Structural and biochemical analysis of atypically low dephosphorylating activity of human dual-specificity phosphatase 28

Abstract

Dual-specificity phosphatases (DUSPs) constitute a subfamily of protein tyrosine phosphatases, and are intimately involved in the regulation of diverse parameters of cellular signaling and essential biological processes. DUSP28 is one of the DUSP subfamily members that is known to be implicated in the progression of hepatocellular and pancreatic cancers, and its biological functions and enzymatic characteristics are mostly unknown. Herein, we present the crystal structure of human DUSP28 determined to 2.1 Å resolution. DUSP28 adopts a typical DUSP fold, which is composed of a central β-sheet covered by α-helices on both sides and contains a well-ordered activation loop, as do other enzymatically active DUSP proteins. The catalytic pocket of DUSP28, however, appears hardly accessible to a substrate because of the presence of nonconserved bulky residues in the protein tyrosine phosphatase signature motif. Accordingly, DUSP28 showed an atypically low phosphatase activity in the biochemical assay, which was remarkably improved by mutations of two nonconserved residues in the activation loop. Overall, this work reports the structural and biochemical basis for understanding a putative oncological therapeutic target, DUSP28, and also provides a unique mechanism for the regulation of enzymatic activity in the DUSP subfamily proteins.

Structural and biochemical characterization of Siw14: A protein-tyrosine phosphatase fold that metabolizes inositol pyrophosphates

“…Therefore, we conclude that the oligomerization reflects crystallographic packing effects. Such artifacts have been observed for some other DUSPs, most of which also appear to be monomers in solution (26,27).…”

Structural study reveals the temperature-dependent conformational flexibility of Tk-PTP, a protein tyrosine phosphatase from Thermococcus kodakaraensis KOD1

“…coli BL21(DE3) RIL strain at 25°C and purified using a Ni-NTA column. SP-PTP and three human DUSP proteins, DUSP3, DUSP15, and DUSP28, were prepared and purified as previously described [ 29 , 37 ].…”

In Vitro and In Silico Investigation of BCI Anticancer Properties and Its Potential for Chemotherapy-Combined Treatments

“…The energy-minimized three-dimensional structure of BCI was procured from the NCBI PubChem database. The prepared ligand was computationally screened against calcium sensing receptor (CASR) (PDB ID: 7dtt) [ 21 ], C-X-C chemokine receptor type 3 (CXCR3) (PDB ID: 6wzk) [ 22 ], cyclin-dependent kinase-5 (CDK5) (PDB ID: 1unl) [ 23 ], cathepsin D (CPSD) (PDB ID: 4od9) [ 24 ], casein kinase II subunit alpha (CK2A1) (PDB ID: 6tls) [ 25 ], cyclin-dependent kinase-1 (CDK1) (PDB ID: 6gu2) [ 26 ], dopamine D1 receptor (DRD1) (PDB ID: 7ckx) [ 27 ], dual specificity phosphatase 13a (DUSP13) (PDB ID: 5xjv) [ 28 ], dual specificity phosphatase 14 (DUSP14) (PDB ID: 2wgp) [ 29 ], dual specificity phosphatase 18 (DUSP18) (PDB ID: 2esb) [ 30 ], dual specificity phosphatase 2 (DUSP2) (PDB ID: 1m3g) [ 31 ], dual specificity phosphatase 28 (DUSP28) (PDB ID: 5y15) [ 32 ], dual specificity phosphatase 5 (DUSP5) (PDB ID: 2g6z) [ 33 ], dual specificity phosphatase 6 (DUSP6) (PDB ID: 1hzm) [ 34 ], dual specificity phosphatase 7 (DUPS7) (PDB ID: 4y2e) [ 35 ], dual specificity phosphatase 8 (DUSP8) (PDB ID: 4jmk) [ 36 ], dipeptidyl peptidase IV (DPP4) (PDB ID: 4pv7) [ 37 ], glucagon-like peptide-1 receptor (GLP-1R) (PDB ID: 5vai) [ 38 ], human apurinic/apyrimidinic endonuclease 1 (APE1) (PDB ID: 6bow) [ 39 ], human indoleamine 2,3-dioxygenase-1 (IDO1) (PDB ID: 6e43) [ 40 ], human topoisomerase-II beta (TOP2β) (PDB ID: 3qx3) [ 41 ], intercellular adhesion molecule (ICAM-1) (PDB ID: 5mza) [ 42 ], lysosomal pro-X carboxypeptidase (PRCP) (PDB ID: 3n2z) [ 43 ], Mu opioid receptor (OPRM1) (PDB ID: 4dkl) [ 44 ], plasminogen activator inhibitor type-1 (PAI-1) (PDB ID: 3cvm) [ 45 ], rho-associated protein kinase-1 (ROCK1) (PDB ID: 3v8s) [ 46 ], rho-associated protein kinase-2 (ROCK2) (PDB ID: 6ed6) [ 47 ], serotonin 5a (5-HT5a) receptor (PDB ID: 7x5h) [ 48 ], signal transducer and activator of transcription-3 (STAT3) (PDB ID: 6nuq) [ 49 ], somatostatin receptor 3 (SSTR3) (PDB ID: 7xms) [ 50 ], tripartite motif-containing 24 ...…”