Voltage sensitive phosphatases: Emerging kinship to protein tyrosine phosphatases from structure-function research

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Abstract

The transmembrane protein Ci-VSP from the ascidian Ciona intestinalis was described as first member of a fascinating family of enzymes, the voltage sensitive phosphatases (VSPs). Ci-VSP and its voltage-activated homologs from other species are stimulated by positive membrane potentials and dephosphorylate the head groups of negatively charged phosphoinositide phosphates (PIPs). In doing so, VSPs act as control centers at the cytosolic membrane surface, because they intervene in signaling cascades that are mediated by PIP lipids. The characteristic motif CX5RT/S in the active site classifies VSPs as members of the huge family of cysteine-based protein tyrosine phosphatases (PTPs). Although PTPs have already been well-characterized regarding both, structure and function, their relationship to VSPs has drawn only limited attention so far. Therefore, the intention of this review is to give a short overview about the extensive knowledge about PTPs in relation to the facts known about VSPs. Here, we concentrate on the structural features of the catalytic domain which are similar between both classes of phosphatases and their consequences for the enzymatic function. By discussing results obtained from crystal structures, molecular dynamics simulations, and mutagenesis studies, a possible mechanism for the catalytic cycle of VSPs is presented based on that one proposed for PTPs. In this way, we want to link the knowledge about the catalytic activity of VSPs and PTPs.

Figures

  • FIGURE 1 | Overview about the classification scheme of cysteine-based PTPs. Members of individual subfamilies, which were exemplarily chosen and discussed in the main text, are listed in their respective PTP subclass. The preferred substrates of these phosphatases are given. Substrates that can be dephosphorylated, but with less preference are mentioned in parentheses.
  • FIGURE 2 | Structural comparison of the catalytic domains of cysteine-based PTPs. (A) Catalytic domains of exemplary chosen phosphatases are shown. The twisted β-sheet core is colored in blue; the α-helices surrounding the core are shown in red. The α-helix C-terminal to the active site loop is depicted in cyan, and the regions corresponding to the P-, TI- andWPD-loop of class I PTPs in yellow (see text for details). In case of Cdc25s, noTI- andWPD-loop exist. The structure of Ci-VSP was taken from the MD simulation (Hobiger et al., 2013) which was performed on the basis of the crystal structure by Matsuda et al. (2011; PDB accession number 3awe). All other structures were created based on the crystal structures available in the RCSB protein data bank. The accession numbers are: 1nwe (hu-PTP1B), 1ygu (hu-CD45. Here, the catalytically active domain D1 is shown.), 1d5r (hu-PTEN), 1vhr (hu-VHR), 1dg9 (bt-BHPTP), and 1qb0 (hu-Cdc25B).
  • FIGURE 3 | Loop regions determine the conformation of the substrate binding pocket in cysteine-based PTPs. (A) Sequence alignment of the three loops which specify the conformation of the substrate binding pocket. The P-loop contains the highly conserved CX5R motif that serves as active site. The WPD-/DPYY- and the TI-/V-loops form the side walls of the substrate binding pocket in class I and II PTPs. Because class III PTPs lack the two latter loops, no sequence alignment could be performed for these regions. Amino acids identified as identical to Ci-VSP are marked in gray. Yellow colored residues are crucial for catalysis and widely conserved among PTPs. UniProt accession numbers are indicated for all sequences
  • FIGURE 4 | Catalytic cycle for cysteine-based PTPs. (A) In the resting state, the sulfur of the catalytic cysteine is stabilized in an anionic thiolate form. This is mediated by a hydrogen bond between the sulfur and the hydroxyl oxygen of the conserved Thr-/Ser-side chain located in the P-loop. Upon binding of the substrate, where the P-loop arginine is particularly involved in the positioning of the substrate, the thiolate acts as catalytic nucleophile by attacking the phosphorus atom of the substrate. The formation of a cysteinyl-phosphate intermediate is facilitated by a general acid (usually an aspartate from the WPD- or DPYY-loop flanking the active site), which donates a proton to the substrate leaving group. Subsequently,
  • FIGURE 5 | Redox modification of the catalytically active side chain in cysteine-based PTPs. (A)The amino acid motif of Ci-VSP, which contains Cys310 as putative interaction partner for the disulfide-bridge with the catalytic Cys363, is aligned with sequences of VSP homologs from various species (Dr, Danio rerio; Gg, Gallus gallus; Xl, Xenopus laevis; hu, human). Additionally, PTEN isoforms from different species are included in this alignment. Amino acid identities to Ci-VSP are colored in gray. Cys310 and the corresponding position in the respective proteins are marked in yellow. (B) For Ci-VSP, the disulfide bridge between Cys310 and the catalytic Cys363 is shown as it has been identified in a crystal structure of the cytosolic domain (PDB accession number 3awg; Matsuda et al., 2011). (C) In crystal structures of the human PTP1B, the formation of a sulphenyl-amide bond has been observed between the P-loop Ser216 and the catalytically active Cys215 (PDB 1oes; van Montfort et al., 2003).
  • FIGURE 6 | An activated water molecule is required for the second step in catalysis of class I PTPs. (A)The substrate binding pocket is structurally aligned for the human PTP1B (in light blue, PDB accession number 3ib0), human PTEN (in yellow, PDB 1d5r), and Ci-VSP [in orange, modeled by MD simulation based on the crystal structure of Matsuda et al. (2011) and Hobiger et al. (2013) PDB 3awe]. The glutamines from theTI-loop of hu-PTP1B and the corresponding amino acids in the other PTPs, the invariant aspartate from theWPD-loop, and the catalytic cysteine from the P-loop are represented as sticks. (B–D)The substrate binding pockets are shown individually for the three PTPs with the following ligands bound to the active site, as found in the respective crystal structures: L(+)-tartrate in hu-PTEN, vanadate in hu-PTP1B, and sulfate in Ci-VSP. One water molecule is coordinated adjacently to the aspartate and the ligand by theTI-loop glutamines in hu-PTP1B (C) and by corresponding residues in Ci-VSP (D). (B)This water molecule is absent in hu-PTEN. Thr167 that corresponds to Gln262 in hu-PTP1B and Glu411 in Ci-VSP is oriented away from the active site. One of the oxygen atoms of the bound tartrate forms a hydrogen bond with the nitrogen of Gln171.

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Hobiger, K., & Friedrich, T. (2015). Voltage sensitive phosphatases: Emerging kinship to protein tyrosine phosphatases from structure-function research. Frontiers in Pharmacology. Frontiers Media S.A. https://doi.org/10.3389/fphar.2015.00020

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