Molecular mechanism of Afadin substrate recruitment to the receptor phosphatase PTPRK via its pseudophosphatase domain

  1. Iain M Hay
  2. Katie E Mulholland
  3. Tiffany Lai
  4. Stephen C Graham
  5. Hayley J Sharpe  Is a corresponding author
  6. Janet E Deane  Is a corresponding author
  1. Cambridge Institute for Medical Research, University of Cambridge, United Kingdom
  2. Signalling Programme, Babraham Institute, United Kingdom
  3. Department of Pathology, University of Cambridge, United Kingdom
5 figures, 1 table and 1 additional file

Figures

Figure 1 with 3 supplements
PTPRK interacts directly with the Afadin C-terminal coiled-coil (CC) region.

(A) Top: schematic of full-length human Afadin, with domain annotation based on UniProt ID P55196, showing Ras-association (RAS, yellow), CC (green), forkhead-associated (FHA, orange), dilute (DIL, …

Figure 1—figure supplement 1
Disorder predictions for Afadin.

Top: schematic of full-length human Afadin (also known as AF6 or MLLT4), with domain annotation based on UniProt ID P55196, colored as in main Figure 1A. The predicted local distance difference test …

Figure 1—figure supplement 2
Afadin-pY1230 antibody validation.

(A) Top: phosphopeptide antigen used to generate a sheep polyclonal anti-Afadin-pY1230 antibody (tthis study). Middle: amino acid numbers of epitope used to generate a mouse monoclonal against …

Figure 1—figure supplement 3
Purification of in vivo biotinylated PTP domains.

(A) Left: following Ni-NTA affinity chromatography, in vivo biotinylated PTPRK D1 and D2 domains were purified by size-exclusion chromatography (SEC) on an S75 16/600 column. Right: after SEC …

Figure 2 with 1 supplement
PTPRK:Afadin-CC forms an equimolar complex with micromolar affinity.

(A) Size-exclusion chromatography coupled to multi-angle light scattering (SEC-MALS) analysis of Afadin-CC. The SEC elution profile (normalized differential refractive index [dRI]; thin red line) …

Figure 2—figure supplement 1
GST-tag removal from Afadin-CC for size-exclusion chromatography coupled to multi-angle light scattering (SEC-MALS) and isothermal titration calorimetry (ITC) experiments.

(A) GST was removed from GST-Afadin-CC by overnight cleavage with GST-3C protease. Cleaved GST and GST-3C were removed by incubation with GSH-sepharose 4B (GSH-resin). (B) Residual cleaved GST was …

Figure 3 with 3 supplements
Structural prediction of the PTPRK-D2:Afadin-CC complex.

(A) Top: schematic of different GST-Afadin-CC truncations used for further interaction mapping experiments. Regions within the predicted helix are marked by a green bar. Dashed lines indicate …

Figure 3—figure supplement 1
Structural prediction of the PTPRK-D2:Afadin-CC complex.

(A) Ribbon diagram of the AF2-Multimer prediction for the PTPRK-D2 domain (blue) in complex with the full Afadin-CC (aa. 1393–1455, green). Afadin-CC residues that contribute to the interaction …

Figure 3—figure supplement 2
Species conservation of Afadin-CC.

Multiple-sequence alignment of the equivalent Afadin-CC region (hsAFDN aa. 1393–1455) from human (Homo sapiens), mouse (Mus musculus), dog (Canis familiaris), frog (Xenopus laevis), zebrafish (Danio …

Figure 3—figure supplement 3
Prediction quality analysis of AF2 multimer-generated PTPRK-D2:Afadin-CC complex models.

(A) The five AF2-Multimer-generated PTPRK-D2:Afadin-CC models were superposed using the PTPRK-D2 chain only. The Afadin-CC chains of each ranked model are shown as cylinders (colored as indicated) …

Figure 4 with 4 supplements
PTPRK binds Afadin-CC via an acidic pocket distal from the D2 ‘active’ site.

