Journal of Molecular Biology
ReviewStructural and Evolutionary Division of Phosphotyrosine Binding (PTB) Domains
Introduction
PTB-containing proteins have quickly gained notoriety as critical regulators for the spatio-temporal organization of signaling networks. The importance of PTBs is represented by the range of physiological processes they modulate, including neuronal development, immune response, tissue homeostasis, and cell growth. Indeed, the list of PTB adapter/scaffold proteins linked to human disease and pathological conditions is ever growing. Mutations in PTB domain-encoded proteins so far have been identified in five human inherited diseases including hypercholesteremia, familial stroke, coronary artery disease, Alzheimer's disease, and diabetes.1, 2, 3, 4, 5, 6, 7, 8
Since 1994, when the initial characterization of PTB domains as modular phosphotyrosine-specific peptide binding domains was made, a rather large and steady body of data concerning PTBs has been amassed. Over the past ten years, several twists on common themes have emerged that necessitates the redefining of PTB domains. Some PTB domains require phosphorylation of a tyrosine in the peptide ligand for high affinity binding, but many more PTB domains bind their target substrates independent of phosphorylated tyrosine residues. PTB domains also bind head groups of acidic phospholipids, consistent with the nearly universal subcellular localization of PTB domains to membrane or juxtamembrane regions; suggesting most PTB domains are multifunctional in their interactions with the unique ability to target both proteins and phospholipids. Historically, PTB domains were segregated into two distinct subgroups: the shorter IRS-like and the longer Shc-like PTB domains. Herein, we integrate structural, evolutionary, and functional analysis that necessitates a division of the PTB domain family into three distinct subgroups.
Section snippets
Structural features of PTB domains
A clear functional dichotomy exists within the PTB domain family that is based upon the requirement of phosphotyrosine in the peptide ligand for binding. This division places Shc/IRS/Dok/SNT PTBs in one group (pY-dependent) and all others in a separate pY-independent group (see Table 1). PTB domains have historically been categorized as “IRS-like” or “Shc-like”, because of overt structural differences.9 We have identified key structural variations in PTB domains that reveal three distinct modes
Basic anatomy of a PTB domain
Shortly, after the identification of Shc as the founding member of PTB domain proteins,10 a 3D structure of the Shc PTB domain was solved.11 The Shc PTB domain was found to adopt a structural conformation similar to that of pleckstrin homology (PH) domains. This was a bit surprising considering the low level of primary sequence conservation between these two domains. Nevertheless, each of the ten different PTB domains with structures obtained thus far share this folding pattern, commonly
Structural analysis of peptide binding
The location and spatial arrangement of the peptide binding pocket is conserved in all PTB domain structures obtained thus far.11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 Furthermore, the general mode of peptide binding within this groove is also shared (Figure 1). PTB peptide ligands are bound as an anti-parallel pseudo-β sheet forming extensive contacts with the β5 strand and the C-terminal α helix. The peptides themselves form a type I β turn towards their distal end. This kink is
Structural analysis of phospholipid binding
One common trait that all PTB domain-containing proteins appear to share is that they are localized either to juxtamembrane regions or to membranes themselves under at least a subset of conditions. This can be explained in part because most of the ligands of PTB domains are transmembrane or membrane-associated proteins, further discussed below. However, a growing number of PTB domains have been found to bind directly to liposome-associated or free phospholipid head groups. Since PTB domains
Evolutionary analysis of PTB domains
PTB domains from different classes share the general functions of peptide and phospholipid binding, but at some point must have diverged evolutionarily in their modes of peptide recognition. Using algorithms developed from structure-based sequence alignments of PTB domains it is clear that a large evolutionary divergence exists between the IRS-like and Shc/Dab-like PTBs. A search of three non-redundant protein databases (Swiss-Prot, TREMBL, and TREMBL-new) with an algorithm built upon an
Functions of PTB domains
Almost 220 distinct PTB domains have been identified in a variety of eukaryotic organisms including Caenorhabditis elegans, Anopheles gambiae, Drosophila melanogaster, Xenopus laevis, and mammals. PTB domains have not been found in Saccharomyces cerevisiae or Arabidopsis thaliana, but two PTBs do exist in Dictyostelium discoidium (Talin A and Talin B). A majority of the known PTB domains are found in mammals (around 150 total), with approximately 60 PTB-encoded proteins present in humans.
