DEPOD - human DEPhOsphorylation Database

Basic Information
Phosphatases
Pathway
Interacting Proteins
Phosphorylating Kinases

Gene Name	NTRK1 (QuickGO)	Interactive visualization of NTRK1 structures (A quick tutorial to explore the interctive visulaization) Representative structure: 6DKB
Synonyms	NTRK1, MTC, TRK
Protein Name	NTRK1
Alternative Name(s)	High affinity nerve growth factor receptor;2.7.10.1;Neurotrophic tyrosine kinase receptor type 1;TRK1-transforming tyrosine kinase protein;Tropomyosin-related kinase A;Tyrosine kinase receptor;Tyrosine kinase receptor A;Trk-A;gp140trk;p140-TrkA;
Protein Family	Belongs to the protein kinase superfamily Tyr proteinkinase family Insulin receptor subfamily
EntrezGene ID	4914 (Comparitive Toxicogenomics)
UniProt AC (Human)	P04629 (protein sequence)
Enzyme Class	2.7.10.1 (BRENDA )
Molecular Weight	87497 Dalton
Protein Length	796 amino acids (AA)
Genome Browsers	NCBI \| ENSG00000198400 (Ensembl) \| UCSC \| 1000 Genomes
Crosslinking annotations	Query our ID-mapping table
Orthologues	Quest For Orthologues (QFO) \| GeneTree \| eggNOG - ENOG410IMMI \| eggNOG - ENOG410XTGG
Phosphorylation Network	Visualize

Domain organization, Expression, Diseases

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Localization, Function, Catalytic activity and Sequence

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Localization (UniProt annotation)
Cell membrane Early endosome membrane Late endosome membrane Note=Rapidly internalizedafter NGF binding (PubMed:1281417) Internalized to endosomes uponbinding of NGF or NTF3 and further transported to the cell bodyvia a retrograde axonal transport Localized at cell membrane andearly endosomes before nerve growth factor (NGF) stimulationRecruited to late endosomes after NGF stimulation Colocalizedwith RAPGEF2 at late endosomes
Function (UniProt annotation)
Receptor tyrosine kinase involved in the development andthe maturation of the central and peripheral nervous systemsthrough regulation of proliferation, differentiation and survivalof sympathetic and nervous neurons High affinity receptor for NGFwhich is its primary ligand (PubMed:1850821, PubMed:1849459,PubMed:1281417, PubMed:8325889, PubMed:15488758, PubMed:17196528,PubMed:27445338) Can also bind and be activated byNTF3/neurotrophin-3 However, NTF3 only supports axonal extensionthrough NTRK1 but has no effect on neuron survival (Bysimilarity) Upon dimeric NGF ligand-binding, undergoeshomodimerization, autophosphorylation and activation(PubMed:1281417) Recruits, phosphorylates and/or activatesseveral downstream effectors including SHC1, FRS2, SH2B1, SH2B2and PLCG1 that regulate distinct overlapping signaling cascadesdriving cell survival and differentiation Through SHC1 and FRS2activates a GRB2-Ras-MAPK cascade that regulates celldifferentiation and survival Through PLCG1 controls NF-Kappa-Bactivation and the transcription of genes involved in cellsurvival Through SHC1 and SH2B1 controls a Ras-PI3 kinase-AKT1signaling cascade that is also regulating survival In absence ofligand and activation, may promote cell death, making the survivalof neurons dependent on trophic factors Isoform TrkA-III: Resistant to NGF, it constitutivelyactivates AKT1 and NF-kappa-B and is unable to activate the Ras-MAPK signaling cascade Antagonizes the anti-proliferative NGF-NTRK1 signaling that promotes neuronal precursors differentiationIsoform TrkA-III promotes angiogenesis and has oncogenic activitywhen overexpressed
Catalytic Activity (UniProt annotation)
ATP + a [protein]-L-tyrosine = ADP + a[protein]-L-tyrosine phosphate
Protein Sequence
MLRGGRRGQLGWHSWAAGPGSLLAWLILASAGAAPCPDACCPHGSSGLRCTRDGALDSLHHLPGAENLTELYIENQQHLQ HLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLSWKTVQGLSLQELVLSGNPLHCSCALRWLQ RWEEEGLGGVPEQKLQCHGQGPLAHMPNASCGVPTLKVQVPNASVDVGDDVLLRCQVEGRGLEQAGWILTELEQSATVMK SGGLPSLGLTLANVTSDLNRKNVTCWAENDVGRAEVSVQVNVSFPASVQLHTAVEMHHWCIPFSVDGQPAPSLRWLFNGS VLNETSFIFTEFLEPAANETVRHGCLRLNQPTHVNNGNYTLLAANPFGQASASIMAAFMDNPFEFNPEDPIPVSFSPVDT NSTSGDPVEKKDETPFGVSVAVGLAVFACLFLSTLLLVLNKCGRRNKFGINRPAVLAPEDGLAMSLHFMTLGGSSLSPTE GKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQRE AELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVY LAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEI FTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG

