Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases.

PubWeight™: 0.77‹?›

🔗 View Article (PMID 26628682)

Published in Sci Signal on December 01, 2015

Authors

Qifang Xu1, Kimberly L Malecka1, Lauren Fink1, E Joseph Jordan2, Erin Duffy1, Samuel Kolander1, Jeffrey R Peterson1, Roland L Dunbrack3

Author Affiliations

1: Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
2: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
3: Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA. roland.dunbrack@fccc.edu.

Articles cited by this

(truncated to the top 100)

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

Clustal W and Clustal X version 2.0. Bioinformatics (2007) 126.47

The Pfam protein families database. Nucleic Acids Res (2011) 33.46

Gain-of-function mutations of c-kit in human gastrointestinal stromal tumors. Science (1998) 21.13

UniProt: a hub for protein information. Nucleic Acids Res (2014) 16.72

Cell signaling by receptor tyrosine kinases. Cell (2010) 12.39

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (2013) 11.01

An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell (2006) 10.28

A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci U S A (2008) 10.07

The Uppsala Electron-Density Server. Acta Crystallogr D Biol Crystallogr (2004) 9.60

Targeting the mitogen-activated protein kinase cascade to treat cancer. Nat Rev Cancer (2004) 6.07

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures. Bioinformatics (2006) 5.46

Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol (2006) 5.03

Two-stage PCR protocol allowing introduction of multiple mutations, deletions and insertions using QuikChange Site-Directed Mutagenesis. Biotechniques (1999) 4.97

Mechanism for activation of the EGF receptor catalytic domain by the juxtamembrane segment. Cell (2009) 4.78

Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and ATP analog. EMBO J (1997) 4.59

Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism. Proc Natl Acad Sci U S A (2006) 4.09

Kinetic and catalytic mechanisms of protein kinases. Chem Rev (2001) 3.80

Protein kinases: evolution of dynamic regulatory proteins. Trends Biochem Sci (2010) 3.61

Gastrointestinal stromal tumours: origin and molecular oncology. Nat Rev Cancer (2011) 3.55

Transformations, means, and confidence intervals. BMJ (1996) 3.42

Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme. Cell (2005) 3.08

Identification of six novel autophosphorylation sites on fibroblast growth factor receptor 1 and elucidation of their importance in receptor activation and signal transduction. Mol Cell Biol (1996) 2.80

A molecular brake in the kinase hinge region regulates the activity of receptor tyrosine kinases. Mol Cell (2007) 2.70

Beta-turns and their distortions: a proposed new nomenclature. Protein Eng (1990) 2.67

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. Nucleic Acids Res (2012) 2.61

A helix scaffold for the assembly of active protein kinases. Proc Natl Acad Sci U S A (2008) 2.51

Identification of two juxtamembrane autophosphorylation sites in the PDGF beta-receptor; involvement in the interaction with Src family tyrosine kinases. EMBO J (1993) 2.46

All autophosphorylation sites of epidermal growth factor (EGF) receptor and HER2/neu are located in their carboxyl-terminal tails. Identification of a novel site in EGF receptor. J Biol Chem (1989) 2.46

Structure and autoregulation of the insulin-like growth factor 1 receptor kinase. Nat Struct Biol (2001) 2.45

Regulation of PDGF signalling and vascular remodelling by peroxiredoxin II. Nature (2005) 2.29

Structure of the CaMKIIdelta/calmodulin complex reveals the molecular mechanism of CaMKII kinase activation. PLoS Biol (2010) 2.22

The structural basis for control of eukaryotic protein kinases. Annu Rev Biochem (2012) 2.21

Activation segment dimerization: a mechanism for kinase autophosphorylation of non-consensus sites. EMBO J (2008) 2.12

Structural analysis of the lymphocyte-specific kinase Lck in complex with non-selective and Src family selective kinase inhibitors. Structure (1999) 2.09

Structural basis and prediction of substrate specificity in protein serine/threonine kinases. Proc Natl Acad Sci U S A (2002) 2.07

Specific CLK inhibitors from a novel chemotype for regulation of alternative splicing. Chem Biol (2011) 2.06

Structure of a c-kit product complex reveals the basis for kinase transactivation. J Biol Chem (2003) 1.95

Regulation of cell cycle progression and apoptosis by the Ras/Raf/MEK/ERK pathway (Review). Int J Oncol (2003) 1.91

