Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states

  1. David Yin-wei Lin
  2. Lauren E Kueffer
  3. Puneet Juneja
  4. Thomas E Wales
  5. John R Engen
  6. Amy H Andreotti  Is a corresponding author
  1. Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, United States
  2. Cryo-EM Facility, Office of Biotechnology, Iowa State University, United States
  3. Department of Chemistry and Chemical Biology, Northeastern University, United States
8 figures, 3 tables and 2 additional files

Figures

Current Bruton’s tyrosine kinase (BTK) structural data.

(a) Comparison of the SRC and TEC domain architectures. Linker regions and domains are labeled, residue numbering shows BTK domain boundaries. The ‘Src module’ is the SH3–SH2–kinase region shred by both families. (b) Autoinhibited BTK core (Src module). The compact structure of the SH3–SH2–kinase region of BTK is exacted from the domain swapped dimer structure (PDB: 4XI2) solved by Wang et al., 2015. The three domains (SH3, SH2, and kinase), the SH2–kinase linker, the activation loop and the active site are labeled. (c) Structure of the BTK Pleckstrin homology/Tec homology (PHTH) domain bound to inositol 1,3,4,5-tetrakisphosphate (IP4; PDB: 1B55) (Baraldi et al., 1999). The monomer is shown for clarity and the TH region bound to Zn2+ is circled. (d) Structure of the tethered PHTH–kinase construct (PDB: 4Y93). (e) Solution-based mapping of BTK PHTH interaction across the activation loop face of the kinase domain.

Figure 2 with 1 supplement
Stabilization of the Bruton’s tyrosine kinase (BTK) SH3–SH2–kinase core.

(a) Mutations introduced into the SH2–kinase linker region of BTK (residues 382–396). PXPP indicates the region that adopts the left-handed, type II polyproline helix in the autoinhibited structure of BTK SH3–SH2–kinase. (b) Western blot showing the kinase activity of wild-type (WT) BTK, 4P, L390F, 4P1F, and ITKLoop BTK variants. Autophosphorylation on BTK is monitored using an anti-pY551 antibody and total protein levels are monitored by Coomassie stain. (c) Melting temperatures of BTK WT and variants (see Figure 2—figure supplement 1). (d) Distance distribution functions and structural parameters (Rg and Dmax) comparing the SH3–SH2–kinase fragment and full-length BTK (wild-type and 4P1F). (e) Surface representation of ab initio envelope reconstructions obtained from small angle X-ray scattering (SAXS) superimposed on the crystal structures for the BTK SH3–SH2–kinase fragment (top). Elongated envelopes for both full-length wild-type (FL WT) BTK and the full-length 4P1F mutant of BTK are shown without structure superposition (bottom). Figure 2—figure supplement 1 provides Guinier and Kratky plots for all four BTK proteins. SASBDB accession codes are as follows: SASDRB9, SASDRC9, SASDRD9, and SASDRE9.

Figure 2—figure supplement 1
Tm and SAXS analyses.

(a) Tm curves and (b) first derivatives for panel of Bruton’s tyrosine kinase (BTK) variants (c) Guinier and (d) Kratky plots for BTK variants.

Crystallization of full-length Bruton’s tyrosine kinase (BTK).

(a) The crystallization target, full-length BTK with stabilized core (FL BTKsc), included (1) SH2–kinase linker mutations (4P1F: A384P, S386P, T387P, A388P, and L390F); (2) activation loop mutations (ITKLoop: L542M, S543T, V555T, R562K, S564A, and P565S); (3) catalytic residue mutation (K430R); and (4) surface entropy reduction mutations (E298A, K300A, and E301A). The N-terminal domains, Pleckstrin homology/Tec homology (PHTH)–proline-rich region (PRR)–SH3, are wild-type BTK sequence. (b, c) Structure of the BTK domain swapped dimer that results from crystallization of full-length BTK (PDB: 8GMB). PHTH–PRR region is missing from the electron density. One SH3–SH2–kinase monomer is shown in (b) and the autoinhibited SH3–SH2–kinase arrangement is circled in (c). Domain colors match those in (a) and the activation loop in the kinase domain is orange. (d) Sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE) showing full-length BTK protein from crystals. Lane 1 is a purified full-length BTK control and lane 2 is protein derived from harvested and washed crystals. (e) Two views of crystal packing with the PHTH domain (red) modeled into one of the solvent channels.

