Structural characterization of the cyclin-dependent protein kinase family.

Structural studies of members of the CDK (cyclin-dependent protein kinase) family have made a significant contribution to our understanding of the regulation of protein kinases. The structure of monomeric unphosphorylated CDK2 was the first of an inactive protein kinase to be determined and, since then, structures of other members of the CDK family, alone, in complex with regulatory proteins and in differing phosphorylation states, have enhanced our understanding of the molecular mechanisms regulating protein kinase activity. Recently, our knowledge of the structural biology of the CDK family has been extended by determination of structures for members of the transcriptional CDK and CDK-like kinase branches of the extended family. We include these recent structures in the present review and consider them in the light of current models for CDK activation and regulation.

[1]  L. Tsai,et al.  A family of human cdc2‐related protein kinases. , 1992, The EMBO journal.

[2]  L. Johnson,et al.  The structural basis for control of eukaryotic protein kinases. , 2012, Annual review of biochemistry.

[3]  L. Johnson,et al.  The structural basis for specificity of substrate and recruitment peptides for cyclin-dependent kinases , 1999, Nature Cell Biology.

[4]  D O Morgan,et al.  Cyclin-dependent kinases: engines, clocks, and microprocessors. , 1997, Annual review of cell and developmental biology.

[5]  F. Sladeczek,et al.  Characterization of brain PCTAIRE-1 kinase immunoreactivity and its interactions with p11 and 14-3-3 proteins. , 1998, European journal of biochemistry.

[6]  Ping Zhang,et al.  Assembly of allosteric macromolecular switches: lessons from PKA , 2012, Nature Reviews Molecular Cell Biology.

[7]  Sung-Hou Kim,et al.  Crystal structure of cyclin-dependent kinase 2 , 1993, Nature.

[8]  A. Reményi,et al.  Protein–peptide complex crystallization: a case study on the ERK2 mitogen-activated protein kinase , 2013, Acta crystallographica. Section D, Biological crystallography.

[9]  T. Hunter,et al.  The Protein Kinase Complement of the Human Genome , 2002, Science.

[10]  Chao Zhang,et al.  Cyclin-dependent kinase control of the initiation-to-elongation switch of RNA polymerase II , 2012, Nature Structural &Molecular Biology.

[11]  Ke Gong,et al.  Pctaire1 Phosphorylates N-Ethylmaleimide-sensitive Fusion Protein , 2006, Journal of Biological Chemistry.

[12]  F. Sladeczek,et al.  The Cdk-like protein PCTAIRE-1 from mouse brain associates with p11 and 14-3-3 proteins , 1997, Molecular and General Genetics MGG.

[13]  A. Mayeda,et al.  CDK11 Complexes Promote Pre-mRNA Splicing* , 2003, The Journal of Biological Chemistry.

[14]  J. Kuriyan,et al.  Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms. , 2011, Molecular cell.

[15]  Elizabeth J. Goldsmith,et al.  Activation Mechanism of the MAP Kinase ERK2 by Dual Phosphorylation , 1997, Cell.

[16]  James M. Roberts,et al.  Living with or without cyclins and cyclin-dependent kinases. , 2004, Genes & development.

[17]  R. Conaway,et al.  Function and regulation of the Mediator complex. , 2011, Current opinion in genetics & development.

[18]  L. Bardwell,et al.  Mechanisms of MAPK signalling specificity. , 2006, Biochemical Society transactions.

[19]  Rajiv Chopra,et al.  Crystal structure of human CDK4 in complex with a D-type cyclin , 2009, Proceedings of the National Academy of Sciences.

[20]  A. Shilatifard,et al.  The Super Elongation Complex Family of RNA Polymerase II Elongation Factors: Gene Target Specificity and Transcriptional Output , 2012, Molecular and Cellular Biology.

[21]  N. Krogan,et al.  The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat , 2013, eLife.

[22]  B. Turk,et al.  Analysis of substrate specificity and cyclin Y binding of PCTAIRE-1 kinase , 2012, Cellular signalling.

[23]  N. Ip,et al.  Pctaire1 Interacts with p35 and Is a Novel Substrate for Cdk5/p35* , 2002, The Journal of Biological Chemistry.

[24]  M. Garber,et al.  CDK9 Autophosphorylation Regulates High-Affinity Binding of the Human Immunodeficiency Virus Type 1 Tat–P-TEFb Complex to TAR RNA , 2000, Molecular and Cellular Biology.

[25]  A. Cole PCTK Proteins: The Forgotten Brain Kinases? , 2009, Neurosignals.

[26]  D. Stephens,et al.  PCTAIRE protein kinases interact directly with the COPII complex and modulate secretory cargo transport , 2005, Journal of Cell Science.

[27]  T. Hunt,et al.  Regulation of the CDK-related protein kinase PCTAIRE-1 and its possible role in neurite outgrowth in Neuro-2A cells. , 2002, Journal of cell science.

[28]  D. Moras,et al.  The crystal structure of human cyclin H , 1996, FEBS letters.

[29]  M. Noble,et al.  The CDK9 Tail Determines the Reaction Pathway of Positive Transcription Elongation Factor b , 2012, Structure.