Motif information from Eukaryotic Linear Motif atlas (ELM)

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Gene Ontology (P: Process; F: Function and C: Component terms)

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GO:0000186	P:activation of MAPKK activity
GO:0001934	P:positive regulation of protein phosphorylation
GO:0004713	F:protein tyrosine kinase activity
GO:0004714	F:transmembrane receptor protein tyrosine kinase activity
GO:0005004	F:GPI-linked ephrin receptor activity
GO:0005166	F:neurotrophin p75 receptor binding
GO:0005524	F:ATP binding
GO:0005768	C:endosome
GO:0005769	C:early endosome
GO:0005770	C:late endosome
GO:0005886	C:plasma membrane
GO:0005887	C:integral component of plasma membrane
GO:0006468	P:protein phosphorylation
GO:0007411	P:axon guidance
GO:0007568	P:aging
GO:0007611	P:learning or memory
GO:0007623	P:circadian rhythm
GO:0008285	P:negative regulation of cell proliferation
GO:0009314	P:response to radiation
GO:0009986	C:cell surface
GO:0010465	F:nerve growth factor receptor activity
GO:0010623	P:programmed cell death involved in cell development
GO:0010976	P:positive regulation of neuron projection development
GO:0018108	P:peptidyl-tyrosine phosphorylation
GO:0019900	F:kinase binding
GO:0021553	P:olfactory nerve development
GO:0030183	P:B cell differentiation
GO:0030424	C:axon
GO:0030425	C:dendrite
GO:0031175	P:neuron projection development
GO:0031667	P:response to nutrient levels
GO:0031901	C:early endosome membrane
GO:0031902	C:late endosome membrane
GO:0032991	C:protein-containing complex
GO:0038083	P:peptidyl-tyrosine autophosphorylation
GO:0038180	P:nerve growth factor signaling pathway
GO:0042490	P:mechanoreceptor differentiation
GO:0042803	F:protein homodimerization activity
GO:0043025	C:neuronal cell body
GO:0043066	P:negative regulation of apoptotic process
GO:0043068	P:positive regulation of programmed cell death
GO:0043121	F:neurotrophin binding
GO:0043235	C:receptor complex
GO:0043524	P:negative regulation of neuron apoptotic process
GO:0043547	P:positive regulation of GTPase activity
GO:0045766	P:positive regulation of angiogenesis
GO:0046579	P:positive regulation of Ras protein signal transduction
GO:0046777	P:protein autophosphorylation
GO:0048011	P:neurotrophin TRK receptor signaling pathway
GO:0048015	P:phosphatidylinositol-mediated signaling
GO:0048406	F:nerve growth factor binding
GO:0048485	P:sympathetic nervous system development
GO:0048666	P:neuron development
GO:0048678	P:response to axon injury
GO:0050965	P:detection of temperature stimulus involved in sensory perception of pain
GO:0050966	P:detection of mechanical stimulus involved in sensory perception of pain
GO:0051092	P:positive regulation of NF-kappaB transcription factor activity
GO:0051599	P:response to hydrostatic pressure
GO:0051602	P:response to electrical stimulus
GO:0051965	P:positive regulation of synapse assembly
GO:0051968	P:positive regulation of synaptic transmission
GO:0060009	glutamatergic
GO:0060385	P:Sertoli cell development
GO:0061368	P:axonogenesis involved in innervation
GO:0070374	P:behavioral response to formalin induced pain
GO:0071316	P:positive regulation of ERK1 and ERK2 cascade
GO:1990090	P:cellular response to nicotine