Figure 4 with 2 supplements
Full-length Bruton’s tyrosine kinase (BTK) cryo-electron microscopy (cryoEM) analysis.

(a) 2D class averages of full-length BTK. (b) Representative 2D class averages. White arrow indicates extra density adjacent to the BTK SH3–SH2–kinase core density. (c–e) Three final 3D reconstructions (see workflow in Figure 4—figure supplement 1). (c) Two views of the Class 0 map with the SH3–SH2–kinase fragment (PDB: 8GMB) fit into the larger density and monomeric Pleckstrin homology/Tec homology (PHTH) domain (PDB: 1B55) fit into the smaller globular density. Continuous density between the large and small density is indicated with a dashed circle. (d) Two views of the Class 1 map with globular density fit as described for (c). The smaller globular density is located in a distinct position with respect to the SH3–SH2–kinase core compared to that shown in (c). Additionally, unmodeled density is observed adjacent to the BTK SH3–SH2–kinase core (dashed circle); the position is similar to the continuous density observed in Class 0. (e) Three views of the Class 3 map with fitted BTK SH3–SH2–kinase core and unmodeled density that is in the same location as that in (d). EMDB accession codes are as follows: EMD-40585, EMD-40586, and EMD-40587. Map fitting without user input was also carried out using Situs (Wriggers, 2012). The result of that fitting is comparable to results obtained using Chimera.

Figure 4—figure supplement 1
Workflow showing cryo-electron microscopy (cryoEM) analysis of full-length Bruton’s tyrosine kinase (BTK).
Figure 4—figure supplement 2
Deuterium uptake curves for the Pleckstrin homology/Tec homology (PHTH) through SH3 domain of Bruton’s tyrosine kinase (BTK).

Domain boundaries for the PHTH and the start of the SH3 domain are indicated. Uptake curves for peptides derived from the linker between PHTH and SH3 (residues 171–214) are boxed in red. The complete HDX dataset is provided in the supplemental data file.

Crystallization of loosely tethered Pleckstrin homology/Tec homology (PHTH)–kinase.

(a) Architecture of the loosely tethered PHTH–kinase constructs used for crystallography. (b) Crystal structure of the PHTH–kinase protein (PDB: 8S93). The PHTH domain (red) docks onto the back of the kinase domain N-lobe (blue). The location of the phosphatidylinositol (3,4,5)-trisphosphate (PIP3)-binding pocket on PHTH is indicated. (c) Direct comparison of the loosely tethered PHTH–kinase structure solved here (left, PDB: 8S93) and the more tightly tethered PHTH–kinase structure solved previously (right, PDB: 4Y93, right). The PHTH domain helix is colored yellow and the kinase domains are in the same orientation to emphasize the difference between the PHTH domains in the two structures. (d) PHTH/kinase interface. PHTH side chains R133, Y134, and R171 (red) make contacts to the Bruton’s tyrosine kinase (BTK) domain (blue). Dotted lines indicate hydrogen bonds. (e) Close-up view of the hydrophobic stack (flanked by W421 and Y461) on the kinase domain N-lobe. The PHTH Y134 residue (red) inserts into the hydrophobic stack (blue) in the loosely tethered PHTH–kinase structure solved here while L390 from the SH2–kinase linker (gray) completes the hydrophobic stack in the previously solved PHTH–kinase structure (PDB: 4Y93).

Bruton’s tyrosine kinase (BTK) activity assays.

(a–c) Representative progress curves, catalytic rate comparisons, and time to threshold ADP for the PH–KD construct. Wild-type BTK Pleckstrin homology/Tec homology (PHTH)–kinase protein is compared with single, double, and triple mutants to probe the PHTH/kinase interface. Ibrutinib inhibition leads to reduction of ADP production (black curve in all experiments). (d–f) Representative progress curves, catalytic rate comparisons, and time to threshold ADP for full-length BTK. Wild-type BTK is compared to the following full-length BTK mutants: R133E/Y134E/R171E, W251K, or W251K/R133E/Y134E/R171E. (g–i) Representative progress curves, catalytic rate comparisons, and time to threshold ADP for full-length WT BTK and R133E/Y134E/R171E mutant in the presence of either control or phosphatidylinositol (3,4,5)-trisphosphate (PIP3) liposomes. (a, d, g) Representative progress curves of ADP production by BTK are from one of the three independent experiments, and each data point is the average of at least two replicates. Bar graphs (b, e, h) represent the average kinase activity rate ± standard error calculated from the boxed region of the corresponding progress curves. Bar graphs (c, f, i) represent the average time to a threshold value of ADP, indicated by dashed line on progress curves. Open circles on all bar graphs represent specific values in each independent experiment. For reactions for which the threshold ADP value is not reached (WT BTK in panels f and i) the values are reported as 180 min. The effect of mutations compared with the wild-type BTK was evaluated by Student’s t-test (*p < 0.05; **p < 0.01; ***p < 0.001; ns, not significant).

