Protein tyrosine phosphatases: structure, function, and implication in human disease

Abstract

Protein tyrosine phosphorylation is a key regulatory mechanism in eukaryotic cell physiology. Aberrant expression or function of protein tyrosine kinases and protein tyrosine phosphatases can lead to serious human diseases, including cancer, diabetes, as well as cardiovascular, infectious, autoimmune, and neuropsychiatric disorders. Here, we give an overview of the protein tyrosine phosphatase superfamily with its over 100 members in humans. We review their structure, function, and implications in human diseases, and discuss their potential as novel drug targets, as well as current challenges and possible solutions to developing therapeutics based on these enzymes.

Fig. 1

Common PTP catalytic mechanism

Fig. 2

Structures of human PTP catalytic domains. Cartoon representation of human PTP catalytic domain structures, divided by family/subfamily, and colored by secondary structure (α-helices in red, β-strands in yellow, loops in green)

Fig. 3

Ribbon representation of the classical class I PTP catalytic domain, colored by NtoC, with tungstate (shown in ball-and-stick representation) bound into the active site (PTP1B; PDB ID: 2HNQ). Conserved residues important for catalysis are highlighted in ball-and-stick representation: catalytic cysteine (C215) and invariant arginine (R221) of the P-loop; WPD-loop residues, including the catalytic acid/base aspartate (D181); conserved glutamine (Q262) of the Q-loop; tyrosine (Y46) of the pTyr-recognition loop (pTyr-loop); conserved glutamate (E115) of the E-loop

Fig. 4

WPD-loop conformations. PTP1B closed state (magenta; PDB ID: 1SUG), PTP1B open state (lime; PDB ID: 2HNP), STEP atypical open state (blue, PDB ID: 2BV5), and LYP atypical open state (white; PDB ID: 2P6X). Catalytic cysteine and catalytic aspartate residues shown in stick representation, conserved tryptophan and proline shown in line representation

Fig. 5

The pTyr-loop. (a) pTyr-loop (blue) relative to the P-loop (lime), with bound pTyr-peptide (white) (PTP1B; PDB ID: 1PTT). The conserved tyrosine (Y46 in PTP1B) defines the depth of the catalytic pocket and facilitates pTyr binding through aromatic π−π interactions. The conserved aspartate or asparagine (D48 in PTP1B) stabilizes substrate binding through bipartite hydrogen bonding interaction with backbone nitrogen atoms of the substrate peptide. (b) Same complex as in (a) but with PTP1B rendered in surface representation (blue, most positive; red, most negative). (In addition to the interactions listed in (a), R47 of the PTP1B pTyr-loop is labeled, the side chain of which interacts with the glutamate in the −1 position of the substrate peptide, highlighting the fact that PTP1B favors substrates with acidic residues at this position)

Fig. 6

The E-loop. (a) The E-loop (green) relative to the P-loop (red) and WPD-loop (yellow) (PTP1B; PDB ID: 2HNQ). In this structure, the WPD-loop is in the open conformation and the E-loop forms a tight β-hairpin, with the E-loop glutamate (E115, shown in stick representation) neutralizing the charge of the conserved P-loop arginine (R221). (b) The E-loop (green) relative to the P-loop (red) and WPD-loop (yellow) (PTP1B; PDB ID: 2B4S). In this structure, the WPD-loop is in the closed conformation and the E-loop does not form a β-hairpin and is partially disordered. The E-loop lysine (K120) and catalytic aspartate of the WPD-loop (both shown in stick representation) form a hydrogen bond, and a sulfate molecule is bound at the active site (1° SO₄) and at a secondary binding site (2° SO₄), which neutralizes the charge of the P-loop arginine

Fig. 7

Binding of a small-molecule phosphate (methylenebis(4,1-phenylene) bis(dihydrogen phosphate); shown in stick representation) to the “second site” in PTP1B (PDB ID: 1AAX; shown as ribbon diagram (left panel) and surface representation (right panel; blue, most positive; red, most negative). Second-site residues Arg24 and Arg 254, as well as gateway residue Gly259 are shown in stick representation (left panel)

