Structure of the Autoinhibited Kinase Domain of CaMKII and SAXS Analysis of the Holoenzyme

Ca2+/calmodulin-dependent protein kinase-II (CaMKII) is unique among protein kinases for its dodecameric assembly and its complex response to Ca2+. The crystal structure of the autoinhibited kinase domain of CaMKII, determined at 1.8 A resolution, reveals an unexpected dimeric organization in which the calmodulin-responsive regulatory segments form a coiled-coil strut that blocks peptide and ATP binding to the otherwise intrinsically active kinase domains. A threonine residue in the regulatory segment, which when phosphorylated renders CaMKII calmodulin independent, is held apart from the catalytic sites by the organization of the dimer. This ensures a strict Ca2+ dependence for initial activation. The structure of the kinase dimer, when combined with small-angle X-ray scattering data for the holoenzyme, suggests that inactive CaMKII forms tightly packed autoinhibited assemblies that convert upon activation into clusters of loosely tethered and independent kinase domains.

[1]  A. Lupas,et al.  Predicting coiled coils from protein sequences , 1991, Science.

[2]  H. Schulman,et al.  Inhibitory autophosphorylation of multifunctional Ca2+/calmodulin-dependent protein kinase analyzed by site-directed mutagenesis. , 1992, The Journal of biological chemistry.

[3]  J. Lisman,et al.  The molecular basis of CaMKII function in synaptic and behavioural memory , 2002, Nature Reviews Neuroscience.

[4]  Dmitri I. Svergun,et al.  Uniqueness of ab initio shape determination in small-angle scattering , 2003 .

[5]  H. Schulman,et al.  Structural Examination of Autoregulation of Multifunctional Calcium/Calmodulin-dependent Protein Kinase II* , 1999, The Journal of Biological Chemistry.

[6]  Aryn H. Gittis,et al.  Decreases in CaMKII Activity Trigger Persistent Potentiation of Intrinsic Excitability in Spontaneously Firing Vestibular Nucleus Neurons , 2005, Neuron.

[7]  Stephen G. Miller,et al.  Sequences of autophosphorylation sites in neuronal type II CaM kinase that control Ca2+-independent activity , 1988, Neuron.

[8]  E. Morris,et al.  Oligomeric structure of alpha-calmodulin-dependent protein kinase II. , 2001, Journal of molecular biology.

[9]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[10]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[11]  M. Kennedy,et al.  Regulation of brain Type II Ca 2+ calmodulin -dependent protein kinase by autophosphorylation: A Ca2+-triggered molecular switch , 1986, Cell.

[12]  D. Svergun,et al.  CRYSOL : a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates , 1995 .

[13]  F. Crick,et al.  The packing of α‐helices: simple coiled‐coils , 1953 .

[14]  P. De Koninck,et al.  Sensitivity of CaM kinase II to the frequency of Ca2+ oscillations. , 1998, Science.

[15]  M. Waxham,et al.  A Peptide Model for Calmodulin Trapping by Calcium/Calmodulin-dependent Protein Kinase II* , 1996, The Journal of Biological Chemistry.

[16]  P. Greengard,et al.  Ca2+/calmodulin-dependent protein kinase II: identification of threonine-286 as the autophosphorylation site in the alpha subunit associated with the generation of Ca2+-independent activity. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[17]  T. Yamauchi,et al.  [Ca2(+)-calmodulin-dependent protein kinase II]. , 1990, Seikagaku. The Journal of Japanese Biochemical Society.

[18]  R. Colbran,et al.  Inactivation of Ca2+/calmodulin-dependent protein kinase II by basal autophosphorylation. , 1993, The Journal of biological chemistry.

[19]  H. Schulman,et al.  Substrate-directed Function of Calmodulin in Autophosphorylation of Ca2+/Calmodulin-dependent Protein Kinase II* , 1998, The Journal of Biological Chemistry.

[20]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[21]  Giulio Superti-Furga,et al.  Dynamic Coupling between the SH2 and SH3 Domains of c-Src and Hck Underlies Their Inactivation by C-Terminal Tyrosine Phosphorylation , 2001, Cell.

[22]  G J Kleywegt,et al.  Efficient rebuilding of protein structures. , 1996, Acta crystallographica. Section D, Biological crystallography.

[23]  K. Sharp,et al.  Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons , 1991, Proteins.

[24]  F A Quiocho,et al.  Modulation of calmodulin plasticity in molecular recognition on the basis of x-ray structures. , 1993, Science.

[25]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Likelihood-enhanced Fast Translation Functions Biological Crystallography Likelihood-enhanced Fast Translation Functions , 2022 .

[26]  H. Schulman,et al.  Distinct autophosphorylation sites sequentially produce autonomy and inhibition of the multifunctional Ca2+/calmodulin-dependent protein kinase , 1989, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[27]  J. M. Davies,et al.  Conformational changes of p97 during nucleotide hydrolysis determined by small-angle X-Ray scattering. , 2005, Structure.