Bruton’s tyrosine kinase (BTK) dimer.

(a) Crystal structure of the BTK kinase domain dimer (PDB: 8S9F). Monomers are shown in gray and blue with one represented in cartoon and the other surface rendered. The C-helix, β3 strand, G-helix, and bound dasatinib are labeled. The region containing the swapped activation loops is indicated with a dashed circle. The portion of the activation loop for which electron density is missing is indicated with a dashed blue line. (b, c) Side chain interactions mediating the N- and C-lobe dimer interfaces, respectively. (d) Close-up view of activation loop of one monomer extending into the active site of the other monomer. Electron density is absent between Y545 and K558 (indicated with blue spheres). Dashed line indicates possible path for the 13 missing residues that contain Y551. Superimposed on the BTK dimer structure are the PKC kinase domain structure bound to substrate (PDB: 4DC2, green) and insulin-like growth factor 1 receptor kinase bound to substrate (PDB: 1K3A, red); kinase domains are excluded for clarity. The serine and tyrosine phosphoacceptors on these substrates are positioned close to the putative location of BTK Y551 (white circle). (e) Unusual ‘DFG-up’ conformation. In the BTK kinase dimer, F540 inserts between K430 and E445 preventing formation of the salt bridge associated with active kinases. (f) Comparison of regulatory spine structures for active BTK kinase domain (PDB: 3K54), inactive BTK (PDB: 3GEN), and the ‘DFG-up’ structure solved here (PDB: 8S9F). F540 is orange and other R-spine residues are in blue. W395 is at the top of the R-spine in BTK; the ‘DFG-up’ configuration stabilizes the active rotamer of W395 (Joseph et al., 2010; Chopra et al., 2016).

Bruton’s tyrosine kinase (BTK) activation model.

(a) Inactive, autoinhibited BTK, the conformational heterogeneity of the Pleckstrin homology/Tec homology (PHTH) domain is indicated in fuzzy red. The hydrophobic stack residues, W421 and Y461, are indicated on the kinase domain N-lobe as WY . (b) Engagement of the BTK SH3 and SH2 domains with exogenous ligands would allow for the PHTH domain to adopt its autoinhibitory pose. Surface rendering of structure solved here (PDB: 8S93) is included, accessibility of the inositol 1,3,4,5-tetrakisphosphate (IP4)/phosphatidylinositol (3,4,5)-trisphosphate (PIP3)-binding site is shown, and hydrophobic stack resides are indicated as in (a). (c) Two PHTH–kinase structures are superimposed on the Saraste PHTH dimer (PDB: 1B55). The top model indicates potential for electrostatic repulsion between membrane and BTK kinase domain in this arrangement (negative charges indicated by ----- and arrows suggest unfavorable interactions between negatively charged surfaces). A 90° rotation (bottom) shows the acidic patch on the kinase domain and the PIP3-binding sites on the PHTH domain (circled) are on the same surface of the structure. (d) Release of all autoinhibitory contacts and dimerization of the BTK kinase domain (PDB: 8S9F) lead to autophosphorylation on Y551 in the activation loop of each kinase domain.