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. Bioinformatics (2012) 1.82

Autoregulatory mechanisms in protein-tyrosine kinases. J Biol Chem (1998) 1.75

Identification and characterization of signal transducer and activator of transcription 3 recruitment sites within the epidermal growth factor receptor. Cancer Res (2003) 1.73

The crystal structure of a phosphorylase kinase peptide substrate complex: kinase substrate recognition. EMBO J (1997) 1.68

The selectivity of receptor tyrosine kinase signaling is controlled by a secondary SH2 domain binding site. Cell (2009) 1.68

Structural and biochemical characterization of the KRLB region in insulin receptor substrate-2. Nat Struct Mol Biol (2008) 1.67

Structural insights into the autoactivation mechanism of p21-activated protein kinase. Structure (2011) 1.62

How do protein kinases discriminate between serine/threonine and tyrosine? Structural insights from the insulin receptor protein-tyrosine kinase. FASEB J (1995) 1.58

Autocrine CSF-1R activation promotes Src-dependent disruption of mammary epithelial architecture. J Cell Biol (2004) 1.56

Statistical analysis of interface similarity in crystals of homologous proteins. J Mol Biol (2008) 1.55

IRAK4 dimerization and trans-autophosphorylation are induced by Myddosome assembly. Mol Cell (2014) 1.52

The active conformation of the PAK1 kinase domain. Structure (2005) 1.50

The hCds1 (Chk2)-FHA domain is essential for a chain of phosphorylation events on hCds1 that is induced by ionizing radiation. J Biol Chem (2001) 1.48

Phosphorylation of Shc by Src family kinases is necessary for stem cell factor receptor/c-kit mediated activation of the Ras/MAP kinase pathway and c-fos induction. Oncogene (1999) 1.46

Tyrosine 319, a newly identified phosphorylation site of ZAP-70, plays a critical role in T cell antigen receptor signaling. J Biol Chem (1999) 1.45

ROCK1 phosphorylates and activates zipper-interacting protein kinase. J Biol Chem (2006) 1.40

Crystal structure of an Aurora-A mutant that mimics Aurora-B bound to MLN8054: insights into selectivity and drug design. Biochem J (2010) 1.38

Identification of tyrosine residues in constitutively activated fibroblast growth factor receptor 3 involved in mitogenesis, Stat activation, and phosphatidylinositol 3-kinase activation. Mol Biol Cell (2001) 1.36

Crystal structures of IRAK-4 kinase in complex with inhibitors: a serine/threonine kinase with tyrosine as a gatekeeper. Structure (2006) 1.32

The protein common interface database (ProtCID)--a comprehensive database of interactions of homologous proteins in multiple crystal forms. Nucleic Acids Res (2010) 1.30

Specific dephosphorylation of the Lck tyrosine protein kinase at Tyr-394 by the SHP-1 protein-tyrosine phosphatase. J Biol Chem (2001) 1.29

A single pair of acidic residues in the kinase major groove mediates strong substrate preference for P-2 or P-5 arginine in the AGC, CAMK, and STE kinase families. J Biol Chem (2005) 1.28

Regulation of zipper-interacting protein kinase activity in vitro and in vivo by multisite phosphorylation. J Biol Chem (2004) 1.27

Vertebrate non-receptor protein-tyrosine kinase families. Genes Cells (1996) 1.26

A crystallographic snapshot of tyrosine trans-phosphorylation in action. Proc Natl Acad Sci U S A (2008) 1.25

Identification and functional analysis of phosphorylated tyrosine residues within EphA2 receptor tyrosine kinase. J Biol Chem (2008) 1.24

Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: structure of lck/imatinib complex. Proteins (2008) 1.23

Intersubunit capture of regulatory segments is a component of cooperative CaMKII activation. Nat Struct Mol Biol (2010) 1.21

EphB1 recruits c-Src and p52Shc to activate MAPK/ERK and promote chemotaxis. J Cell Biol (2003) 1.20

Oncogenic activation of the Lck protein accompanies translocation of the LCK gene in the human HSB2 T-cell leukemia. Mol Cell Biol (1994) 1.19

A quantitative study of the recruitment potential of all intracellular tyrosine residues on EGFR, FGFR1 and IGF1R. Mol Biosyst (2008) 1.19