Receptor tyrosine kinase and cytokine receptor signaling
The most well characterized PTB domain-containing protein is the Shc adapter protein (reviewed by Ravichandran).48 The presence of both SH2 and PTB domains in Shc allows for its binding to a variety of growth factor receptors upon their ligand-stimulated activation. Upon binding to activated receptors, Shc itself is tyrosine phosphorylated and recruits the Grb2 adapter via Grb2 SH2-mediated binding. Sos, a Ras nucleotide exchange factor, is then bound, whereupon Ras activation stimulates the
Low density lipoprotein receptor signaling
A number of phosphotyrosine-independent PTB adapters have been shown to bind to members of the low density lipoprotein (LDL) receptor family.54 One of the first of these PTB adapters shown to bind LDL receptors was the mammalian disabled-1 (Dab-1).55, 56, 57 The function of Dab1 was initially characterized genetically using mice with the targeted disruption of the mdab1 gene58 or mice with spontaneous autosomal recessive mutations in mdab1.59 Each of these mouse lines exhibited a phenotype
Amyloid precursor protein processing
Several PTB adapter proteins have been recently linked to Alzheimer's disease on the basis of their ability to bind to amyloid precursor protein.71 Alzheimer's disease is characterized by the buildup of miliary amyloid plaques in the brain parenchyma. The major components of these amyloid plaques are the secreted Aβ peptides Aβ40 and Aβ42 derived from the transmembrane amyloid precursor protein (APP). In neuronal cells, β- and γ-secretase-mediated processing of APP occurs in endocytic vesicles.
Asymmetric cell division
Proteins of the Numb family are all involved in mediating asymmetric cell division. The C. elegans Numb homolog, CKA1, binds to the atypical protein kinase C PKC3, via its PTB domain.84, 85 PKC3 function is essential for embryogenesis and asymmetry in early cell divisions. CKA1 functions to properly sequester and localize PKC3 to lateral surfaces of polarized cells. Thus, CKA1 is presumed to be an important regulator of early development in C. elegans. Likewise, the Drosophila Numb (dNumb)
Integrin activation and cell adhesion
Integrins are cell adhesion molecules that bind to the extracellular matrix (ECM) and regulate various cellular processes including motility, polarity, growth, and survival.97 Ligand binding induces integrin clustering and establishment of focal complexes. These focal complexes are composed of adapter and signaling proteins that recruit additional factors. This leads to the development of a focal adhesion, which is a nexus for ECM–integrin–cytoskeleton signaling pathways. Many PTB domain
Future outlook
Table 3 presents a summary of the structural and functional features that define the three subgroups of PTB domains. While significant diversity exists in PTB domains, it is clear that they all function in an adapter/scaffold capacity. Six PTB domain encoded scaffold proteins have been found to have mutations that contribute to human disease (Table 4), demonstrating the importance of these proteins in organizing critical signaling complexes in cells. The signaling complexes controlled by most
References (98)
- et al.
Interaction of CED-6/GULP, an adapter protein involved in engulfment of apoptotic cells with CED-1 and CD91/low density lipoprotein receptor-related protein (LRP)
J. Biol. Chem.
(2002) - et al.
Mutations in a gene encoding a novel protein containing a phosphotyrosine-binding domain cause type 2 cerebral cavernous malformations
Am. J. Hum. Genet.
(2003) - et al.
The function of PTB domain proteins
Kidney Int.
(1999) - et al.
A region in Shc distinct from the SH2 domain can bind tyrosine-phosphorylated growth factor receptors
J. Biol. Chem.
(1994) - et al.
Structure of the IRS-1 PTB domain bound to the juxtamembrane region of the insulin receptor
Cell
(1996) - et al.
Structural basis of SNT PTB domain interactions with distinct neurotrophic receptors
Mol. Cell
(2000) - et al.
Structural basis for the specific recognition of RET by the Dok1 phosphotyrosine binding domain
J. Biol. Chem.
(2004) - et al.
Origins of peptide selectivity and phosphoinositide binding revealed by structures of disabled-1 PTB domain complexes
Structure
(2003) - et al.
Crystal structures of the Dab homology domains of mouse disabled 1 and 2
J. Biol. Chem.
(2003) - et al.
Structural determinants of integrin recognition by talin
Mol. Cell
(2003)
Phosphotyrosine binding domains of Shc and insulin receptor substrate 1 recognize the NPXpY motif in a thermodynamically distinct manner
J. Biol. Chem.
PTB domains of IRS-1 and Shc have distinct but overlapping binding specificities
J. Biol. Chem.
Coupling of folding and binding in the PTB domain of the signaling protein Shc
Structure
The mammalian numb phosphotyrosine-binding domain. Characterization of binding specificity and identification of a novel PDZ domain-containing numb binding protein, LNX
J. Biol. Chem.
FRS2 PTB domain conformation regulates interactions with divergent neurotrophic receptors