Tables

Key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Recombinant DNA reagentFL BTK-C6H pET20 (plasmid)DOI: 10.1016/j.str.2017.07.014Residues 1–659 wIth Y617P mutation, UniProt: P35991
Recombinant DNA reagentFL BTK-C6H Q91A, I92A, I94A, and I95A pET20 (plasmid)This paperResidues 1–659 wIth Y617P mutation
Recombinant DNA reagentFL BTK-C6H A384P, S386P, T387P, and A388P pET20 (plasmid)This paperResidues 1–659 wIth Y617P mutation
Recombinant DNA reagentFL BTK-C6H A384P, S386P, T387P, A388P, and L390F pET20 (plasmid)This paperResidues 1–659 wIth Y617P mutation
Recombinant DNA reagentFL BTK-C6H L542M, S543T, V555T, R562K, S564A, and P565S pET20 (plasmid)This paperResidues 1–659 wIth Y617P mutation
Recombinant DNA reagentSH3-SH2-kinase BTK-C6H pET20 (plasmid)This paperResidues 214–659 wIth Y617P mutation
Recombinant DNA reagentSH3-SH2-kinase BTK-C6H A384P, S386P, T387P, A388P, and L390F pET20 (plasmid)This paperResidues 214–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-FL BTK pET20 (plasmid)This paperResidues 1–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-FL BTK W251K pET20 (plasmid)This paperResidues 1–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-FL BTK R133E/Y134E/R171E pET20 (plasmid)This paperResidues 1–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-FL BTK R133E/Y134E/R171E/W251K pET20 (plasmid)This paperResidues 1–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-FL BTKsc pET20 (plasmid)This paperResidues 1–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-FL BTKsc Δ185–194 pET20 (plasmid)This paperResidues 1–184, 195–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-FL BTKsc Δ185–206 pET20 (plasmid)This paperResidues 1–184, 207–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-FL BTKsc Δ181–206 pET20 (plasmid)This paperResidues 1–180, 207–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-FL BTKsc Δ175–210 pET20 (plasmid)This paperResidues 1–174, 211–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-FL BTKsc Δ173–215 pET20 (plasmid)This paperResidues 1–172, 216–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-1PHTH171-G(GGSGG)4G-396kinase659 Q91A, I92A, I94A, I95A, K430R, L542M, S543T, V555T, R562K, S564A, and P565S pET28 (plasmid)This paperResidues 1–171, 396–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-1PHTH171-G(GGSGG)6G-396kinase659 Q91A, I92A, I94A, I95A, K430R, L542M, S543T, V555T, R562K, S564A, and P565S pET28 (plasmid)This paperResidues 1–171, 396–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-1PHTH176-G(GGSGG)4G-384kinase659 pET28 (plasmid)This paperResidues 1–176, 384–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-1PHTH176-G(GGSGG)4G-384kinase659 R133E pET28 (plasmid)This paperResidues 1–176, 384–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-1PHTH176-G(GGSGG)4G-384kinase659 Y134E pET28 (plasmid)This paperResidues 1–176, 384–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-1PHTH176-G(GGSGG)4G-384kinase659 R133E/Y134E pET28 (plasmid)This paperResidues 1–176, 384–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO-1PHTH176-G(GGSGG)4G-384kinase659 R133E/Y134E/171E pET28 (plasmid)This paperResidues 1–176, 384–659 wIth Y617P mutation
Recombinant DNA reagentN6H-SUMO KD Y551E/L390G pET20 (plasmid)This paperResidues 382–659 wIth Y617P mutation
Recombinant DNA reagentpCDFDuet YopHThomas E. Smithgall
Strain, strain background (Escherichia coli)BL21 (DE3)Thermo Fisher Scientific Cat#C600003https://www.thermofisher.com/order/catalog/product/C600003
Other1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC)Avanti Polar Lipids Cat#850375Phttps://avantilipids.com/product/850375
Other1,2-Dioleoyl-sn-glycero-3-phospho-L-serine (DOPS)Avanti Polar Lipids Cat#840035Phttps://avantilipids.com/product/840035
Other1,2-Dioleoyl-sn-glycero-3-phosphoinositol-3,4,5-trisphosphate (tetra-ammonium salt) (PIP3)Avanti Polar Lipids Cat#850156Phttps://avantilipids.com/product/850156
