4EKU

Crystal Structure of FERM Domain of Proline-rich Tyrosine Kinase 2

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	FERM_C_FAK1	e4ekuA4	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: FERM_C_FAK1	ECOD (1.6)
A	FERM_M	e4ekuA1	A: alpha bundles	X: Acyl-CoA binding protein-like (From Topology)	H: Acyl-CoA binding protein-like (From Topology)	T: Acyl-CoA binding protein-like	F: FERM_M	ECOD (1.6)
A	KOG4257	e4ekuA3	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG4257	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	1.20.80.10	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein		CATH (4.3.0)
A	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21477	FAK1/PYK2, FERM domain C-lobe (FERM_C_FAK1)	FAK1/PYK2, FERM domain C-lobe	FAK1 (focal adhesion kinase 1) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells and it is involved in diverse cellular roles. The N-terminal region of FAK1 contains a FERM domain which is subdivided FERM_N or A-lo ...	FAK1 (focal adhesion kinase 1) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells and it is involved in diverse cellular roles. The N-terminal region of FAK1 contains a FERM domain which is subdivided FERM_N or A-lobe, FERM_M or B-lobe and FERM_C or C-lobe. This entry represents the C-lobe, which is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites [1-5]. This domain is also present in protein-tyrosine kinase 2-beta (also known as PYK2), a cytoplasmic, non-receptor tyrosine kinase which is a close paralogue to FAK in vertebrates. FRMPD1/3/4 also contain this domain; FRMPD1 regulates the subcellular location of activator of G-protein signaling 3 and its interaction with G-proteins. FRMPD4 has been shown to regulate dendritic spine morphogenesis and the function of FRMPD3 is not clear.	Domain
A	PF00373	FERM central domain (FERM_M)	FERM central domain	This domain is the central structural domain of the FERM domain.	Domain
A	PF18038	FERM N-terminal domain (FERM_N_2)	FERM N-terminal domain	This entry represents the FERM N-terminal domain found in focal adhesion kinases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Protein-tyrosine kinase 2-beta	protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 3-phosphoinositide-dependent protein kinase binding protein binding kinase binding enzyme binding protein kinase binding non-membrane spanning protein tyrosine kinase activity protein-containing complex binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding histone H2AXY142 kinase activity histone modifying activity histone kinase activity histone H2AX kinase activity protein serine/threonine kinase activity calcium/calmodulin-dependent protein kinase activity histone H3Y41 kinase activity histone H3 kinase activity neurotransmitter receptor regulator activity molecular function regulator activity signaling receptor regulator activity signaling receptor binding glutamate receptor binding	regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process positive regulation of nitric oxide metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process reactive nitrogen species metabolic process positive regulation of nitric oxide metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process cellular process metabolic process regulation of nitric oxide metabolic process positive regulation of nitric oxide biosynthetic process regulation of metabolic process positive regulation of cellular process response to stimulus response to chemical response to xenobiotic stimulus cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process positive regulation of signal transduction signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality trans-synaptic signaling regulation of signaling cell surface receptor signaling pathway nervous system process cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion cell adhesion cell-matrix adhesion positive regulation of cell-substrate adhesion regulation of cell-matrix adhesion response to stress response to ischemia apoptotic process cell death programmed cell death response to lipid response to oxygen-containing compound cellular response to oxygen-containing compound response to retinoic acid cellular response to chemical stimulus cellular response to retinoic acid cellular response to lipid developmental process sexual reproduction cellular developmental process reproductive process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism developmental maturation developmental process involved in reproduction female gamete generation gamete generation oocyte development anatomical structure maturation cell differentiation anatomical structure development germ cell development oocyte maturation oocyte differentiation cell maturation regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cell projection organization neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development positive regulation of cell projection organization cellular component organization or biogenesis system development plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization response to cation stress response to osmotic stress response to abiotic stimulus response to salt stress regulation of postsynaptic specialization assembly cellular component biogenesis cellular component assembly cell junction assembly regulation of excitatory synapse assembly postsynaptic density organization regulation of synapse structure or activity synapse organization regulation of synapse assembly regulation of postsynaptic density organization postsynapse organization organelle assembly postsynaptic specialization assembly postsynapse assembly regulation of postsynapse organization regulation of cellular component biogenesis regulation of organelle organization excitatory synapse assembly regulation of cell junction assembly regulation of synapse organization organelle organization cell junction organization regulation of organelle assembly postsynaptic specialization organization synapse assembly postsynaptic density assembly regulation of postsynaptic density assembly cellular response to stress response to fluid shear stress cellular response to fluid shear stress mononuclear cell differentiation mature B cell differentiation B cell activation involved in immune response lymphocyte activation cell activation involved in immune response lymphocyte differentiation marginal zone B cell differentiation leukocyte activation B cell differentiation leukocyte activation involved in immune response lymphocyte activation