SASDFC2: Urokinase plasminogen activator surface receptor, uPAR K50C-V70C,...

Basic information

• Entry: Database: SASBDB / ID: SASDFC2

Sample

Urokinase plasminogen activator surface receptor, uPAR K50C-V70C, complex with urokinase-type plasminogen activator (Amino Terminal Fragment, ATF).

• Urokinase plasminogen activator surface receptor (protein), uPAR, Homo sapiens
• Urokinase-type plasminogen activator (Amino Terminal Fragment) (protein), ATF, Homo sapiens

Function / homology

Function:

cell-matrix adhesion mediator activity / urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / protein complex involved in cell-matrix adhesion / Regulation of FXIIa and plasma kallikrein activity / positive regulation of extracellular matrix disassembly / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of integrin-mediated signaling pathway / positive regulation of homotypic cell-cell adhesion / regulation of fibrinolysis / regulation of wound healing / negative regulation of plasminogen activation / serine-type endopeptidase complex / regulation of smooth muscle cell migration / Dissolution of Fibrin Clot / regulation of cell adhesion mediated by integrin / protein localization to cell surface / positive regulation of DNA binding / extrinsic component of membrane / plasminogen activation / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of release of cytochrome c from mitochondria / regulation of proteolysis / tertiary granule membrane / negative regulation of fibrinolysis / FXIIa activates plasma kallikrein-kinin system / regulation of cell adhesion / fibrinolysis / cell-matrix adhesion / specific granule membrane / positive regulation of protein phosphorylation / blood coagulation / chemotaxis / enzyme activator activity / signaling receptor activity / positive regulation of cell migration / receptor ligand activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / external side of plasma membrane / protein domain specific binding / signaling receptor binding / focal adhesion / negative regulation of apoptotic process / Neutrophil degranulation / endoplasmic reticulum membrane / enzyme binding / cell surface / signal transduction / : / proteolysis / extracellular exosome / extracellular region / membrane / plasma membrane

Domain/homology:

CD59 antigen, conserved site / Ly-6 / u-PAR domain signature. / u-PAR/Ly-6 domain / Ly-6 antigen / uPA receptor -like domain / Ly-6 antigen/uPA receptor-like / Snake toxin-like superfamily / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan

Component:

Urokinase-type plasminogen activator / Urokinase plasminogen activator surface receptor

• Biological species: Homo sapiens (human)
• Citation: Journal: J Biol Chem / Year: 2019; Title: Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?; Authors: Julie M Leth / Haydyn D T Mertens / Katrine Zinck Leth-Espensen / Thomas J D Jørgensen / Michael Ploug / ; Abstract: The urokinase receptor (uPAR) is a founding member of a small protein family with multiple Ly6/uPAR (LU) domains. The motif defining these LU domains contains five plesiotypic disulfide bonds stabilizing its prototypical three-fingered fold having three protruding loops. Notwithstanding the detailed knowledge on structure-function relationships in uPAR, one puzzling enigma remains unexplored. Why does the first LU domain in uPAR (DI) lack one of its consensus disulfide bonds, when the absence of this particular disulfide bond impairs the correct folding of other single LU domain-containing proteins? Here, using a variety of contemporary biophysical methods, we found that reintroducing the two missing half-cystines in uPAR DI caused the spontaneous formation of the corresponding consensus 7-8 LU domain disulfide bond. Importantly, constraints due to this cross-link impaired (i) the binding of uPAR to its primary ligand urokinase and (ii) the flexible interdomain assembly of the three LU domains in uPAR. We conclude that the evolutionary deletion of this particular disulfide bond in uPAR DI may have enabled the assembly of a high-affinity urokinase-binding cavity involving all three LU domains in uPAR. Of note, an analogous neofunctionalization occurred in snake venom α-neurotoxins upon loss of another pair of the plesiotypic LU domain half-cystines. In summary, elimination of the 7-8 consensus disulfide bond in the first LU domain of uPAR have significant functional and structural consequences.

Contact author

• Haydyn Mertens (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #2811: ; Type: dummy / Radius of dummy atoms: 3.00 A; Comment: Refined DAMMIN model from average volume (10 DAMMIF iterations); Chi-square value: 1.433; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Urokinase plasminogen activator surface receptor, uPAR K50C-V70C, complex with urokinase-type plasminogen activator (Amino Terminal Fragment, ATF).; Specimen concentration: 0.30-2.50 / Entity id: 66 / 1481
• Buffer: Name: 20 mM PBS, 5 %(v/v) glycerol / pH: 7.4

Entity #66

Name: uPAR / Type: protein
Description: Urokinase plasminogen activator surface receptor
Formula weight: 36.98 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q03405
Sequence:

MGHPPLLPLL LLLHTCVPAS WGLRCMQCKT NGDCRVEECA LGQDLCRTTI VRLWEEGEEL ELVEKSCTHS EKTNRTLSYR TGLKITSLTE VVCGLDLCNQ GNSGRAVTYS RSRYLECISC GSSDMSCERG RHQSLQCRSP EEQCLDVVTH WIQEGEEGRP KDDRHLRGCG YLPGCPGSNG FHNNDTFHFL KCCNTTKCNE GPILELENLP QNGRQCYSCK GNSTHGCSSE ETFLIDCRGP MNQCLVATGT HEPKNQSYMV RGCATASMCQ HAHLGDAFSM NHIDVSCCTK SGCNHPDLDV QYRSGAAPQP GPAHLSLTIT LLMTARLWGG TLLWT

Entity #1481

Name: ATF / Type: protein
Description: Urokinase-type plasminogen activator (Amino Terminal Fragment)
Formula weight: 16.099 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P00749
Sequence:

MRALLARLLL CVLVVSDSKG SNELHQVPSN CDCLNGGTCV SNKYFSNIHW CNCPKKFGGQ HCEIDKSKTC YEGNGHFYRG KASTDTMGRP CLPWNSATVL QQTYHAHRSD ALQLGLGKHN YCRNPDNRRR PWCYVQVGLK PLV

Experimental information

• Beam: Instrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: Urokinase plasminogen activator surface receptor, uPAR K50C-V70C, complex with urokinase-type plasminogen activator (Amino Terminal Fragment, ATF).
Measurement date: May 5, 2017 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.0226	5.0354

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 1074 /

	Min	Max
Q	0.0913838	3.04188
P(R) point	1	1074
R	0	9

Result

Type of curve: extrapolated
Comments: Introduced disulfide in the first LU domain, DI, of uPAR (K50C-V70C).

	Experimental	Standard	Porod
MW	51.9 kDa	51.9 kDa	38.6 kDa
Volume	-	-	65.6 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.04019	0.001	0.04024	0.001
Radius of gyration, Rg	2.659 nm	0.01	2.64 nm	0.01

	Min	Max	Error
D	-	9	0.5
Guinier point	1	146	-