[30]  J. Kohoutek,et al.  Cyclin K goes with Cdk12 and Cdk13 , 2012, Cell Division.

[31]  Lynn F. Ten Eyck,et al.  A helix scaffold for the assembly of active protein kinases , 2008, Proceedings of the National Academy of Sciences.

[32]  Richard F. Thompson,et al.  Involvement of cyclin-dependent kinase-like 2 in cognitive function required for contextual and spatial learning in mice , 2022 .

[33]  Wei Chen,et al.  Differential regulation and properties of MAPKs , 2007, Oncogene.

[34]  Meredith Wilson,et al.  The CDKL5 disorder is an independent clinical entity associated with early-onset encephalopathy , 2012, European Journal of Human Genetics.

[35]  L. Tsai,et al.  Structure and Regulation of the CDK5-p25nck5a Complex , 2001 .

[36]  W. El-Deiry,et al.  p21WAF1 and tumourigenesis: 20 years after , 2013, Current opinion in oncology.

[37]  J. Diffley Quality control in the initiation of eukaryotic DNA replication , 2011, Philosophical Transactions of the Royal Society B: Biological Sciences.

[38]  P. Jeffrey,et al.  Structural basis of cyclin-dependent kinase activation by phosphorylation , 1996, Nature Structural Biology.

[39]  A. Hanauer,et al.  Inactivation of the CDKL3 gene at 5q31.1 by a balanced t(X;5) translocation associated with nonspecific mild mental retardation , 2008, American journal of medical genetics. Part A.

[40]  J. Egly,et al.  A history of TFIIH: two decades of molecular biology on a pivotal transcription/repair factor. , 2011, DNA repair.

[41]  Kornelia Polyak,et al.  Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex , 1995, Nature.

[42]  L. Johnson,et al.  The structure of P‐TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation , 2008, The EMBO journal.

[43]  S. Geley,et al.  Cyclin-Dependent Kinase 16/PCTAIRE Kinase 1 Is Activated by Cyclin Y and Is Essential for Spermatogenesis , 2011, Molecular and Cellular Biology.

[44]  Sung-Hou Kim,et al.  Three-dimensional structure of human cyclin H, a positive regulator of the CDK-activating kinase , 1996, Nature Structural Biology.

[45]  Xin Wang,et al.  Functional characterization of human PFTK1 as a cyclin-dependent kinase , 2007, Proceedings of the National Academy of Sciences.

[46]  R. Fisher Secrets of a double agent: CDK7 in cell-cycle control and transcription , 2005, Journal of Cell Science.

[47]  N. Landsberger,et al.  What We Know and Would Like to Know about CDKL5 and Its Involvement in Epileptic Encephalopathy , 2012, Neural plasticity.

[48]  T. Tahirov,et al.  Crystal structure of HIV-1 Tat complexed with human P-TEFb , 2010, Nature.

[49]  Martin E M Noble,et al.  The Role of the Phospho-CDK2/Cyclin A Recruitment Site in Substrate Recognition* , 2006, Journal of Biological Chemistry.

[50]  P. Cramer,et al.  Structure of the mediator subunit cyclin C and its implications for CDK8 function. , 2005, Journal of molecular biology.

[51]  L. Johnson,et al.  Protein Kinase Inhibitors: Insights into Drug Design from Structure , 2004, Science.

[52]  W. Lim,et al.  Docking interactions in protein kinase and phosphatase networks. , 2006, Current opinion in structural biology.

[53]  David O. Morgan,et al.  The Cell Cycle: Principles of Control , 2014 .

[54]  M. E. M. Noble,et al.  The structure of CDK4/cyclin D3 has implications for models of CDK activation , 2009, Proceedings of the National Academy of Sciences.

[55]  Philip D. Jeffrey,et al.  Crystal structure of the p27Kip1 cyclin-dependent-kinase inibitor bound to the cyclin A–Cdk2 complex , 1996, Nature.

[56]  Emily K. Lehrman,et al.  Two Cyclin-Dependent Kinase Pathways Are Essential for Polarized Trafficking of Presynaptic Components , 2010, Cell.

[57]  J. Sack CRYSTAL STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2-WT) COMPLEX WITH N-[5-[[[5-(1,1-DIMETHYLETHYL)-2-OXAZOLYL] METHYL]THIO]-2-THIAZOLYL]-4-PIPERIDINECARBOXAMIDE (BMS-387032) , 2015 .

[58]  Susan S. Taylor,et al.  Defining the Conserved Internal Architecture of a Protein Kinase , 2010, Biochimica et biophysica acta.

[59]  Li-Huei Tsai,et al.  Cyclin-dependent kinases: a family portrait , 2009, Nature Cell Biology.

[60]  M. Noble,et al.  Recent developments in cyclin-dependent kinase biochemical and structural studies. , 2010, Biochimica et biophysica acta.

[61]  R. Huber,et al.  The structure of CDK8/CycC implicates specificity in the CDK/cyclin family and reveals interaction with a deep pocket binder. , 2011, Journal of molecular biology.