(A) Conservation mapping of the PTPRK-D2:Afadin-CC interface. PTPRK-D2 is shown (blue surface representation) in complex with Afadin-CC (green ribbons). Residues that are conserved in both …

Figure 4—figure supplement 1
Mapping of unique PTPRM residues.

Multiple-sequence alignment of human PTPRK, PTPRU, and PTPRM D2 domain sequences. Residues that are conserved in both PTPRK and PTPRU, but differ in PTPRM, which were used for interaction site …

Figure 4—figure supplement 2
Localization of additional PTPRK D2 mutations.

(A) Ribbon diagram of PTPRK-D2 (blue) and PTPRM-D2 (wheat) in complex with Afadin-CC (green). PTPRK-F1225 stacks with hydrophobic W1418-Y1419 residues of Afadin-CC and this residue is conserved in …

Figure 4—figure supplement 3
Thermal stability of PTPRK-D2 mutants.

Differential scanning fluorimetry of PTPRK-D2 WT (black), F1255A (red), M-loop (blue), and double mutant (DM, yellow) recombinant proteins. Curves and melting temperature (Tm) values shown represent …

Figure 4—figure supplement 4
Prediction quality of models prior to biochemical mapping.

(A) The 5 AF2-Multimer generated PTPRK-ICD:Afadin-CC models were superposed using the PTPRK-ICD chain only. The Afadin-CC chains of each ranked model are shown as cylinders (colored as indicated). (B

Figure 5 with 1 supplement
Mutation of residues at the interaction interface inhibit dephosphorylation of Afadin by PTPRK.

(A) Time course of pNPP dephosphorylation by WT (black) and double mutant (DM, red) PTPRK-ICD. Error bars represent ± SEM of n = 2 independent experiments. (B) Immunoblot analysis of …

Figure 5—figure supplement 1
PTPRK-ICD-DM displays impaired dephosphorylation of Afadin-pY1230, but not p120Cat-pY228.

Densitometric quantification of immunoblots in Figure 5B (90 min time point shown) at indicated time points. Top: Afadin-pY1230 normalized against no protein control. Middle: p120Cat-pY228 …