OtherPyruvate Kinase/Lactic DehydrogenaseMilliporeSigma Cat#P0294https://www.sigmaaldrich.com/US/en/product/sigma/p0294?gclid=EAIaIQobChMIobDx8MqZgwMVyVdyCh1-egAIEAAYASAAEgLOzPD_BwE
OtherSYPRO Protein Gel StainsThermo Fisher Scientific Cat#S6650https://www.thermofisher.com/order/catalog/product/S6650
OtherPhusion Hot Start II DNA PolymeraseThermo Fisher Scientific Cat#F549Lhttps://www.thermofisher.com/order/catalog/product/F549L?SID=srch-srp-F549L
AntibodyBD Pharmingen Purified Mouse anti-Btk (pY551)/Itk (pY511) (mouse monoclonal)BD Biosciences Cat#558034WB (1:1000)
Software, algorithmCootDOI: 10.1107/S0907444910007493 v0.9.8.8https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Software, algorithmautoPROCDOI: 10.1107/S0907444911007773 v20211020https://www.globalphasing.com/autoproc/
Software, algorithmXDSDOI: 10.1107/S0907444909047337 v20220110https://xds.mr.mpg.de/
Software, algorithmSTARANISODOI: 10.1107/S010876731809640X v3.350https://staraniso.globalphasing.org/staraniso_about.html
Software, algorithmCCP4i suiteDOI:10.1107/S2059798323003595 v0.8https://www.ccp4.ac.uk/
Software, algorithmPhaserDOI: 10.1107/S0021889807021206 v2.8https://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software
Software, algorithmPhenixDOI: 10.1107/S2059798319011471 v1.20-4459https://phenix-online.org/
Software, algorithmCryoSparcStructura Biotechnology Inc v4.1.2https://cryosparc.com/
Software, algorithmPyMOLShrodinger LLC v2.5.5https://www.pymol.org/
Software, algorithmDynamXWATERS v3.0https://www.waters.com/nextgen/us/en.html
Software, algorithmPLGSWATERS v3.0https://www.waters.com/nextgen/us/en.html
Software, algorithmFrameSliceThe SIBYLS Beamline N/Ahttps://sibyls.als.lbl.gov/ran
Software, algorithmBioXTAS RAWDOI: 10.1107/S1600576717011438 v2.1.4https://bioxtas-raw.readthedocs.io/en/latest/
Software, algorithmATSAS: ALMERGEEMBL Hamburg v3.2.1https://www.embl-hamburg.de/biosaxs/manuals/almerge.html
Software, algorithmChimeraUCSF v1.15https://www.cgl.ucsf.edu/chimera/
Table 1
Data collection and refinement statistics.
FL Btk,PHTH/KD complex*,KD with dasatinib,
PDB codes8GMB8S938S9F
Data collection
Space groupP 31 2 1P 1 21 1P 1 21 1
Cell dimensions
a, b, c (Å)125.72, 125.72, 110.0938.38, 77.38, 82.3255.24, 110.04, 61.14
α, β, γ (°)90, 90, 12090, 97.98, 9090, 99.51, 90
Resolution (Å)§108.88–3.19 (3.53–3.19)81.53–2.00 (2.20–2.00)55.02–2.50 (2.79–2.50)
Spherical data completeness (%)§67.7 (13.2)54.5 (13.6)69.7 (12.5)
Ellipsoidal data completeness (%)§94.2 (70.4)84.1 (78.5)91.8 (52.0)
Rmerge§0.27 (>1)0.13 (0.80)0.26 (>1)
Rmeas§0.27 (>1)0.16 (0.95)0.396 (>1)
CC1/2§0.998 (0.74)0.99 (0.54)0.99 (0.56)
Mean I /σ§17.8 (2.0)7.1 (1.6)11.2 (1.4)
Multiplicity§88.5 (82.2)3.7 (3.3)14.8 (14.9)
Refinement
Resolution (Å)§19.58–3.40 (3.52–3.40)19.71–2.10 (2.18–2.10)19.96–2.60 (2.69–2.60)
Number of reflections§11,205 (295)21,392 (572)17,286 (300)
Rwork / Rfree (%)27.63/28.9319.95/24.8624.34/28.95
Number of non-hydrogen atoms316837594167
Protein311935254034
Ligand/ion93108118
Water017867
Average B-factor157.6939.8978.30
Protein158.1540.1578.73
Ligand/ion128.6036.7374.73
Water35.7456.37
Ramachandran statistics
Favored (%)93.7297.6296.59
Allowed (%)6.052.383.41
Outliers (%)0.230.000.00
Clashscore6.561.693.27
R.m.s. deviations
Bond lengths (Å)0.0020.0020.002
Bond angles (°)0.430.490.43
  1. *

    X-ray data from a single crystal.

  2. X-ray data from multiple crystals.

  3. X-ray data anisotropically corrected with the STARANISO webserver (Global Phasing).

  4. §

    Statistics for the highest resolution shell are shown in parentheses.

Author response table 1
Fit-in-mapSitus
Class 00.71810.6144
Class 10.70030.6277
Class 30.62730.5798

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  1. David Yin-wei Lin
  2. Lauren E Kueffer
  3. Puneet Juneja
  4. Thomas E Wales
  5. John R Engen
  6. Amy H Andreotti
(2024)
Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states
eLife 12:RP89489.
https://doi.org/10.7554/eLife.89489.3