KEGG Pathway
Reactome Pathway

Pathway ID	Pathway Name	Pathway Description (KEGG)
hsa04010	MAPK signaling pathway	The mitogen-activated protein kinase (MAPK) cascade is a highly conserved module that is involved in various cellular functions, including cell proliferation, differentiation and migration. Mammals express at least four distinctly regulated groups of MAPKs, extracellular signal-related kinases (ERK)-1/2, Jun amino-terminal kinases (JNK1/2/3), p38 proteins (p38alpha/beta/gamma/delta) and ERK5, that are activated by specific MAPKKs: MEK1/2 for ERK1/2, MKK3/6 for the p38, MKK4/7 (JNKK1/2) for the JNKs, and MEK5 for ERK5. Each MAPKK, however, can be activated by more than one MAPKKK, increasing the complexity and diversity of MAPK signalling. Presumably each MAPKKK confers responsiveness to distinct stimuli. For example, activation of ERK1/2 by growth factors depends on the MAPKKK c-Raf, but other MAPKKKs may activate ERK1/2 in response to pro-inflammatory stimuli.
hsa04014	Ras signaling pathway	The Ras proteins are GTPases that function as molecular switches for signaling pathways regulating cell proliferation, survival, growth, migration, differentiation or cytoskeletal dynamism. Ras proteins transduce signals from extracellular growth factors by cycling between inactive GDP-bound and active GTP-bound states. The exchange of GTP for GDP on RAS is regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Activated RAS (RAS-GTP) regulates multiple cellular functions through effectors including Raf, phosphatidylinositol 3-kinase (PI3K) and Ral guanine nucleotide-dissociation stimulator (RALGDS).
hsa04151	PI3K-Akt signaling pathway	The phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, translation, proliferation, growth, and survival. The binding of growth factors to their receptor tyrosine kinase (RTK) or G protein-coupled receptors (GPCR) stimulates class Ia and Ib PI3K isoforms, respectively. PI3K catalyzes the production of phosphatidylinositol-3,4,5-triphosphate (PIP3) at the cell membrane. PIP3 in turn serves as a second messenger that helps to activate Akt. Once active, Akt can control key cellular processes by phosphorylating substrates involved in apoptosis, protein synthesis, metabolism, and cell cycle.
hsa04210	Apoptosis	Apoptosis is a genetically programmed process for the elimination of damaged or redundant cells by activation of caspases (aspartate-specific cysteine proteases). The onset of apoptosis is controlled by numerous interrelating processes. The 'extrinsic' pathway involves stimulation of members of the tumor necrosis factor (TNF) receptor subfamily, such as TNFRI, CD95/Fas or TRAILR (death receptors), located at the cell surface, by their specific ligands, such as TNF-alpha, FasL or TRAIL, respectively. The 'intrinsic' pathway is activated mainly by non-receptor stimuli, such as DNA damage, ER stress, metabolic stress, UV radiation or growth-factor deprivation. The central event in the 'intrinsic' pathway is the mitochondrial outer membrane permeabilization (MOMP), which leads to the release of cytochrome c. These two pathways converge at the level of effector caspases, such as caspase-3 and caspase-7. The third major pathway is initiated by the constituents of cytotoxic granules (e.g. Perforin and Granzyme B) that are released by CTLs (cytotoxic T-cells) and NK (natural killer) cells. Granzyme B, similarly to the caspases, cleaves its substrates after aspartic acid residues, suggesting that this protease has the ability to activate members of the caspase family directly. It is the balance between the pro-apoptotic and anti-apoptotic signals that eventually determines whether cells will undergo apoptosis, survive or proliferate. TNF family of ligands activates anti-apoptotic or cell-survival signals as well as apoptotic signals. NGF and Interleukin-3 promotes the survival, proliferation and differentiation of neurons or hematopoietic cells, respectively. Withdrawal of these growth factors leads to cell death, as described above.
