Structural basis for the specificity of PPM1H phosphatase for Rab GTPases. (28th September 2021)

• Record Type: Journal Article
• Authors: Waschbüsch, Dieter; Berndsen, Kerryn; Lis, Pawel; Knebel, Axel; Lam, Yuko PY; Alessi, Dario R; Khan, Amir R
• Is Part Of: EMBO reports. Volume 22:Number 11(2021)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2021-09-28
• Subjects: crystal structure -- LRRK2 kinase -- membrane trafficking -- PPM1H phosphatase -- Rab GTPase; Molecular biology -- Periodicals; Molecular Biology -- Periodicals; Molecular biology; Periodicals; 572.8
• DOI: 10.15252/embr.202152675
• Languages: English
• ISSNs: 1469-221X

Abstract

Abstract: LRRK2 serine/threonine kinase is associated with inherited Parkinson's disease. LRRK2 phosphorylates a subset of Rab GTPases within their switch 2 motif to control their interactions with effectors. Recent work has shown that the metal‐dependent protein phosphatase PPM1H counteracts LRRK2 by dephosphorylating Rabs. PPM1H is highly selective for LRRK2 phosphorylated Rabs, and closely related PPM1J exhibits no activity towards substrates such as Rab8a phosphorylated at Thr72 (pThr72). Here, we have identified the molecular determinant of PPM1H specificity for Rabs. The crystal structure of PPM1H reveals a structurally conserved phosphatase fold that strikingly has evolved a 110‐residue flap domain adjacent to the active site. The flap domain distantly resembles tudor domains that interact with histones in the context of epigenetics. Cellular assays, crosslinking and 3‐D modelling suggest that the flap domain encodes the docking motif for phosphorylated Rabs. Consistent with this hypothesis, a PPM1J chimaera with the PPM1H flap domain dephosphorylates pThr72 of Rab8a both in vitro and in cellular assays. Therefore, PPM1H has acquired a Rab‐specific interaction domain within a conserved phosphatase fold. Synopsis: PPM1H phosphatase belongs to the PPM (PP2C) family of enzymes that have a conserved Mg 2+ /Mn 2+ ‐dependent catalytic domain. PPM1H counters the LRRK2 kinase pathway by dephosphorylating a subset of Rab GTPases. Through X‐ray, biochemical and cellular studies, the molecular basis for specificity can be attributed to a novel flap domain that has evolved to recognize Rab GTPases. Mutations in the flap domain reduce the ability of PPM1H to hydrolyze a phosphorylated threonine in the switch 2 helix of Rab8a and Rab10 Grafting of the PPM1H flap domain onto PPM1J phosphatase is sufficient to enable PPM1J to dephosphorylate Rab8a and Rab10 both in vitro and in cellular assays A hydrophobic N‐terminal anchor that is conserved in PPM1H, PPM1J and PPM1M contributes to folding of their catalytic domains Abstract : PPM1H phosphatase counters the LRRK2 kinase pathway by dephosphorylating a subset of Rab GTPases. Structural, biochemical and cellular assays attribute the molecular basis for substrate specificity to a novel flap domain that has evolved to recognize Rab GTPases.