Research ArticleStructural Biology

Structural basis for the preference of the Arabidopsis thaliana phosphatase RLPH2 for tyrosine-phosphorylated substrates

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Science Signaling  03 Apr 2018:
Vol. 11, Issue 524, eaan8804
DOI: 10.1126/scisignal.aan8804

Substrate specificity of an unusual phosphatase

The plant phosphatase RLPH2 is a member of the phosphoserine- and phosphothreonine-specific protein phosphatase (PPP) family; however, it prefers substrates that contain phosphotyrosine residues to those that contain phosphoserine or phosphothreonine residues. Labandera et al. solved crystal structures of RLPH2 both in its native form and in complex with the phosphate mimic tungstate and performed biochemical assays with various mutant forms of RLPH2. These approaches revealed the structural basis for the preference of RLPH2 for phosphotyrosine, particularly substrates that are dually phosphorylated on both tyrosine and a nearby threonine residue. These findings explain the unusual properties of this phosphatase, and the preference for substrates containing a pTxpY motif suggests that mitogen-activated protein kinases (MAPKs) may be substrates for RLPH2 in vivo.


Despite belonging to the phosphoserine- and phosphothreonine-specific phosphoprotein phosphatase (PPP) family, Arabidopsis thaliana Rhizobiales-like phosphatase 2 (RLPH2) strongly prefers substrates bearing phosphorylated tyrosine residues. We solved the structures of RLPH2 crystallized in the presence or absence of sodium tungstate. These structures revealed the presence of a central domain that forms a binding site for two divalent metal ions that closely resembles that of other PPP-family enzymes. Unique structural elements from two flanking domains suggest a mechanism for the selective dephosphorylation of phosphotyrosine residues. Cocrystallization with the phosphate mimetic tungstate also suggests how positively charged residues that are highly conserved in the RLPH2 class form an additional pocket that is specific for a phosphothreonine residue located near the phosphotyrosine residue that is bound to the active site. Site-directed mutagenesis confirmed that this auxiliary recognition element facilitates the recruitment of dual-phosphorylated substrates containing a pTxpY motif.

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