Fig. 8

Activation of SHP2 by binding of specific pTyr-containing proteins

Fig. 9

SHP2 interactions and signaling pathways in hematopoietic cells. Direct interactions are indicated by solid lines, indirect interactions by dashed lines (adapted from ref. 158)

Fig. 10

Model of glutamate receptor internalization through Aβ-mediated activation of STEP. Aβ activates the α7 nicotinic receptor, leading to Ca²⁺ influx and activation of calcineurin [197]. Calcineurin subsequently dephosphorylates and activates STEP. Concomitantly, Aβ also elevates STEP protein levels through inhibition of the ubiquitin proteasome system [203]. STEP dephosphorylates a regulatory tyrosine residue in both the NR2B and GluR2 glutamate receptor subunits, leading to internalization of the receptors [199, 200]. As a result, synaptic function is disrupted (Figure from ref. , with permission)

Fig. 11

(a–d) Comparison of ligand binding to PTP1B in closed state (a/b; PDB ID: 2QBS) and open state (c/d; PDB ID: 3EAX). The protein surface in (a) and (c) is colored by electrostatic potential as calculated and rendered in ICM (blue, most positive; red, most negative; the colors were capped at ±5 kcal/electron units). Macroshape representations as rendered in ICM (blue, deepest depression; green, largest protrusion) illustrate the differences between the active site pockets in closed (b) and open conformation (d). White arrows indicate the position of the P-loop, black arrows indicate the WPD-loop in closed state (a) and open state (c). (e) Comparison of PTP1B with WPD-loop in closed (blue; PDB ID 2QBS) and open (grey; PDB ID 3EAX) conformation. The white arrow indicates the P-loop, the green arrow indicates the WPD-loop. (f–j) Comparison of open state conformation in PTP1B (f; PDB ID 3EB1), TCPTP (g; PDB ID 1L8K), LYP (h; PDB ID 2P6X), LAR (i; PDB ID 1LAR), and RPTPγ (j; PDB ID 2H4V). The protein surface is colored by electrostatic potential as calculated and rendered in ICM (blue, most positive; red, most negative; the colors were capped at ±5 kcal/electron units)

Fig. 12

Allosteric inhibition of PTPs. (a) Crystal structure of PTP1B complexed with an allosteric inhibitor (compound 2, shown in ball-and-stick representation); catalytic Cys215 and Asp181 are shown as spheres (PDB ID: 1T49, ref. 34). (b) Comparison of the allosteric site in PTP1B (as in (a)) with corresponding sites in STEP (PDB ID: 2BV5), SHP2 (PDB ID: 3B7O), and SHP1 (PDB ID: 1GWZ). Structures are superimposed; proteins are shown in surface representation (blue, most positive; red, most negative); compound 2 is shown as reference in all structures. (c) Scanning-insertional mutagenesis using FlAsH and a FlAsH-binding peptide (TetraCys: CCPGCC) inserted at position Ala79 identifies a potential allosteric site in TCPTP. To illustrate the location of the identified allosteric site, the crystal structure of TCPTP (PDB ID: 1L8K) is shown as surface and ribbon representation; Ala79, Cys216, and D182 are shown as spheres. The PTP allosteric inhibitor (compound 2) is superimposed for orientation

Fig. 13

Comparison of reduced and oxidized states of PTP1B. (a) Ribbon diagram of PTP1B in reduced state (blue; PDB ID: 2HNP) and PTP1B in oxidized, sulphenyl-amide state (green, PDB ID: 1OEM). P-loop Cys215 and Ser216 residues, which form the sulphenyl-amide five-membered ring, and pTyr-loop Tyr46 residues are shown in stick representation. (b/c) Surface representation (blue, most positive; red, most negative) of PTP1B in the reduced state (b) and oxidized state (c)