hsa04722	Neurotrophin signaling pathway	Neurotrophins are a family of trophic factors involved in differentiation and survival of neural cells. The neurotrophin family consists of nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), neurotrophin 3 (NT-3), and neurotrophin 4 (NT-4). Neurotrophins exert their functions through engagement of Trk tyrosine kinase receptors or p75 neurotrophin receptor (p75NTR). Neurotrophin/Trk signaling is regulated by connecting a variety of intracellular signaling cascades, which include MAPK pathway, PI-3 kinase pathway, and PLC pathway, transmitting positive signals like enhanced survival and growth. On the other hand, p75NTR transmits both positive and nagative signals. These signals play an important role for neural development and additional higher-order activities such as learning and memory.
hsa04750	Inflammatory mediator regulation of TRP channels	The TRP channels that exhibit a unique response to temperature have been given the name thermo-TRPs. Among all thermo- TRP channels, TRPV1-4, TRPM8, and TRPA1 are expressed in subsets of nociceptive dorsal root ganglion (DRG) neuron cell bodies including their peripheral and central projections. These channels can be modulated indirectly by inflammatory mediators such as PGE2, bradykinin, ATP, NGF, and proinflammatory cytokines that are generated during tissue injury. While the noxious heat receptor TRPV1 is sensitized (that is, their excitability can be increased) by post-translational modifications upon activation of G-protein coupled receptors (GPCRs) or tyrosine kinase receptors, the receptors for inflammatory mediators, the same action appears to mainly desensitize TRPM8, the main somatic innocuous cold sensor. This aforementioned sensitization could allow the receptor to become active at body temperature, so it not only contributes toward thermal hypersensitivity but also is possibly a substrate for ongoing persistent pain.
hsa05200	Pathways in cancer
hsa05202	Transcriptional misregulation in cancer	In tumor cells, genes encoding transcription factors (TFs) are often amplified, deleted, rearranged via chromosomal translocation and inversion, or subjected to point mutations that result in a gain- or loss-of- function. In hematopoietic cancers and solid tumors, the translocations and inversions increase or deregulate transcription of the oncogene. Recurrent chromosome translocations generate novel fusion oncoproteins, which are common in myeloid cancers and soft-tissue sarcomas. The fusion proteins have aberrant transcriptional function compared to their wild-type counterparts. These fusion transcription factors alter expression of target genes, and thereby result in a variety of altered cellular properties that contribute to the tumourigenic process.
hsa05216	Thyroid cancer	Thyroid cancer is the most common endocrine malignancy and accounts for the majority of endocrine cancer- related deaths each year. More than 95% of thyroid carcinomas are derived from follicular cells. Their behavior varies from the indolent growing, well-differentiated papillary and follicular carcinomas (PTC and FTC, respectively) to the extremely aggressive undifferentiated carcinoma (UC). Somatic rearrangements of RET and TRK are almost exclusively found in PTC and may be found in early stages. The most distinctive molecular features of FTC are the prominence of aneuploidy and the high prevalence of RAS mutations and PAX8-PPAR{gamma} rearrangements. p53 seems to play a crucial role in the dedifferentiation process of thyroid carcinoma.
hsa05230	Central carbon metabolism in cancer	Malignant transformation of cells requires specific adaptations of cellular metabolism to support growth and survival. In the early twentieth century, Otto Warburg established that there are fundamental differences in the central metabolic pathways operating in malignant tissue. He showed that cancer cells consume a large amount of glucose, maintain high rate of glycolysis and convert a majority of glucose into lactic acid even under normal oxygen concentrations (Warburg's Effects). More recently, it has been recognized that the 'Warburg effect' encompasses a similarly increased utilization of glutamine. From the intermediate molecules provided by enhanced glycolysis and glutaminolysis, cancer cells synthesize most of the macromolecules required for the duplication of their biomass and genome. These cancer-specific alterations represent a major consequence of genetic mutations and the ensuing changes of signalling pathways in cancer cells. Three transcription factors, c-MYC, HIF-1 and p53, are key regulators and coordinate regulation of cancer metabolism in different ways, and many other oncogenes and tumor suppressor genes cluster along the signaling pathways that regulate c-MYC, HIF-1 and p53.

