Serine/threonine-protein phosphatase 5

 

Serine/threonine protein phosphatase 5 (PP5) from Homo sapiens hydrolyses a phosphoprotein substrate into a protein and a phosphate group. It is implicated in wide ranging cellular processes, including apoptosis, differentiation, DNA damage response, cell survival, regulation of ion channels or circadian rhythms, in response to steroid and thyroid hormones, calcium, fatty acids, TGF-beta as well as oxidative and genotoxic stresses. It is a member of the PPP gene family of protein phosphatases that is widely expressed in mammalian tissues.

 

Reference Protein and Structure

Sequence
P53041 UniProt (3.1.3.16) IPR011236 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1s95 - Structure of serine/threonine protein phosphatase 5 (1.6 Å) PDBe PDBsum 1s95
Catalytic CATH Domains
3.60.21.10 CATHdb (see all for 1s95)
Cofactors
Manganese(2+) (2)
Click To Show Structure

Enzyme Reaction (EC:3.1.3.16)

O-phospho-L-serine(2-) residue
CHEBI:83421ChEBI
+
water
CHEBI:15377ChEBI
→
L-serine residue
CHEBI:29999ChEBI
+
hydrogenphosphate
CHEBI:43474ChEBI
Alternative enzyme names: 3-hydroxy 3-methylglutaryl coenzymeA reductase phosphatase, Aspergillus awamori acid protein phosphatase, BCKDH phosphatase, HMG-CoA reductase phosphatase, Branched-chain alpha-keto acid dehydrogenase phosphatase, Calcineurin, Casein phosphatase, Phosphatase 2A, Phosphatase 2B, Phosphatase C-II, Phosphatase H-II, Phosphatase I, Phosphatase IB, Phosphatase II, Phosphatase III, Phosphatase IV, Phosphatase SP, Phosphopyruvate dehydrogenase phosphatase, Phosphospectrin phosphatase, Polycation modulated (PCM-) phosphatase, Protein D phosphatase, Protein phosphatase, Protein phosphatase-1, Protein phosphatase-2A, Protein phosphatase-2B, Protein phosphatase-2C, Serine/threonine specific protein phosphatase, Phosphoprotein phosphatase,

Enzyme Mechanism

Introduction

DFT calculations suggest that the reaction proceeds via an in-line concerted transition state, without intermediates. A water molecule is activated by two Mn(II) ions and His427 which lower its pKa such that it is present as a hydroxide ion. This hydroxide ion performs a nucleophilic attack on the phosphorus atom of the substrate, causing the P-O4 bond to break. The transition state is stabilised by Arg275 (H bonding to O1 and O4), Arg400 (H bonding to O3) and Asn303 (H bonding to O2). Asp274 hydrogen bonds to His304, lowering its pKa, facilitating deprotonation of His304. The leaving alcohol group is protonated by His304 and His304 is protonated by Asp274.

Catalytic Residues Roles

UniProt PDB* (1s95)
Asp242, His244, Asp271 Asp242(76)A, His244(78)A, Asp271(105)A Forms the manganese 1 binding site. metal ligand
Asp274 Asp274(108)A Hydrogen bonds to His 304, lowering its pKa, aiding His 304 to donate a proton to the leaving group. activator, proton donor
His304 His304(138)A Acts as an acid by donating a proton to the leaving alcohol group. proton relay, proton acceptor, proton donor
Arg275 Arg275(109)A Hydrogen bonds to atoms O1 and O4, helping to stabilise the transition state. transition state stabiliser
Asn303 Asn303(137)A Hydrogen bonds to atom O2 of the substrate, helping to stabilise the transition state. metal ligand, transition state stabiliser
Arg400 Arg400(234)A Hydrogen bonds to atom O3 of the substrate, helping to stabilise the transition state. transition state stabiliser
Asp271, His352, Asn303, His427 Asp271(105)A, His352(186)A, Asn303(137)A, His427(261)A Forms the manganese 2 binding site. metal ligand
His427 His427(261)A Helps lower the pKa of a bound water molecule to such an extent as to cause it to 'spontaneously deprotonate'. activator, metal ligand
*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

bimolecular nucleophilic substitution, proton transfer, overall product formed

References

  1. Ribeiro AJ et al. (2013), Chemistry, 19, 14081-14089. The Catalytic Mechanism of Protein Phosphatase 5 Established by DFT Calculations. DOI:10.1002/chem.201301565. PMID:24014428.
  2. McConnell JL et al. (2009), Mol Pharmacol, 75, 1249-1261. Targeting Protein Serine/Threonine Phosphatases for Drug Development. DOI:10.1124/mol.108.053140. PMID:19299564.
  3. Shi Y (2009), Cell, 139, 468-484. Serine/Threonine Phosphatases: Mechanism through Structure. DOI:10.1016/j.cell.2009.10.006. PMID:19879837.
  4. Hinds TD Jr et al. (2008), Int J Biochem Cell Biol, 40, 2358-2362. Protein phosphatase 5. DOI:10.1016/j.biocel.2007.08.010. PMID:17951098.
  5. Swingle MR et al. (2004), J Biol Chem, 279, 33992-33999. Structural Basis for the Catalytic Activity of Human Serine/Threonine Protein Phosphatase-5. DOI:10.1074/jbc.m402855200. PMID:15155720.

Step 1. The bound hydroxide performs a nucleophilic attack on the phosphate group causing it to be cleaved from the main substrate molecule. The oxygen of the dephosphorylated protein deprotonates His304 which in turn deprotonates Asp274.

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Catalytic Residues Roles

Residue Roles
Asp242(76)A metal ligand
His244(78)A metal ligand
Asp271(105)A metal ligand
Asn303(137)A metal ligand
His352(186)A metal ligand
His427(261)A metal ligand
Asp274(108)A activator
Arg400(234)A transition state stabiliser
His427(261)A activator
Asn303(137)A transition state stabiliser
Arg275(109)A transition state stabiliser
His304(138)A proton donor, proton acceptor
Asp274(108)A proton donor
His304(138)A proton relay

Chemical Components

ingold: bimolecular nucleophilic substitution, proton transfer, overall product formed
Download: Image, Marvin File

Step 1. The bound hydroxide performs a nucleophilic attack on the phosphate group causing it to be cleaved from the main substrate molecule. The oxygen of the dephosphorylated protein deprotonates His304 which in turn deprotonates Asp274.

Products.

Contributors

Gemma L. Holliday, Ellie Wright, Marko Babić, Noa Marson