1G4U

CRYSTAL STRUCTURE OF THE SALMONELLA TYROSINE PHOSPHATASE AND GTPASE ACTIVATING PROTEIN SPTP BOUND TO RAC1

Functional Information from GO Data

Chain	GOid	namespace	contents
R	0000166	molecular_function	nucleotide binding
R	0000242	cellular_component	pericentriolar material
R	0001764	biological_process	neuron migration
R	0001891	cellular_component	phagocytic cup
R	0001934	biological_process	positive regulation of protein phosphorylation
R	0003376	biological_process	sphingosine-1-phosphate receptor signaling pathway
R	0003924	molecular_function	GTPase activity
R	0003925	molecular_function	G protein activity
R	0005515	molecular_function	protein binding
R	0005525	molecular_function	GTP binding
R	0005634	cellular_component	nucleus
R	0005654	cellular_component	nucleoplasm
R	0005730	cellular_component	nucleolus
R	0005737	cellular_component	cytoplasm
R	0005789	cellular_component	endoplasmic reticulum membrane
R	0005802	cellular_component	trans-Golgi network
R	0005829	cellular_component	cytosol
R	0005856	cellular_component	cytoskeleton
R	0005884	cellular_component	actin filament
R	0005886	cellular_component	plasma membrane
R	0005925	cellular_component	focal adhesion
R	0005938	cellular_component	cell cortex
R	0006911	biological_process	phagocytosis, engulfment
R	0006954	biological_process	inflammatory response
R	0007015	biological_process	actin filament organization
R	0007155	biological_process	cell adhesion
R	0007160	biological_process	cell-matrix adhesion
R	0007163	biological_process	establishment or maintenance of cell polarity
R	0007167	biological_process	enzyme-linked receptor protein signaling pathway
R	0007264	biological_process	small GTPase-mediated signal transduction
R	0008045	biological_process	motor neuron axon guidance
R	0008360	biological_process	regulation of cell shape
R	0009611	biological_process	response to wounding
R	0009653	biological_process	anatomical structure morphogenesis
R	0010310	biological_process	regulation of hydrogen peroxide metabolic process
R	0010591	biological_process	regulation of lamellipodium assembly
R	0010592	biological_process	positive regulation of lamellipodium assembly
R	0010595	biological_process	positive regulation of endothelial cell migration
R	0010762	biological_process	regulation of fibroblast migration
R	0010764	biological_process	negative regulation of fibroblast migration
R	0010810	biological_process	regulation of cell-substrate adhesion
R	0016020	cellular_component	membrane
R	0016477	biological_process	cell migration
R	0016601	biological_process	Rac protein signal transduction
R	0016787	molecular_function	hydrolase activity
R	0019899	molecular_function	enzyme binding
R	0019901	molecular_function	protein kinase binding
R	0030027	cellular_component	lamellipodium
R	0030031	biological_process	cell projection assembly
R	0030032	biological_process	lamellipodium assembly
R	0030036	biological_process	actin cytoskeleton organization
R	0030041	biological_process	actin filament polymerization
R	0030334	biological_process	regulation of cell migration
R	0030425	cellular_component	dendrite
R	0030667	cellular_component	secretory granule membrane
R	0030672	cellular_component	synaptic vesicle membrane
R	0030742	molecular_function	GTP-dependent protein binding
R	0030865	biological_process	cortical cytoskeleton organization
R	0030900	biological_process	forebrain development
R	0031410	cellular_component	cytoplasmic vesicle
R	0031529	biological_process	ruffle organization
R	0031901	cellular_component	early endosome membrane
R	0031996	molecular_function	thioesterase binding
R	0032496	biological_process	response to lipopolysaccharide
R	0032587	cellular_component	ruffle membrane
R	0032707	biological_process	negative regulation of interleukin-23 production
R	0032956	biological_process	regulation of actin cytoskeleton organization
R	0034446	biological_process	substrate adhesion-dependent cell spreading
R	0035025	biological_process	positive regulation of Rho protein signal transduction
R	0035556	biological_process	intracellular signal transduction
R	0035567	biological_process	non-canonical Wnt signaling pathway
R	0035774	biological_process	positive regulation of insulin secretion involved in cellular response to glucose stimulus
R	0036464	cellular_component	cytoplasmic ribonucleoprotein granule
R	0042470	cellular_component	melanosome
R	0042554	biological_process	superoxide anion generation
R	0042734	cellular_component	presynaptic membrane
R	0042995	cellular_component	cell projection
R	0043020	cellular_component	NADPH oxidase complex
R	0043652	biological_process	engulfment of apoptotic cell
R	0044877	molecular_function	protein-containing complex binding
R	0045202	cellular_component	synapse
R	0045211	cellular_component	postsynaptic membrane
R	0045428	biological_process	regulation of nitric oxide biosynthetic process
R	0045730	biological_process	respiratory burst
R	0046425	biological_process	regulation of receptor signaling pathway via JAK-STAT
R	0048012	biological_process	hepatocyte growth factor receptor signaling pathway
R	0048261	biological_process	negative regulation of receptor-mediated endocytosis
R	0048812	biological_process	neuron projection morphogenesis
R	0048870	biological_process	cell motility
R	0051022	molecular_function	Rho GDP-dissociation inhibitor binding
R	0051492	biological_process	regulation of stress fiber assembly
R	0051496	biological_process	positive regulation of stress fiber assembly
R	0051668	biological_process	localization within membrane
R	0051894	biological_process	positive regulation of focal adhesion assembly
R	0055038	cellular_component	recycling endosome membrane
R	0060071	biological_process	Wnt signaling pathway, planar cell polarity pathway
R	0060091	cellular_component	kinocilium
R	0060263	biological_process	regulation of respiratory burst
R	0060326	biological_process	cell chemotaxis
R	0061344	biological_process	regulation of cell adhesion involved in heart morphogenesis
R	0070062	cellular_component	extracellular exosome
R	0071526	biological_process	semaphorin-plexin signaling pathway
R	0090023	biological_process	positive regulation of neutrophil chemotaxis
R	0097178	biological_process	ruffle assembly
R	0098794	cellular_component	postsynapse
R	0098978	cellular_component	glutamatergic synapse
R	0101003	cellular_component	ficolin-1-rich granule membrane
R	0150052	biological_process	regulation of postsynapse assembly
R	1900026	biological_process	positive regulation of substrate adhesion-dependent cell spreading
R	1900029	biological_process	positive regulation of ruffle assembly
R	1900242	biological_process	regulation of synaptic vesicle endocytosis
R	1902622	biological_process	regulation of neutrophil migration
R	1903348	biological_process	positive regulation of bicellular tight junction assembly
R	1904948	biological_process	midbrain dopaminergic neuron differentiation
R	2000386	biological_process	positive regulation of ovarian follicle development
S	0004725	molecular_function	protein tyrosine phosphatase activity
S	0006470	biological_process	protein dephosphorylation
S	0016311	biological_process	dephosphorylation