Tables

Appendix 1—key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Gene (human)PTPRKENSEMBL: ENSG00000152894
Gene (human)AFDNENSEMBL: ENSG00000130396
Cell line (human)MCF10AATCCCRL-10317
Cell line (human)HEK293TD. RonN/A
Transfected
construct (human)
MCF10A PTPRK
KO pooled.tGFP
Fearnley et al., 2019N/ALentivirally transduced stable cell line
Transfected
construct (human)
MCF10A PTPRK KO pooled.tGFP.
P2A.PTPRK
Fearnley et al., 2019N/ALentivirally transduced stable cell line
Transfected
construct (human)
MCF10A PTPRK KO
pooled.tGFP.P2A.
PTPRK.C1089S
Fearnley et al., 2019N/ALentivirally transduced stable cell line
Transfected
construct (human)
MCF10A tGFPFearnley et al., 2019N/ALentivirally transduced stable cell line
AntibodyAnti-PTPRK
(rabbit monoclonal)
Fearnley et al., 20192.H4Western blot: 1:1000
AntibodyAnti-Afadin-pY1230
(sheep polyclonal)
This studyN/ACharacterized in Figure 1—figure supplement 2
Western blot: 1 µg/ml
(with 10 µg/ml
non-phosphopeptide)
Available on request from Sharpe lab, Babraham Institute
AntibodyAnti-Afadin
(mouse monoclonal)
BD Transduction LaboratoriesCat#610732Western blot: 1:1000
AntibodyAnti-p120 catenin
(mouse monoclonal)
BD Transduction LaboratoriesCat#610133Western blot: 1:1000
AntibodyAnti-RFP
(mouse monoclonal)
Thermo Fisher ScientificCat#MA5-15257Western blot: 1:1000
AntibodyAnti-Turbo-GFP
(mouse monoclonal)
OriGeneTA150041Western blot: 1:1000
AntibodyAnti-Afadin
(rabbit monoclonal)
Cell Signaling TechnologyCat#13531Western blot: 1:1000
AntibodyAnti-His (mouse
monoclonal)
Cell Signaling TechnologyCat#2366Western blot: 1:1000
AntibodyAnti-phospho-tyrosine
(P-Tyr-1000) (rabbit
monoclonal)
Cell Signaling TechnologyCat#8954Western blot: 1:2000
AntibodyAnti-paxillin (rabbit monoclonal)Cell Signaling TechnologyCat#12065 (D9G12)Western blot: 1:1000
AntibodyAnti-phospho-p120
catenin (Y904)
(rabbit polyclonal)
Cell Signaling TechnologyCat#2910Western blot: 1:1000
AntibodyAnti-phospho-p120
catenin (Y228)
(rabbit polyclonal)
Cell Signaling TechnologyCat#2911Western blot: 1:1000
AntibodyAnti-phospho-
paxillin (Y118)
Cell Signaling TechnologyCat#2541Western blot: 1:1000
AntibodyAnti-Tubulin (alpha)
(mouse monoclonal)
SigmaCat#T6199Western blot: 1:1000
AntibodyHRP-conjugated-
donkey anti-goat IgG
Jackson ImmunoResearchCat#705-035-147Western blot: 1:5000
AntibodyHRP-conjugated-
donkey anti-rabbit IgG
Jackson ImmunoResearchCat#711-035-152Western blot: 1:5000
AntibodyHRP-conjugated-
donkey anti-mouse IgG
Jackson ImmunoResearchCat#711-035-152Western blot: 1:5000
AntibodyHRP-conjugated-mouse anti-
rabbit IgG (conformation specific)
Cell Signaling TechnologyCat#5127SWestern blot: 1:2000
Recombinant
DNA reagent
pET15bJ. DeaneN/A
Recombinant
DNA reagent
pET15b.His.TEV.AviFearnley et al., 2019N/A
Recombinant
DNA reagent
pET15b.His.TEV.Avi.
PTPRK.ICD
Fearnley et al., 2019UniProt: Q15262-3
Recombinant
DNA reagent
pET15b.His.TEV.Avi.
PTPRK.ICD.D1057A
Fearnley et al., 2019UniProt: Q15262-3
Recombinant
DNA reagent
pET15b.His.TEV.Avi.
PTPRK.ICD.C1089S
Fearnley et al., 2019UniProt: Q15262-3
Recombinant
DNA reagent
pET15b.His.TEV.Avi.
PTPRK.D1
Fearnley et al., 2019UniProt: Q15262-3
Recombinant
DNA reagent
pET15b.His.TEV.Avi.
PTPRK.D2
Fearnley et al., 2019UniProt: Q15262-3
Recombinant
DNA reagent
PET15b.His.TEV.Avi.
PTPRK.D2.G1273H
This studyUniProt: Q15262-3Mutations: G1273H
See Figure 4
Recombinant
DNA reagent
pET15b.His.TEV.Avi.
PTPRK.D2.L1335R
This studyUniProt: Q15262-3Mutations: L1335R

