34, Issue 12
  • DOI: 10.1128/MCB.00388-14

Protein kinases: evolution of dynamic regulatory proteins
journal, February 2011


The Molecular Mechanism of Eukaryotic Elongation Factor 2 Kinase Activation
journal, July 2014

  • Tavares, Clint D. J.; Ferguson, Scarlett B.; Giles, David H.
  • Journal of Biological Chemistry, Vol. 289, Issue 34
  • DOI: 10.1074/jbc.M114.577148

Myosin-based cortical tension in Dictyostelium resolved into heavy and light chain-regulated components
journal, April 1996

  • Egelhoff, Thomas T.; Naismith, Teresa V.; Brozovich, Frank V.
  • Journal of Muscle Research and Cell Motility, Vol. 17, Issue 2
  • DOI: 10.1007/bf00124248

TRPM7, a novel regulator of actomyosin contractility and cell adhesion
journal, January 2006

  • Clark, Kristopher; Langeslag, Michiel; van Leeuwen, Bart
  • The EMBO Journal, Vol. 25, Issue 2
  • DOI: 10.1038/sj.emboj.7600931

Structural Evolution of the Protein Kinase–Like Superfamily
journal, January 2005


Recruitment of a myosin heavy chain kinase to actin-rich protrusions in Dictyostelium
journal, May 2001


The eEF2 Kinase Confers Resistance to Nutrient Deprivation by Blocking Translation Elongation
journal, May 2013


Myosin heavy chain kinases play essential roles in Ca2+, but not cAMP, chemotaxis and the natural aggregation of Dictyostelium discoideum
journal, August 2012

  • Wessels, D.; Lusche, D. F.; Steimle, P. A.
  • Journal of Cell Science, Vol. 125, Issue 20
  • DOI: 10.1242/jcs.112474

Myosin heavy chain kinases play essential roles in Ca2+, but not cAMP, chemotaxis and the natural aggregation of Dictyostelium discoideum
journal, August 2012

  • Wessels, D.; Lusche, D. F.; Steimle, P. A.
  • Journal of Cell Science, Vol. 125, Issue 20
  • DOI: 10.1242/jcs.112474

Crystal Structure of the  -Kinase Domain of Dictyostelium Myosin Heavy Chain Kinase A
journal, March 2010


Eukaryotic elongation factor 2 kinase, an unusual enzyme with multiple roles
journal, May 2014


Kinetic and Catalytic Mechanisms of Protein Kinases
journal, August 2001


MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Eukaryotic elongation factor 2 kinase, an unusual enzyme with multiple roles
journal, May 2014


Kinetic and Catalytic Mechanisms of Protein Kinases
journal, August 2001


REFMAC 5 for the refinement of macromolecular crystal structures
journal, March 2011

  • Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911001314

Myosin Heavy Chain Phosphorylation Sites Regulate Myosin Localization during Cytokinesis in Live Cells
journal, December 1997

  • Sabry, James H.; Moores, Sheri L.; Ryan, Shannon
  • Molecular Biology of the Cell, Vol. 8, Issue 12
  • DOI: 10.1091/mbc.8.12.2605

Dictyostelium Myosin Heavy Chain Kinase A Subdomains: COILED-COIL AND WD REPEAT ROLES IN OLIGOMERIZATION AND SUBSTRATE TARGETING
journal, July 1997

  • Kolman, Michael F.; Egelhoff, Thomas T.
  • Journal of Biological Chemistry, Vol. 272, Issue 27
  • DOI: 10.1074/jbc.272.27.16904

Adaptation to Starvation: Translating a Matter of Life or Death
journal, June 2013


Insights into the regulation of eukaryotic elongation factor 2 kinase and the interplay between its domains
journal, January 2012

  • Pigott, Craig R.; Mikolajek, Halina; Moore, Claire E.
  • Biochemical Journal, Vol. 442, Issue 1
  • DOI: 10.1042/BJ20111536

Catalytic Control in the EGF Receptor and Its Connection to General Kinase Regulatory Mechanisms
journal, April 2011


Dictyostelium myosin heavy chain kinase A regulates myosin localization during growth and development.
journal, January 1996

  • Kolman, M. F.; Futey, L. M.; Egelhoff, T. T.
  • The Journal of Cell Biology, Vol. 132, Issue 1
  • DOI: 10.1083/jcb.132.1.101

TRPM7, the Mg2+ Inhibited Channel and Kinase
book, December 2010


Dominant Rio1 kinase/ATPase catalytic mutant induces trapping of late pre-40S biogenesis factors in 80S-like ribosomes
journal, June 2014

  • Ferreira-Cerca, Sébastien; Kiburu, Irene; Thomson, Emma
  • Nucleic Acids Research, Vol. 42, Issue 13
  • DOI: 10.1093/nar/gku542

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
journal, July 2006

  • Dundas, J.; Ouyang, Z.; Tseng, J.
  • Nucleic Acids Research, Vol. 34, Issue Web Server
  • DOI: 10.1093/nar/gkl282

The TRPM7 Chanzyme Is Cleaved to Release a Chromatin-Modifying Kinase
journal, May 2014


[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997


Mapping of the Novel Protein Kinase Catalytic Domain of Dictyostelium Myosin II Heavy Chain Kinase A
journal, March 1997

  • Côté, Graham P.; Luo, Xia; Murphy, Michael B.
  • Journal of Biological Chemistry, Vol. 272, Issue 11
  • DOI: 10.1074/jbc.272.11.6846

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

Purification and characterization of a myosin heavy chain kinase from Dictyostelium discoideum.
journal, January 1987


Identification of two phosphorylated threonines in the tail region of Dictyostelium myosin II.
journal, July 1988


Works referencing / citing this record:

Mass Spectrometric Analysis of TRPM6 and TRPM7 Phosphorylation Reveals Regulatory Mechanisms of the Channel-Kinases
journal, February 2017

  • Cai, Na; Bai, Zhiyong; Nanda, Vikas
  • Scientific Reports, Vol. 7, Issue 1
  • DOI: 10.1038/srep42739