Grb10, a positive, stimulatory signaling adapter in platelet-derived growth factor BB-, insulin-like growth factor I-, and insulin-mediated mitogenesis. Mol Cell Biol (1999) 1.18

Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor c-Met and its complex with the microbial alkaloid K-252a. Proc Natl Acad Sci U S A (2003) 1.15

Direct binding of Cbl to Tyr568 and Tyr936 of the stem cell factor receptor/c-Kit is required for ligand-induced ubiquitination, internalization and degradation. Biochem J (2006) 1.12

Crystal structure of the protein kinase domain of yeast AMP-activated protein kinase Snf1. Biochem Biophys Res Commun (2005) 1.12

The cellular localization of the murine serine/arginine-rich protein kinase CLK2 is regulated by serine 141 autophosphorylation. J Biol Chem (1998) 1.11

Identification of Y589 and Y599 in the juxtamembrane domain of Flt3 as ligand-induced autophosphorylation sites involved in binding of Src family kinases and the protein tyrosine phosphatase SHP2. Blood (2006) 1.10

Asymmetric receptor contact is required for tyrosine autophosphorylation of fibroblast growth factor receptor in living cells. Proc Natl Acad Sci U S A (2010) 1.10

On the molecular mechanisms of mitotic kinase activation. Open Biol (2012) 1.08

High accuracy mutation detection in leukemia on a selected panel of cancer genes. PLoS One (2012) 1.08

Small-molecule inhibition and activation-loop trans-phosphorylation of the IGF1 receptor. EMBO J (2008) 1.07

Crystal structure of the Apo, unactivated insulin-like growth factor-1 receptor kinase. Implication for inhibitor specificity. J Biol Chem (2002) 1.06

Insights into the aberrant activity of mutant EGFR kinase domain and drug recognition. Structure (2012) 1.04

Structures of Down syndrome kinases, DYRKs, reveal mechanisms of kinase activation and substrate recognition. Structure (2013) 1.03

Modulation of kinase-inhibitor interactions by auxiliary protein binding: crystallography studies on Aurora A interactions with VX-680 and with TPX2. Protein Sci (2008) 1.02

Molecular mechanism of Aurora A kinase autophosphorylation and its allosteric activation by TPX2. Elife (2014) 1.01

Direct association of Csk homologous kinase (CHK) with the diphosphorylated site Tyr568/570 of the activated c-KIT in megakaryocytes. J Biol Chem (1997) 1.01

Structural studies on phospho-CDK2/cyclin A bound to nitrate, a transition state analogue: implications for the protein kinase mechanism. Biochemistry (2002) 0.99

Crystal structures of the Mnk2 kinase domain reveal an inhibitory conformation and a zinc binding site. Structure (2005) 0.99

Mitogen-activated protein kinases interacting kinases are autoinhibited by a reprogrammed activation segment. EMBO J (2006) 0.99

Oncogenic Flt3 receptors display different specificity and kinetics of autophosphorylation. Exp Hematol (2009) 0.98

MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes. Nucleic Acids Res (2007) 0.96

Identification of a major determinant for serine-threonine kinase phosphoacceptor specificity. Mol Cell (2013) 0.96

Leucettines, a class of potent inhibitors of cdc2-like kinases and dual specificity, tyrosine phosphorylation regulated kinases derived from the marine sponge leucettamine B: modulation of alternative pre-RNA splicing. J Med Chem (2011) 0.96

Protein-tyrosine phosphatase DEP-1 controls receptor tyrosine kinase FLT3 signaling. J Biol Chem (2011) 0.95

Structural recognition of an optimized substrate for the ephrin family of receptor tyrosine kinases. FEBS J (2009) 0.93

Structure of the OSR1 kinase, a hypertension drug target. Proteins (2008) 0.91

Src family kinases negatively regulate platelet-derived growth factor alpha receptor-dependent signaling and disease progression. J Biol Chem (2000) 0.91

7,8-dichloro-1-oxo-β-carbolines as a versatile scaffold for the development of potent and selective kinase inhibitors with unusual binding modes. J Med Chem (2012) 0.90

Predicting protein kinase specificity: Predikin update and performance in the DREAM4 challenge. PLoS One (2011) 0.90

Back pocket flexibility provides group II p21-activated kinase (PAK) selectivity for type I 1/2 kinase inhibitors. J Med Chem (2014) 0.90