See Figure 4D
Recombinant
DNA reagent
pET15b.His.TEV.Avi.
PTPRK.ICD.DM
This studyUniProt: Q15262-3Mutations: G1273H L1335R
See Figure 4E
Recombinant
DNA reagent
pET15b.His.TEV.Avi.
PTPRK.D2.DM
This studyUniProt: Q15262-3Mutations: G1273H L1335R
See Figure 4E
Recombinant
DNA reagent
pET15b.His.TEV.Avi.
PTPRK.D2.F1225A
This studyUniProt: Q15262-3Mutation: F1225A
See Figure 4H
Recombinant
DNA reagent
pET15b.His.TEV.Avi.
PTPRK.D2.M-loop
This studyUniProt: Q15262-3Mutations: C1372Y E1373N
E1374G
See Figure 4H
Recombinant
DNA reagent
pGEX-6P-1J. DeaneN/A
Recombinant
DNA reagent
pGEX-6P-Afadin-1098-C*This studyUniProt: P55196-4See Figure 1E
Recombinant
DNA reagent
pGEX-6P-Afadin-1098-1507This studyUniProt: P55196-4See Figure 1E
Recombinant
DNA reagent
pGEX-6P-Afadin-1098-1407This studyUniProt: P55196-4See Figure 1
Recombinant DNA reagentpGEX-6P-Afadin-1514-C*This studyUniProt: P55196-4See Figure 1E
Recombinant DNA reagentpGEX-6P-Afadin-1393-C*This studyUniProt: P55196-4See Figure 1E
Recombinant DNA reagentpGEX-6P-Afadin-1393-1507This studyUniProt: P55196-4See Figure 1E
Recombinant DNA reagentpGEX-6P-Afadin-CCThis studyUniProt: P55196-4Encoding amino acids: 1393–1455

