Protein-tyrosine-phosphatase non-receptor type 1

 

Protein tyrosine phosphatases catalyse the removal of phosphoryl groups from tyrosine residues in proteins. They play important roles in the control of biological processes such as cell cycles and signal transduction pathways.

The human tyrosine-protein phosphatase PTPN1 acts as a regulator of endoplasmic reticulum unfolded protein response. Mediates dephosphorylation of EIF2AK3/PERK; inactivating the protein kinase activity of EIF2AK3/PERK. It may also play an important role in CKII- and p60c-src-induced signal transduction cascades, regulate the EFNA5-EPHA3 signaling pathway which modulates cell reorganisation and cell-cell repulsion, and may also regulate the hepatocyte growth factor receptor signaling pathway through dephosphorylation of MET.

 

Reference Protein and Structure

Sequence
P18031 UniProt (3.1.3.48) IPR012265 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1bzc - HUMAN PTP1B CATALYTIC DOMAIN COMPLEXED WITH TPI (2.35 Å) PDBe PDBsum 1bzc
Catalytic CATH Domains
3.90.190.10 CATHdb (see all for 1bzc)
Click To Show Structure

Enzyme Reaction (EC:3.1.3.48)

L-tyrosine-O-phosphate(2-) residue
CHEBI:82620ChEBI
+
water
CHEBI:15377ChEBI
→
hydrogenphosphate
CHEBI:43474ChEBI
+
L-tyrosine residue
CHEBI:46858ChEBI
Alternative enzyme names: PPT-phosphatase, PTP-phosphatase, PTPase, (Phosphotyrosine)protein phosphatase, Phosphoprotein phosphatase (phosphotyrosine), Phosphotyrosine histone phosphatase, Phosphotyrosine phosphatase, Phosphotyrosine protein phosphatase, Phosphotyrosylprotein phosphatase, Protein phosphotyrosine phosphatase, Tyrosine O-phosphate phosphatase, Tyrosylprotein phosphatase,

Enzyme Mechanism

Introduction

The reaction occurs via a double displacement mechanism. First, Cys 215 acts as a nucleophile to attack the phosphate of the phosphotyrosine substrate and displace the tyrosine. Cys 215 is present as a thiolate in the ground state; its pKa is reduced by interactions with Ser 222 and Arg 221. The departing tyrosine leaving group is protonated by Asp 181 acting as a general acid.

In the second step, the cysteinyl-phosphate is hydrolysed. Asp 181 deprotonates the nucleophilic water molecule while the negative charge that accumulates on the departing thiolate leaving group is stabilised by a hydrogen bond from Ser 222.

Catalytic Residues Roles

UniProt PDB* (1bzc)
Gln262 Gln262A Plays an important role in positioning the nucleophilic water molecule steric role
Asp181 Asp181A Protonates the departing tyrosine during formation of the cysteinyl phosphate intermediate. Deprotonates the nucleophilic water molecule during hydrolysis of the intermediate. proton shuttle (general acid/base)
Cys215 Cys215A Acts as the catalytic nucleophile. Attacks the phosphate of the phosphotyrosine substrate, forming a cysteinyl-phosphate intermediate which is subsequently hydrolysed. covalent catalysis
Arg221 Arg221A Lowers the pKa of Cys 215 to allow it to exist as a thiolate. Also helps stabilise the negatively charged transition states. activator, electrostatic stabiliser
Ser222 Ser222A Lowers the pKa of Cys 215 to allow it to exist as a thiolate. Stabilises accumulation of negative charge on the departing cysteine thiolate during hydrolysis of the cysteinyl-phosphate. activator, electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Asthagiri D et al. (2002), J Am Chem Soc, 124, 10225-10235. Density Functional Study of the Mechanism of a Tyrosine Phosphatase:  I. Intermediate Formation. DOI:10.1021/ja020046n. PMID:12188687.
  2. Ozcan A et al. (2013), Proteins, 81, 788-804. Effects of protonation state of Asp181 and position of active site water molecules on the conformation of PTP1B. DOI:10.1002/prot.24234. PMID:23239271.
  3. Brandão TA et al. (2012), Arch Biochem Biophys, 525, 53-59. The molecular details of WPD-loop movement differ in the protein-tyrosine phosphatases YopH and PTP1B. DOI:10.1016/j.abb.2012.06.002. PMID:22698963.
  4. Romsicki Y et al. (2003), J Biol Chem, 278, 29009-29015. Functional Characterization and Crystal Structure of the C215D Mutant of Protein-tyrosine Phosphatase-1B. DOI:10.1074/jbc.m303817200. PMID:12748196.
  5. Dillet V et al. (2000), J Phys Chem B, 104, 11321-11333. Stabilization of Charges and Protonation States in the Active Site of the Protein Tyrosine Phosphatases:  A Computational Study†. DOI:10.1021/jp001575l.
  6. Pannifer AD et al. (1998), J Biol Chem, 273, 10454-10462. Visualization of the Cysteinyl-phosphate Intermediate of a Protein-tyrosine Phosphatase by X-ray Crystallography. DOI:10.1074/jbc.273.17.10454. PMID:9553104.
  7. Barford D et al. (1994), Science, 263, 1397-1404. Crystal structure of human protein tyrosine phosphatase 1B. DOI:10.2210/pdb2hnp/pdb. PMID:8128219.

Step 1.

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Catalytic Residues Roles

Residue Roles
Gln262A steric role
Arg221A activator, electrostatic stabiliser
Asp181A proton shuttle (general acid/base)
Cys215A covalent catalysis
Ser222A activator, electrostatic stabiliser

Chemical Components

Step 1.

Contributors

Gemma L. Holliday, Steven Smith