involved in immune response mature B cell differentiation involved in immune response immune response hemopoiesis B cell activation cell activation immune effector process immune system process leukocyte differentiation protein phosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process defense response cellular defense response regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of molecular function positive regulation of protein modification process regulation of phosphate metabolic process positive regulation of macromolecule metabolic process positive regulation of protein kinase activity positive regulation of protein phosphorylation positive regulation of transferase activity positive regulation of phosphorus metabolic process regulation of protein metabolic process positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of phosphorylation regulation of phosphorus metabolic process response to organophosphorus response to nitrogen compound response to purine-containing compound response to cAMP protein-containing complex organization signal complex assembly protein-containing complex assembly response to hydrogen peroxide response to oxidative stress response to reactive oxygen species regulation of growth growth positive regulation of cell growth regulation of cell growth cell growth positive regulation of growth negative regulation of potassium ion transport regulation of localization regulation of potassium ion transport transport regulation of transport negative regulation of monoatomic ion transport regulation of monoatomic ion transport negative regulation of biological process negative regulation of transport establishment of localization metal ion transport localization monoatomic ion transport potassium ion transport monoatomic cation transport regulation of metal ion transport intracellular signal transduction positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission positive regulation of synaptic transmission, glutamatergic negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process negative regulation of cellular process regulation of cytoskeleton organization regulation of actin filament-based process actin cytoskeleton organization regulation of actin cytoskeleton organization actin filament-based process cytoskeleton organization response to cytokine response to chemokine cytokine-mediated signaling pathway cellular response to chemokine chemokine-mediated signaling pathway response to peptide G protein-coupled receptor signaling pathway cellular response to cytokine stimulus response to hexose response to monosaccharide response to carbohydrate response to glucose reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation cortical cytoskeleton organization positive regulation of organelle organization regulation of cellular component size regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of protein polymerization regulation of actin filament polymerization protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin filament polymerization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of actin polymerization or depolymerization actin filament organization positive regulation of supramolecular fiber organization regulation of protein polymerization regulation of actin filament length regulation of supramolecular fiber organization supramolecular fiber organization positive regulation of actin filament polymerization regulation of anatomical structure size response to immobilization stress positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion regulation of developmental process regulation of cell differentiation regulation of cell development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal development negative regulation of developmental process regulation of myeloid cell differentiation negative regulation of myeloid cell differentiation myeloid cell differentiation regulation of hemopoiesis ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway positive regulation of receptor signaling pathway via STAT peptidyl-amino acid modification regulation of receptor signaling pathway via JAK-STAT activation of protein kinase activity regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via STAT peptidyl-tyrosine modification positive regulation of receptor signaling pathway via JAK-STAT activation of Janus kinase activity peptidyl-tyrosine phosphorylation cell surface receptor signaling pathway via JAK-STAT cell surface receptor protein tyrosine kinase signaling pathway vascular endothelial growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway gliogenesis glial cell proliferation protein autophosphorylation peptidyl-tyrosine autophosphorylation regulation of B cell chemotaxis positive regulation of chemotaxis regulation of lymphocyte chemotaxis taxis regulation of mononuclear cell migration positive regulation of immune system process chemotaxis regulation of leukocyte chemotaxis positive regulation of lymphocyte migration regulation of leukocyte migration lymphocyte migration response to external stimulus positive regulation of leukocyte chemotaxis leukocyte migration B cell chemotaxis regulation of response to external stimulus lymphocyte chemotaxis regulation of lymphocyte migration positive regulation of lymphocyte chemotaxis positive regulation of response to external stimulus positive regulation of mononuclear cell migration positive regulation of B cell chemotaxis cell chemotaxis positive regulation of leukocyte migration regulation of chemotaxis mononuclear cell migration leukocyte chemotaxis adaptive immune response response to metal ion response to calcium ion actomyosin structure organization actin filament bundle organization contractile actin filament bundle assembly actin filament bundle assembly stress fiber assembly endothelial cell migration blood vessel endothelial cell migration blood vessel morphogenesis tube development angiogenesis sprouting angiogenesis vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development positive regulation of JNK cascade JNK cascade regulation of JNK cascade postsynaptic modulation of chemical synaptic transmission ERBB signaling pathway epidermal growth factor receptor signaling pathway macrophage chemotaxis macrophage migration regulation of macrophage migration myeloid leukocyte migration regulation of macrophage chemotaxis response to decreased oxygen levels response to hypoxia response to oxygen levels cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway response to tumor necrosis factor focal adhesion assembly cell-substrate junction assembly cell-substrate junction organization regulation of calcium ion transport intracellular calcium ion homeostasis calcium ion transport monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of release of sequestered calcium ion into cytosol inorganic ion transmembrane transport inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol regulation of transmembrane transport chemical homeostasis cellular localization inorganic ion homeostasis homeostatic process monoatomic ion transmembrane transport calcium ion homeostasis regulation of monoatomic ion transmembrane transport negative regulation of sequestering of calcium ion maintenance of location in cell regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis regulation of sequestering of calcium ion calcium ion transmembrane import into cytosol sequestering of calcium ion cellular homeostasis regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis tissue homeostasis bone resorption response to hormone response to endogenous stimulus positive regulation of cytosolic calcium ion concentration positive regulation of endothelial cell migration regulation of endothelial cell migration catabolic process proteolysis involved in protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis protein catabolic process regulation of catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process modification-dependent protein catabolic process positive regulation of proteolysis ubiquitin-dependent protein catabolic process integrin-mediated signaling pathway regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process response to alcohol response to ethanol regulation of cell shape cell morphogenesis regulation of cell morphogenesis regulation of anatomical structure morphogenesis positive regulation of translation positive regulation of macromolecule biosynthetic process post-transcriptional regulation of gene expression gene expression translation macromolecule biosynthetic process regulation of gene expression positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process endothelin receptor signaling pathway response to mechanical stimulus negative regulation of cell population proliferation regulation of vasculature development positive regulation of developmental process positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis positive regulation of multicellular organismal process regulation of synaptic plasticity muscle cell apoptotic process regulation of muscle cell apoptotic process negative regulation of muscle cell apoptotic process regulation of DNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of DNA biosynthetic process DNA metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of DNA metabolic process DNA biosynthetic process regulation of DNA metabolic process negative regulation of signaling negative regulation of synaptic transmission negative regulation of cell communication long-term synaptic depression long-term synaptic potentiation response to cocaine response to alkaloid negative regulation of biomineral tissue development regulation of biomineral tissue development regulation of bone mineralization negative regulation of bone mineralization ossification biomineral tissue development bone mineralization animal organ development tissue development negative regulation of ossification negative regulation of multicellular organismal process regulation of ossification	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol neuron spine synapse neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse cell junction dendrite cellular anatomical structure intracellular anatomical structure cytoplasm cytosol neuron spine synapse neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse cell junction dendrite dendritic tree cell body anchoring junction focal adhesion cell-substrate junction protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex NMDA selective glutamate receptor complex receptor complex cell periphery ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex Schaffer collateral - CA1 synapse apical dendrite cell leading edge lamellipodium glutamatergic synapse intracellular organelle cytoskeleton organelle membraneless organelle intracellular membraneless organelle perinuclear region of cytoplasm neuronal cell body postsynaptic density, intracellular component postsynaptic specialization postsynaptic specialization, intracellular component postsynaptic density neuron to neuron synapse asymmetric synapse cell cortex presynapse growth cone axon distal axon site of polarized growth membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A	IPR000719	Protein kinase domain	Domain
A	IPR017441	Protein kinase, ATP binding site	Binding Site
A	IPR014352	FERM/acyl-CoA-binding protein superfamily	Homologous Superfamily
A	IPR049385	FAK1-like, FERM domain C-lobe	Domain
A	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A	IPR019749	Band 4.1 domain	Domain
A	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A	IPR000299	FERM domain	Domain
A	IPR041784	FAK1/PYK2, FERM domain C-lobe	Domain
A	IPR008266	Tyrosine-protein kinase, active site	Active Site
A	IPR019748	FERM central domain	Domain
A	IPR041390	Focal adhesion kinase, N-terminal	Domain
A	IPR035963	FERM superfamily, second domain	Homologous Superfamily
A	IPR036137	Focal adhesion kinase, targeting (FAT) domain superfamily	Homologous Superfamily
A	IPR011993	PH-like domain superfamily	Homologous Superfamily
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR005189	Focal adhesion kinase, targeting (FAT) domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q14289	melanoma status epilepticus skin neoplasm skin cancer Petit mal status primitive neuroectodermal tumor subependymal giant cell astrocytoma astrocytic tumor malignant ependymoma oligodendroglioma Pick disease Takayasu arteritis atypical teratoid rhabdoid tumor cutaneous melanoma large cell medulloblastoma melanoma status epilepticus skin neoplasm skin cancer Petit mal status primitive neuroectodermal tumor subependymal giant cell astrocytoma astrocytic tumor malignant ependymoma oligodendroglioma Pick disease Takayasu arteritis atypical teratoid rhabdoid tumor cutaneous melanoma large cell medulloblastoma malignant glioma osteosarcoma pilocytic astrocytoma Alzheimer disease autism spectrum disorder glioblastoma lung carcinoma medulloblastoma non-small cell lung carcinoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.