Pathway ID	Pathway Name	Pathway Description (KEGG)
R-HSA-167021	PLC-gamma1 signalling.	The activation of phosphlipase C-gamma (PLC-gamma) and subsequent mobilization of calcium from intracellular stores are essential for neurotrophin secretion. PLC-gamma is activated through the phosphorylation by TrkA receptor kinase and this form hydrolyses PIP2 to generate inositol tris-phosphate (IP3) and diacylglycerol (DAG). IP3 promotes the release of Ca2+ from internal stores and this results in activation of enzymes such as protein kinase C and Ca2+ calmodulin-regulated protein kinases
R-HSA-167044	Signalling to RAS.	Signalling through Shc adaptor proteins appears to be identical for both NGF and EGF. It leads to a fast, but transient, MAPK/ERK activation, which is insufficient to explain the prolonged activation of MAPK found in NGF-treated cells
R-HSA-170968	Frs2-mediated activation.	The adaptor protein Frs2 (Fibroblast growth factor receptor substrate 2) can mediate the prolonged activation of the MAPK (ERK) cascade
R-HSA-170984	ARMS-mediated activation.	ARMS (Ankyrin-Rich Membrane Spanning/Kidins 220) is a 220kD tetraspanning adaptor protein which becomes rapidly tyrosine phosphorylated by active Trk receptors. ARMS is another adaptor protein which is involved in the activation of Rap1 and the subsequent prolonged activation of the MAPK cascade
R-HSA-177504	Retrograde neurotrophin signalling.	Neurotrophin-TRK complexes can be internalized and enter signalling vesicles, which travel retrogradely over long distances from distal nerve terminals to neuronal cell bodies. Such retrograde signalling by neurotrophin-TRK complexes regulates survival, synaptogenesis and maintenance of proper neural connectivity. The neurotrophin-TRK complex may use three distinct internalization pathways. Although Clathrin-mediated endocytosys appears to be the major internalization route, it is controversial whether it also represents the dominant pathway for retrograde transport and signalling. Pyncher-mediated endocytosis might be more relevant in this regard. Moreover, also caveolin-mediated endocytosis may play a role in NGF-TrkA internalization.Retrograde transport of TRKs is microtubule-dependent: TRKs remain activated and bound to neurotrophins during retrograde transport. The current view is reflected in the signalling endosome model. It is a specialized vesicle containing ligand (NGF, BDNF) bound to its activated TRK receptor, together with activated downstream signalling proteins, transported by motor proteins (dyneins) from nerve terminals to remote cell bodies, where the receptors trigger signalling cascades
R-HSA-187024	NGF-independant TRKA activation.	TRK receptors can also be activated by at least two G-protein-coupled receptors (GPCR), the adenosine A2a receptor and the PACAP type I receptor, without involvement of neurotrophins. Activity of both receptors is mediated by G proteins that activate adenyl cyclase. How this leads to TRKA activation has not been fully elucidated, although a SRC-family tyrosine kinase and intracellular Ca2+ appear to play a role. TRKA activation through GPCRs occurs with slow kinetics (over 1 hr adenosine or PACAP treatment is required) in an intracellular location (probably the Golgi apparatus), and requires transcriptional and protein synthesis events that may influence the processing and activation of the receptors. GPCR-mediated transactivation of TRK receptors causes the preferential activation of AKT versus ERKs. This leads to a cell survival response
R-HSA-187042	TRKA activation by NGF.	Neurotrophin functions are mediated by binding of the secreted neurotrophin homodimers to their common neurotrophin receptor p75NTR, and to their cognate tropomyosin related kinase (TRK) receptor. NGF binds to TRKA, BDNF and NT4 bind to TRKB, NT3 binds to TRKC. A tri-molecular signalling complex (NGF-p75NTR-TRKA) might also be possible
R-HSA-187706	Signalling to p38 via RIT and RIN.	RIT and RIN are two small guanine nucleotide binding proteins that share more than 50% sequence identity with RAS, including highly conserved core effector domains. Unlike RAS, the C termini of RIT and RIN lack a typical prenylation motif (CAAX, XXCC, or CXC) required for the association of RAS proteins with the plasma membrane. RIT is expressed in all tissues, whereas RIN is neuron-specific. They have similar signalling properties and are activated by NGF through unknown exchange factors. They signal to ERKs and p38 MAP kinase. They mainly lead to p38 activation via the BRAF-MEK kinase cascade
R-HSA-198203	PI3K/AKT activation.	PI3K/AKT signalling is a major regulator of neuron survival. It blocks cell death by both impinging on the cytoplasmic cell death machinery and by regulating the expression of genes involved in cell death and survival. In addition, it may also use metabolic pathways to regulate cell survival.The PI3K/AKT pathway also affects axon diameter and branching (Marcus et al, 2002) and regulates small G proteins like RhoA (Vanhaesebroeck, B and Waterman, MD, 1999), which control the behaviour of the F-actin cytoskeleton. Moreover, through its connection with the TOR pathway, it promotes translation of a subset of mRNAs
R-HSA-198745	Signalling to STAT3.	Neurotrophin-induced increase in Signal transducer and activator of transcription 3 (STAT3; acute-phase response factor) activation appears to underly several downstream functions of neurotrophin signalling, such as transcription of immediate early genes, proliferation arrest, and neurite outgrowth

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NTRK1