Phosphohistidine phosphatase

 

This eukaryotic enzyme dephosphorylates phosphorylated histidine residues within proteins and peptides. The enzyme acts on phosphate groups attached to both the pros- and tele-nitrogen atoms, but the pros- position is somewhat preferred (by a factor of two at the most) [PMID:19836471]. The substrate specificity depends on the amino acid sequence or structural context of the phosphohistidine in a phosphoprotein. The enzyme is also active on free phosphoramidate [PMID:12383260, PMID:19836471] and peptide-bound phospholysine [PMID:25574816].

 

Reference Protein and Structure

Sequence
Q9NRX4 UniProt (3.9.1.3) IPR028441 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
2hw4 - Crystal structure of human phosphohistidine phosphatase (1.9 Å) PDBe PDBsum 2hw4
Catalytic CATH Domains
3.50.20.20 CATHdb (see all for 2hw4)
Click To Show Structure

Enzyme Reaction (EC:3.9.1.3)

water
CHEBI:15377ChEBI
+
N(pros)-phosphonato-L-histidine residue
CHEBI:64837ChEBI
→
L-histidine residue
CHEBI:29979ChEBI
+
hydrogenphosphate
CHEBI:43474ChEBI
Alternative enzyme names: PHPT1 (gene name), Protein histidine phosphatase, PHP,

Enzyme Mechanism

Introduction

The substrate binds to the protein. His53 acts as a general base to activate a water molecule, which in turn functions as a nucleophile to attack the phosphate of the substrate. The phosphate is eliminated and the substrate histidine abstracts a proton from His53 (inferred).

Catalytic Residues Roles

UniProt PDB* (2hw4)
His53 His53(72)A Acts as a general acid/base. proton acceptor, proton donor
Ala54 (main-N), Ser94, Ala96 (main-N), Arg78 Ala54(73)A (main-N), Ser94(113)A, Ala96(115)A (main-N), Arg78(97)A Form a positively charged phosphate binding site which helps stabilise the reactive intermediates and transition states formed during the course of the reaction. electrostatic stabiliser
Lys21 Lys21(40)A Lys21 helps stabilise the reactive intermediates and transition states formed during the course of the reaction. The amine group of Lys21 is also close to the imidazole ring of His53, and the positive charge may also be a reason for the reduced pKa of the imidazole ring modifies pKa, 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

proton transfer, bimolecular nucleophilic substitution, overall product formed, overall reactant used, inferred reaction step, native state of enzyme regenerated

References

  1. Gong W et al. (2009), Biochem J, 418, 337-344. Solution structure and catalytic mechanism of human protein histidine phosphatase 1. DOI:10.1042/BJ20081571. PMID:18991813.
  2. Ek P et al. (2015), Ups J Med Sci, 120, 20-27. Phosphohistidine phosphatase 1 (PHPT1) also dephosphorylates phospholysine of chemically phosphorylated histone H1 and polylysine. DOI:10.3109/03009734.2014.996720. PMID:25574816.
  3. Attwood PV et al. (2010), Biochim Biophys Acta, 1804, 199-205. Chemical phosphorylation of histidine-containing peptides based on the sequence of histone H4 and their dephosphorylation by protein histidine phosphatase. DOI:10.1016/j.bbapap.2009.10.007. PMID:19836471.
  4. Busam RD et al. (2006), J Biol Chem, 281, 33830-33834. First structure of a eukaryotic phosphohistidine phosphatase. DOI:10.1074/jbc.C600231200. PMID:16990267.
  5. Ma R et al. (2005), Biochem Biophys Res Commun, 337, 887-891. Mutational study of human phosphohistidine phosphatase: effect on enzymatic activity. DOI:10.1016/j.bbrc.2005.09.134. PMID:16219293.
  6. Ek P et al. (2002), Eur J Biochem, 269, 5016-5023. Identification and characterization of a mammalian 14-kDa phosphohistidine phosphatase. PMID:12383260.

Step 1. His53 abstracts a proton from the nucleophilic water, which attacks the phosphate, eliminating the protein histidine intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys21(40)A electrostatic stabiliser
Ala54(73)A (main-N) electrostatic stabiliser
Arg78(97)A electrostatic stabiliser
Ser94(113)A electrostatic stabiliser
Ala96(115)A (main-N) electrostatic stabiliser
Lys21(40)A modifies pKa
His53(72)A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic substitution, overall product formed, overall reactant used

Step 2. Inferred step in which the protein histidine intermediate abstracts a proton from the catalytic histidine residue to regenerate the active site.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys21(40)A modifies pKa
His53(72)A proton donor

Chemical Components

inferred reaction step, native state of enzyme regenerated, proton transfer, overall product formed
Download: Image, Marvin File

Step 1. His53 abstracts a proton from the nucleophilic water, which attacks the phosphate, eliminating the protein histidine intermediate.

Step 2. Inferred step in which the protein histidine intermediate abstracts a proton from the catalytic histidine residue to regenerate the active site.

Products.

Contributors

Gemma L. Holliday