Structural Basis for the Specific Recognition of RET by the Dok1 Phosphotyrosine Binding Domain*

Dok1 is a common substrate of activated protein-tyrosine kinases. It is rapidly tyrosine-phosphorylated in response to receptor tyrosine activation and interacts with ras GTPase-activating protein and Nck, leading to inhibition of ras signaling pathway activation and the c-Jun N-terminal kinase (JNK) and c-Jun activation, respectively. In chronic myelogenous leukemia cells, it has shown constitutive phosphorylation. The N-terminal phosphotyrosine binding (PTB) domain of Dok1 can recognize and bind specifically to phosphotyrosine-containing motifs of receptors. Here we report the crystal structure of the Dok1 PTB domain alone and in complex with a phosphopeptide derived from RET receptor tyrosine kinase. The structure consists of a β-sandwich composed of two nearly orthogonal, 7-stranded, antiparallel β-sheets, and it is capped at one side by a C-terminal α-helix. The RET phosphopeptide binds to Dok1 via a surface groove formed between strand β5 and the C-terminal α-helix of the PTB domain. The structures reveal the molecular basis for the specific recognition of RET by the Dok1 PTB domain. We also show that Dok1 does not recognize peptide sequences from TrkA and IL-4, which are recognized by Shc and IRS1, respectively.

[1]  Thomas C. Terwilliger,et al.  Automated MAD and MIR structure solution , 1999, Acta crystallographica. Section D, Biological crystallography.

[2]  M. White,et al.  PTB Domains of IRS-1 and Shc Have Distinct but Overlapping Binding Specificities (*) , 1995, The Journal of Biological Chemistry.

[3]  R. Meadows,et al.  Structural basis for IL-4 receptor phosphopeptide recognition by thelRS-1 PTB domain , 1996, Nature Structural Biology.

[4]  Thomas C. Terwilliger,et al.  Electronic Reprint Biological Crystallography Maximum-likelihood Density Modification , 2022 .

[5]  A. Petros,et al.  Structure and ligand recognition of the phosphotyrosine binding domain of Shc , 1995, Nature.

[6]  N. Asai,et al.  A Mutation at Tyrosine 1062 in MEN2A-Ret and MEN2B-Ret Impairs Their Transforming Activity and Association with Shc Adaptor Proteins* , 1996, The Journal of Biological Chemistry.

[7]  G. Lenoir,et al.  Oncogenic activation of RET by two distinct FMTC mutations affecting the tyrosine kinase domain , 1997, Oncogene.

[8]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[9]  David A Calderwood,et al.  Integrin β cytoplasmic domain interactions with phosphotyrosine-binding domains: A structural prototype for diversity in integrin signaling , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[10]  S. Shoelson,et al.  Crystal structure of the pleckstrin homology-phosphotyrosine binding (PH-PTB) targeting region of insulin receptor substrate 1. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[11]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[12]  L. Johnson.  Macromolecular crystallography. Part A. Methods in Enzymology, Vol. 276. Edited by Charles W. Carter Jr and Robert M. Sweet. New York: Academic Press, 1997. Pp. xxxii + 700. Price $99.00. ISBN 0-12-182177-3 , 1998 .

[13]  K. Shokat,et al.  A chemical genetic screen for direct v-Src substrates reveals ordered assembly of a retrograde signaling pathway. , 2002, Chemistry & biology.

[14]  R. Kobayashi,et al.  p62 dok : A Constitutively Tyrosine-Phosphorylated, GAP-Associated Protein in Chronic Myelogenous Leukemia Progenitor Cells , 1997, Cell.

[15]  G. D. Vita,et al.  The insulin receptor substrate (IRS)-1 recruits phosphatidylinositol 3-kinase to Ret: evidence for a competition between Shc and IRS-1 for the binding to Ret , 2001, Oncogene.

[16]  T. Gustafson,et al.  Distinct Modes of Interaction of SHC and Insulin Receptor Substrate-1 with the Insulin Receptor NPEY Region via Non-SH2 Domains (*) , 1995, The Journal of Biological Chemistry.

[17]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[18]  Robert M. Sweet,et al.  Macromolecular Crystallography: Part A , 1997 .

[19]  R M Esnouf,et al.  An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. , 1997, Journal of molecular graphics & modelling.

[20]  K. Chan,et al.  RET receptor tyrosine kinase isoforms in kidney function and disease , 2002, Oncogene.

[21]  Masahide Takahashi,et al.  Role of Dok1 in Cell Signaling Mediated by RET Tyrosine Kinase* , 2002, The Journal of Biological Chemistry.

[22]  T. Pawson,et al.  Nck-Interacting Ste20 Kinase Couples Eph Receptors to c-Jun N-Terminal Kinase and Integrin Activation , 2000, Molecular and Cellular Biology.

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

[24]  D. Baltimore,et al.  Domain-dependent Function of the rasGAP-binding Protein p62Dok in Cell Signaling* , 2001, The Journal of Biological Chemistry.

[25]  A. Kudo,et al.  The Pre-B Cell Receptor Signaling for Apoptosis Is Negatively Regulated by FcγRIIB1 , 2002, The Journal of Immunology.

[26]  L. Mulligan,et al.  Conservation of RET proto-oncogene splicing variants and implications for RET isoform function , 2002, Cytogenetic and Genome Research.

[27]  D. Baltimore,et al.  Identification of the Abl- and rasGAP-Associated 62 kDa Protein as a Docking Protein, Dok , 1997, Cell.

[28]  L. Mulligan,et al.  Expression of RET 3′ splicing variants during human kidney development , 1998, Oncogene.