See Figure 1F
Recombinant DNA reagentpGEX-6P-Afadin-CC-WY>AAThis studyUniProt: P55196-4Mutations: W1418A Y1419A
See Figure 3D
Recombinant DNA reagentpGEX-6P-Afadin-CC-ER>AAThis studyUniProt: P55196-4Mutations: E1429A R1430A
See Figure 3D
Recombinant DNA reagentpGEX-6P-Afadin-CC-RK>AAThis studyUniProt: P55196-4Mutations: R1432A K1433A
See Figure 3D
Recombinant DNA reagentpGEX-6P-Afadin-CC-Q>AThis studyUniProt: P55196-4Mutations: Q1443A
See Figure 3D
Recombinant DNA reagentpGEX-6P-Afadin-CC-T>AThis studyUniProt: P55196-4Mutations: T1446A
See Figure 3D
Recombinant DNA reagentpGEX-6P-Afadin-CC-QT>AAThis studyUniProt: P55196-4Mutations: Q1443A T1446A
See Figure 3D
Recombinant DNA reagentpmScarlet-C1Z. KadlecovaN/A
Recombinant DNA reagentpmScarlet-AfadinThis studyUniProt: P55196-4See Figure 1—figure supplement 2D
Recombinant DNA reagentpmScarlet-Afadin-Y1226FThis studyUniProt: P55196-4Mutation: Y1226F
See Figure 1—figure supplement 2D
Recombinant DNA reagentpmScarlet-Afadin-Y1230FThis studyUniProt: P55196-4Mutation: Y1230F
See Figure 1—figure supplement 2D
Recombinant DNA reagentpmScarlet-Afadin-YF YFThis studyUniProt: P55196-4Mutations: Y1226F Y1230F
See Figure 1—figure supplement 2D
Sequence-based reagentON-TARGETplus
Human AFDN siRNA:
Dharmacon, GE HealthcareL-020075-02-0005
Sequence-based reagentON-TARGETplus
Non-targeting pool siRNA:
Dharmacon, GE HealthcareCat#D-001810-10-05
Peptide, recombinant proteinCatalaseSigmaCat#C134514
Peptide, recombinant proteinCholera toxinSigmaCat#C-8052
Peptide, recombinant proteinInsulinSigmaCat#I-1882
Peptide, recombinant proteinEpidermal growth factorPeproTechCat#AF-100-15-1MG
Commercial assay or kitQ5 High-Fidelity
DNA Polymerase
New England BiolabsCat#M0491S
Commercial assay or kitPhusion Hot Start II
DNA polymerase
Thermo Fisher ScientificCat#F549L
Commercial assay or kitEZ-ECL substrateGeneflowCat#K1-0170
Commercial assay or kitInstantBlueExpedeonCat#ISB1L
Commercial assay or kitPhosphatase inhibitor cocktailRocheCat#04906845001
Commercial assay or kitTaqMan Universal Master Mix IIApplied BiosystemsCat#4440040
Chemical compound, drugHydrogen peroxideThermo Fisher ScientificCat#H/1750/15
Chemical compound, drugSodium orthovanadateAlfa AesarCat#J60191
Chemical compound, drug250 kDa-FITC-dextranSigmaCat#FD250S-100MG
Chemical compound, drugPara-Nitrophenol-
phosphate (pNPP)
New England BiolabsCat#P0757
Chemical compound, drugIPTGGeneronCat#GEN-S-02122
Chemical compound, drugD-biotinSigmaCat#B4639
Chemical compound, drugl-GlutamineSigmaCat#G7513
Chemical compound, drugHydrocortisoneSigmaCat#H-0888
Chemical compound, drugNH4OHAcros OrganicsCat#460801000
Chemical compound, drugMethanol-free 16%
(w/v) paraformaldehyde (PFA)
Thermo Fisher ScientificCat#28906
Software, algorithmFIJI/ImageJLaboratory for Optical and
Computational Instrumentation
University of Wisconsin-Madison
Software, algorithmGraphPadPrism
Software, algorithmChimeraUCSF
Strain, strain
background
(Escherichia coli)
STABLE competent E. coliNEBCat#C3040I
Strain, strain
background (E. coli)
DH5alpha competent E. coliInvitrogenCat#18265017
Strain, strain
background (E. coli)
BL21 DE3
Rosetta E. coli
J. DeaneN/A
OtherDMEMThermo Fisher ScientificCat#41965-039Component of cell culture media
OtherHam's F-12SigmaCat#N4888Component of cell culture media
OtherHorse serumThermo Fisher ScientificCat#16050-122Component of cell culture media
OtherHRP-conjugated streptavidinThermo Fisher ScientificCat#434323For detection of biotinylated proteins
OtherFetal bovine serumSigmaCat#F7524-500mlComponent of cell culture media
OtherTrypsin-EDTA solutionSigmaCat#T3924Reagent used to lift cells
from culture vessel
OtherGeneJuiceMerck MilliporeCat#70967-3Transfection reagent
OtherEDTA-free protease inhibitorsRocheCat#11836170001Component of cell lysis buffer
OtherLipofectamine
RNAiMAX
InvitrogenCat#13778075Transfection reagent
OtherOptiMEMThermo Fisher ScientificCat#31985070Component of cell culture media
OtherProtein G agarose
beads
Merck MilliporeCat#16-266Affinity reagent for
immunoprecipitations
OtherNi-NTA agaroseQIAGENCat#1018244Affinity reagent for His-tag purification
OtherStreptavidin-coated
magnetic beads
New England BiolabsCat#S1420SAffinity reagent for Avi-tag pull-downs
OtherStreptavidin agaroseThermo Fisher ScientificCat#20357Affinity reagent for Avi-tag pull-downs
OtherSuperdex 200 16/600 columnGE HealthcareCat#28-9893-35Chromatography column
OtherSuperdex 75 16/600 columnGE HealthcareCat#28-9893-33Chromatography column
OtherUltracel-3K regenerated
cellulose centrifugal filter
Merck MilliporeCat#UFC900324Chromatography column
OtherUltracel-10K regenerated
cellulose centrifugal filter
Merck MilliporeCat#UFC901024Used for protein concentration
OtherUltracel-30K regenerated
cellulose centrifugal filter
Merck MilliporeCat#UFC903024Used for protein concentration
OtherNuPAGE 4–12% Bis-Tris gelThermo Fisher ScientificCat#NP0321BOXSDS PAGE electrophoresis gel
OtherSlide-A-Lyzer 20K MWCOThermo Fisher ScientificCat#66003Dialysis cassette
OtherSYPRO Orange dyeThermo Fisher ScientificCat#S6650Used for thermal shift assays
OtherMycoAlert PLUS
Mycoplasma Detection Kit
Lonza#LT07-705Used for testing cell lines
OtherMycoProbe Mycoplasma
Detection Kit
R&D Systems#CUL001BUsed for testing cell lines

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