Peptidylprolyl isomerase (PpiC-type)

 

Prolyl isomerase is able to convert the cis and trans forms of peptide bonds involving proline. This alters the 3d structure of the target proteins, which activates them or deactivates them so that they can take part in signal pathways inside the cell. The human prolyl isomerase hPin1 targets many important proteins after they have been phosphorylated by ser/thr kinases, being involved specifically in G2/M transitions in the cell cycle. As a result, mutations to the protein have been implicated in many forms of cancer.

 

Reference Protein and Structure

Sequence
Q13526 UniProt (5.2.1.8) IPR000297 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1nmw - Solution structure of the PPIase domain of human Pin1 (solution nmr Å) PDBe PDBsum 1nmw
Catalytic CATH Domains
3.10.50.40 CATHdb (see all for 1nmw)
Click To Show Structure

Enzyme Reaction (EC:5.2.1.8)

peptidylproline (omega=180) residue
CHEBI:83834ChEBI
→
peptidylproline (omega=0) residue
CHEBI:83833ChEBI
Alternative enzyme names: PPIase, Cyclophilin, Peptide bond isomerase, Peptidyl-prolyl cis-trans isomerase, Rotamase, Peptidylprolyl cis-trans isomerase,

Enzyme Mechanism

Introduction

Pin 1 catalyzes the cis-trans isomerization of proline amide bonds and is higly selective for proline residues with a phosphorylated threonine or serine immediately proceeding it. The main effect of Pin1 on the isomerization reaction is the reduction of the free energy barrier. This is accomplished by a combined rotation of the ψ backbone angle of the threonine residue and the amide bond. The enzyme works via the electrostatic stabilization of the phosphate group of the threonine residue through the basic triad and the hydrogen bonds between the enzyme Gln 131 and the peptide which fix one part of the peptide in the catalytic site, hindering its rotation. Cys 113 has a minor role in the stabilization of the cis form and stabilizes the carbonyl group during the initial rotation. Ser 154 is likely to interact with the phosphate group and may even stabilize the transition state via hydrogen bonding to the carbonyl oxygen in the trans form and to the phosphate of a threonine residue in the cis form.

Catalytic Residues Roles

UniProt PDB* (1nmw)
Ser154 Ser154(105)A Thought to interact with the phosphate group and may stabilize the transition state via hydrogen bonding to the carbonyl oxygen in the trans form and to the phosphate of a threonine residue in the cis form. electrostatic stabiliser
Gln131 Gln131(82)A Part of the basic triad which stabilizes the phosphate of the threonine residue this stops the rotation of the peptide within the catalytic site. electrostatic stabiliser
Cys113 Cys113(64)A Helps stabilize the cis isomer and the carbonyl group during the initial rotation. 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. Vöhringer-Martinez E et al. (2014), J Phys Chem B, 118, 9871-9880. The influence of Ser-154, Cys-113, and the phosphorylated threonine residue on the catalytic reaction mechanism of Pin1. DOI:10.1021/jp505638w. PMID:25059768.

Step 1.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser154(105)A electrostatic stabiliser
Cys113(64)A electrostatic stabiliser
Gln131(82)A electrostatic stabiliser

Chemical Components

Step 1.

Introduction

The cis and trans forms of the prolyl peptide bond are, unlike peptide bonds involving other amino acids, very similar in energy levels. However, interconversion involves breaking the resonance overlap of the CN partial double bond, with very high activation energy. The enzyme is able to reduce this activation barrier by the formation of a tetrahedral intermediate: Cys 113, deprotonated by His 57, attacks the carbonyl of the peptide bond to form an oxyanion intermediate stabilised by His 157. As the tetrahedral intermediate does not have partial double bond character, rotation around the CN bond can occur easily. Collapse of the tetrahedral intermediate then occurs with Cys 113 protonated by His 57 to allow it to act as a leaving group.

Catalytic Residues Roles

UniProt PDB* (1nmw)
His59 His59(10)A Acts to deprotonate the catalytic nucleophile Cys 113 thus allowing it to form the tetrahedral intermediate. proton shuttle (general acid/base)
Cys113 Cys113(64)A Acts as nucleophile to attack the carbonyl moiety of the prolyl peptide bond leading to a tetrahedral intermediate which then collapses to form the cis/trans product. covalently attached
His157 His157(108)A Stabilises the oxyanion transition state through hydrogen bonding between its protonated form and the negative charge on the oxygen. 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. Ranganathan R et al. (1997), Cell, 89, 875-886. Structural and Functional Analysis of the Mitotic Rotamase Pin1 Suggests Substrate Recognition Is Phosphorylation Dependent. DOI:10.1016/s0092-8674(00)80273-1. PMID:9200606.

Step 1.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Cys113(64)A covalently attached
His59(10)A proton shuttle (general acid/base)
His157(108)A electrostatic stabiliser
Ser154(105)A electrostatic stabiliser

Chemical Components

Step 1.

Contributors

Peter Sarkies, Gemma L. Holliday, James Willey