J. Biol. Chem.
Mints, Munc18-interacting proteins in synaptic vesicle exocytosis
J. Biol. Chem.
Characterization of four mammalian numb protein isoforms. Identification of cytoplasmic and membrane-associated variants of the phosphotyrosine binding domain
J. Biol. Chem.
Conformation, localization, and integrin binding of talin depend on its interaction with phosphoinositides
J. Biol. Chem.
Specificity in pleckstrin homology (PH) domain membrane targeting: a role for a phosphoinositide–protein co-operative mechanism
FEBS Letters
Pleckstrin homology and phosphotyrosine-binding domain-dependent membrane association and tyrosine phosphorylation of Dok-4, an inhibitory adapter molecule expressed in epithelial cells
J. Biol. Chem.
Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors
J. Mol. Biol.
Identification of residues within the SHC phosphotyrosine binding/phosphotyrosine interaction domain crucial for phosphopeptide interaction
J. Biol. Chem.
Protein tyrosine phosphatases in the human genome
Cell
The phosphotyrosine interaction domain of SHC recognizes tyrosine-phosphorylated NPXY motif
J. Biol. Chem.
Binding specificity and mutational analysis of the phosphotyrosine binding domain of the brain-specific adaptor protein ShcC
J. Biol. Chem.
Modified phage peptide libraries as a tool to study specificity of phosphorylation and recognition of tyrosine containing peptides
J. Mol. Biol.
Dockers at the crossroads
Cell. Signal.
Interactions of the low density lipoprotein receptor gene family with cytosolic adaptor and scaffold proteins suggest diverse biological functions in cellular communication and signal transduction
J. Biol. Chem.
Reeler/Disabled-like disruption of neuronal migration in knockout mice lacking the VLDL receptor and ApoE receptor 2
Cell
Interaction of cytosolic adaptor proteins with neuronal apolipoprotein E receptors and the amyloid precursor protein
J. Biol. Chem.
Direct binding of Reelin to VLDL receptor and ApoE receptor 2 induces tyrosine phosphorylation of disabled-1 and modulates tau phosphorylation
Neuron
Events governing organization of postmigratory neurons: studies on brain development in normal and reeler mice
Brain Res.
Reelin is a ligand for lipoprotein receptors
Neuron
Tyrosine-phosphorylated low density lipoprotein receptor-related protein 1 (Lrp1) associates with the adaptor protein SHC in SRC-transformed cells
J. Biol. Chem.
The reelin receptor ApoER2 recruits JNK-interacting proteins-1 and -2
J. Biol. Chem.
LDL receptor-related protein, a multifunctional ApoE receptor, binds secreted beta-amyloid precursor protein and mediates its degradation
Cell
The J.D. mutation in familial hypercholesterolemia: amino acid substitution in cytoplasmic domain impedes internalization of LDL receptors
Cell
NPXY, a sequence often found in cytoplasmic tails, is required for coated pit-mediated internalization of the low density lipoprotein receptor
J. Biol. Chem.
Adaptor protein interactions: modulators of amyloid precursor protein metabolism and Alzheimer's disease risk?
Expt. Neurol.
Autosomal recessive hypercholesterolemia protein interacts with and regulates the cell surface level of Alzheimer's amyloid beta precursor protein
J. Biol. Chem.
X11L2, a new member of the X11 protein family, interacts with Alzheimer's beta-amyloid precursor protein
Biochem. Biophys. Res. Commun.
The X11alpha protein slows cellular amyloid precursor protein processing and reduces Abeta40 and Abeta42 secretion
J. Biol. Chem.
Interaction of the phosphotyrosine interaction/phosphotyrosine binding-related domains of Fe65 with wild-type and mutant Alzheimer's beta-amyloid precursor proteins
J. Biol. Chem.
Molecular cloning of human Fe65L2 and its interaction with the Alzheimer's beta-amyloid precursor protein
Neurosci. Letters
Regulation of beta-amyloid secretion by FE65, an amyloid protein precursor-binding protein
J. Biol. Chem.
Munc18 interacting proteins: ADP-ribosylation factor-dependent coat proteins that regulate the traffic of beta-Alzheimer's precursor protein
J. Biol. Chem.
A novel adapter protein employs a phosphotyrosine binding domain and exceptionally basic N-terminal domains to capture and localize an atypical protein kinase C: characterization of Caenorhabditis elegans C kinase adapter 1, a protein that avidly binds protein kinase C3
J. Biol. Chem.
Structural properties and mechanisms that govern association of C kinase adapter 1 with protein kinase C3 and the cell periphery
J. Biol. Chem.
numb, a gene required in determination of cell fate during sensory organ formation in Drosophila embryos
Cell
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