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG R 1001

Chain	Residue
R	THR17
R	THR35
R	GDP1000
R	AF31002
R	HOH1072
R	HOH1073

---

site_id	AC2
Number of Residues	22
Details	BINDING SITE FOR RESIDUE GDP R 1000

Chain	Residue
R	LYS16
R	THR17
R	CYS18
R	LYS116
R	ASP118
R	SER158
R	ALA159
R	LEU160
R	MG1001
R	AF31002
R	HOH1004
R	HOH1010
R	HOH1042
R	HOH1072
R	HOH1073
S	ARG209
S	THR249
S	CYS250
S	HOH680
R	ALA13
R	VAL14
R	GLY15

---

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE AF3 R 1002

Chain	Residue
R	GLY12
R	ALA13
R	LYS16
R	THR35
R	GLY60
R	GLN61
R	GDP1000
R	MG1001
R	HOH1071
S	ARG209

---

Functional Information from PROSITE/UniProt

site_id	PS00383
Number of Residues	11
Details	TYR_PHOSPHATASE_1 Tyrosine specific protein phosphatases active site. IHClgGvgRTG

Chain	Residue	Details
S	ILE479-GLY489

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Active site: {"description":"Phosphocysteine intermediate"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	Site: {"description":"Arginine finger; crucial for GTP hydrolysis by stabilizing the transition state","evidences":[{"source":"PROSITE-ProRule","id":"PRU01404","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	8
Details	Motif: {"description":"Effector region","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"38332367","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8Q0N","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11090627","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38332367","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38355798","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1E96","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WKP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WKQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WKR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q0N","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8WEJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11090627","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38332367","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1E96","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WKP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WKQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WKR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q0N","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11090627","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1E96","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WKP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WKQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WKR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"38355798","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8WEJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	Modified residue: {"description":"(Microbial infection) O-AMP-tyrosine; by Haemophilus IbpA; alternate","evidences":[{"source":"PubMed","id":"19362538","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	Modified residue: {"description":"(Microbial infection) O-AMP-threonine; by Vibrio VopS","evidences":[{"source":"PubMed","id":"19039103","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	1
Details	Glycosylation: {"description":"(Microbial infection) O-linked (GlcNAc) tyrosine; by Photorhabdus PAU_02230; alternate","evidences":[{"source":"PubMed","id":"24141704","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	1
Details	Glycosylation: {"description":"(Microbial infection) O-linked (Glc) threonine; by C.difficile toxins TcdA and TcdB, and by P.sordellii toxin TcsL; alternate","evidences":[{"source":"PubMed","id":"19744486","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24905543","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7775453","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7777059","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"18093184","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38332367","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"23512198","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	1
Details	Annotated By Reference To The Literature 1ksj

Chain	Residue	Details
R	GLN61

---

site_id	CSA2
Number of Residues	1
Details	Annotated By Reference To The Literature 1ksj

Chain	Residue	Details
R	ALA13

---

site_id	CSA3
Number of Residues	4
Details	Annotated By Reference To The Literature 1ksj

Chain	Residue	Details
S	ASP441
S	ARG487
S	THR488
S	CYS481

---