[28]  Dmitri I. Svergun,et al.  PRIMUS: a Windows PC-based system for small-angle scattering data analysis , 2003 .

[29]  Paul Young,et al.  Structural basis for activation of the titin kinase domain during myofibrillogenesis , 1998, Nature.

[30]  Lubert Stryer,et al.  Dual role of calmodulin in autophosphorylation of multifunctional cam kinase may underlie decoding of calcium signals , 1994, Neuron.

[31]  M. King,et al.  Affinity labeling of the ATP-binding site of type II calmodulin-dependent protein kinase by 5'-p-fluorosulfonylbenzoyl adenosine. , 1988, Archives of biochemistry and biophysics.

[32]  P. Greengard,et al.  Autophosphorylation reversibly regulates the Ca2+/calmodulin-dependence of Ca2+/calmodulin-dependent protein kinase II. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Angus C Nairn,et al.  Crystal structure of a tetradecameric assembly of the association domain of Ca2+/calmodulin-dependent kinase II. , 2003, Molecular cell.

[34]  J. M. Bradshaw,et al.  Chemical Quenched Flow Kinetic Studies Indicate an Intraholoenzyme Autophosphorylation Mechanism for Ca2+/Calmodulin-dependent Protein Kinase II* , 2002, The Journal of Biological Chemistry.

[35]  Dmitri I. Svergun,et al.  Determination of the regularization parameter in indirect-transform methods using perceptual criteria , 1992 .

[36]  L. Johnson,et al.  The crystal structure of a phosphorylase kinase peptide substrate complex: kinase substrate recognition , 1997, The EMBO journal.

[37]  Susan S. Taylor,et al.  Regulation of protein kinases; controlling activity through activation segment conformation. , 2004, Molecular cell.

[38]  J. Mccammon,et al.  Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. , 1999, Journal of structural biology.

[39]  Dan Wang,et al.  Comparative Analyses of the Three-dimensional Structures and Enzymatic Properties of α, β, γ, and δ Isoforms of Ca2+-Calmodulin-dependent Protein Kinase II* , 2004, Journal of Biological Chemistry.

[40]  T. Soderling,et al.  Ca2+/calmodulin-dependent protein kinase II. Identification of a regulatory autophosphorylation site adjacent to the inhibitory and calmodulin-binding domains. , 1988, The Journal of biological chemistry.

[41]  M. T. Davison,et al.  The calmodulin-dependent glycogen synthase kinase from rabbit skeletal muscle. Purification, subunit structure and substrate specificity. , 1983, European journal of biochemistry.

[42]  P. J. Vernon,et al.  Autophosphorylation of Calmodulin‐Kinase II in Synaptic Junctions Modulates Endogenous Kinase Activity , 1984, Journal of neurochemistry.

[43]  T. Soderling,et al.  Mutational analysis of the autoinhibitory domain of calmodulin kinase II. , 1994, The Journal of biological chemistry.

[44]  Chi-Ying F. Huang,et al.  Identification of the Substrate and Pseudosubstrate Binding Sites of Phosphorylase Kinase γ-Subunit (*) , 1995, The Journal of Biological Chemistry.

[45]  A. Nairn,et al.  Structural Basis for the Autoinhibition of Calcium/Calmodulin-Dependent Protein Kinase I , 1996, Cell.

[46]  B. Kemp,et al.  Insights into autoregulation from the crystal structure of twitchin kinase , 1994, Nature.

[47]  H. Schulman,et al.  Calmodulin Trapping by Calcium-Calmodulin-Dependent Protein Kinase , 1992, Science.

[48]  Tobias Meyer,et al.  An ultrasensitive Ca2+/calmodulin-dependent protein kinase II-protein phosphatase 1 switch facilitates specificity in postsynaptic calcium signaling , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[49]  M K Smith,et al.  Functional determinants in the autoinhibitory domain of calcium/calmodulin-dependent protein kinase II. Role of His282 and multiple basic residues. , 1992, The Journal of biological chemistry.

[50]  M. Waxham,et al.  Three-dimensional Reconstructions of Calcium/Calmodulin-dependent (CaM) Kinase IIα and Truncated CaM Kinase IIα Reveal a Unique Organization for Its Structural Core and Functional Domains* , 2000, The Journal of Biological Chemistry.

[51]  John M Koomen,et al.  Comparative analyses of the three-dimensional structures and enzymatic properties of alpha, beta, gamma and delta isoforms of Ca2+-calmodulin-dependent protein kinase II. , 2004, The Journal of biological chemistry.

[52]  Andy Hudmon,et al.  Structure-function of the multifunctional Ca2+/calmodulin-dependent protein kinase II. , 2002, The Biochemical journal.

[53]  J Walshaw,et al.  Socket: a program for identifying and analysing coiled-coil motifs within protein structures. , 2001, Journal of molecular biology.

[54]  C. Lu,et al.  Regulation of the Ca2+/CaM-Responsive Pool of CaMKII by Scaffold-Dependent Autophosphorylation , 2003, Neuron.

[55]  D I Svergun,et al.  Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. , 1999, Biophysical journal.