Prolyl oligopeptidase

 

This group of serine peptidases belong to MEROPS peptidase family S9 (clan SC), subfamily S9A (prolyl oligopeptidase). The active site of members of this clan consists of a linear arrangement of serine, histidine and threonine catalytic residues [PMID:7845208]. Prolyl oligopeptidases are either located in the cytosol or they are membrane bound, where they cleave peptide bonds with prolyl P1 specificities (but cleavage of alanyl bonds has been detected). The proline must adopt a trans configuration within the chain. Peptides of up to 30 residues are cleaved [PMID:7845208].

 

Reference Protein and Structure

Sequence
P23687 UniProt (3.4.21.26) IPR002470 (Sequence Homologues) (PDB Homologues)
Biological species
Sus scrofa (pig) Uniprot
PDB
1qfm - PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE (1.4 Å) PDBe PDBsum 1qfm
Catalytic CATH Domains
3.40.50.1820 CATHdb (see all for 1qfm)
Click To Show Structure

Enzyme Reaction (EC:3.4.21.26)

water
CHEBI:15377ChEBI
+
dipeptide zwitterion
CHEBI:90799ChEBI
→
L-alpha-amino acid zwitterion
CHEBI:59869ChEBI
Alternative enzyme names: Endoprolylpeptidase, Post-proline cleaving enzyme, Post-proline endopeptidase, Proline endopeptidase, Proline-specific endopeptidase, Prolyl endopeptidase,

Enzyme Mechanism

Introduction

This peptidase functions in much the same way as other serine peptidases. The Ser-His-Asp catalytic triad activates the serine through general acid/base catalysis. The serine then attacks the carbonyl group of the peptide bond, cleaving the C-N bond. Water is activated by the histidine of the triad and then cleaves the remaining product from the enzyme.

Catalytic Residues Roles

UniProt PDB* (1qfm)
Tyr473 Tyr473A Forms an oxyanion hole, stabilises the transition states formed during the course of the reaction. electrostatic stabiliser
Ser554 Ser554A Part of the Ser-His-Asp catalytic triad; acts as a general acid/base and forms an acyl-enzyme intermediate during the course of the reaction. covalent catalysis, proton shuttle (general acid/base)
Asp641 Asp641A Part of the Ser-His-Asp catalytic triad; acts to stabilise and activate the general acid/base histidine. modifies pKa, electrostatic stabiliser
His680 His680A Part of the Ser-His-Asp catalytic triad; acts as a general acid/base to activate the nucleophile serine and later the catalytic water molecule. proton shuttle (general acid/base)
*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. Szeltner Z et al. (2002), J Biol Chem, 277, 44597-44605. Substrate-dependent Competency of the Catalytic Triad of Prolyl Oligopeptidase. DOI:10.1074/jbc.m207386200. PMID:12228249.
  2. Szeltner Z et al. (2013), Biochim Biophys Acta, 1834, 98-111. The loops facing the active site of prolyl oligopeptidase are crucial components in substrate gating and specificity. DOI:10.1016/j.bbapap.2012.08.012. PMID:22940581.
  3. Kaszuba K et al. (2012), Biochimie, 94, 1398-1411. Molecular dynamics, crystallography and mutagenesis studies on the substrate gating mechanism of prolyl oligopeptidase. DOI:10.1016/j.biochi.2012.03.012. PMID:22484394.
  4. Kaushik S et al. (2011), PLoS One, 6, e26251-. Structural analysis of prolyl oligopeptidases using molecular docking and dynamics: insights into conformational changes and ligand binding. DOI:10.1371/journal.pone.0026251. PMID:22132071.
  5. Kaszuba K et al. (2009), SAR QSAR Environ Res, 20, 595-609. Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity. DOI:10.1080/10629360903438198. PMID:20024801.
  6. Shan L et al. (2005), Proc Natl Acad Sci U S A, 102, 3599-3604. Structural and mechanistic analysis of two prolyl endopeptidases: role of interdomain dynamics in catalysis and specificity. DOI:10.1073/pnas.0408286102. PMID:15738423.
  7. Szeltner Z et al. (2004), J Mol Biol, 340, 627-637. Concerted structural changes in the peptidase and the propeller domains of prolyl oligopeptidase are required for substrate binding. DOI:10.1016/j.jmb.2004.05.011. PMID:15210359.
  8. Szeltner Z et al. (2003), J Biol Chem, 278, 48786-48793. Electrostatic environment at the active site of prolyl oligopeptidase is highly influential during substrate binding. DOI:10.1074/jbc.M309555200. PMID:14514675.
  9. Szeltner Z et al. (2002), J Biol Chem, 277, 42613-42622. Electrostatic Effects and Binding Determinants in the Catalysis of Prolyl Oligopeptidase. SITE-SPECIFIC MUTAGENESIS AT THE OXYANION BINDING SITE. DOI:10.1074/jbc.m208043200. PMID:12202494.
  10. Polgár L (2002), Cell Mol Life Sci, 59, 349-362. The prolyl oligopeptidase family. DOI:10.1007/s00018-002-8427-5. PMID:11915948.
  11. Szeltner Z et al. (2000), Protein Sci, 9, 353-360. Substrate- and pH-dependent contribution of oxyanion binding site to the catalysis of prolyl oligopeptidase, a paradigm of the serine oligopeptidase family. DOI:10.1110/ps.9.2.353. PMID:10716187.
  12. Fülöp V et al. (1998), Cell, 94, 161-170. Prolyl Oligopeptidase. DOI:10.1016/s0092-8674(00)81416-6. PMID:9695945.
  13. Rawlings ND et al. (1994), Methods Enzymol, 244, 19-61. Families of serine peptidases. PMID:7845208.
  14. Rennex D et al. (1991), Biochemistry, 30, 2195-2203. cDNA cloning of porcine brain prolyl endopeptidase and identification of the active-site seryl residue. PMID:1900195.
  15. Stone SR et al. (1991), Biochem J, 276 ( Pt 3), 837-840. Inactivation of prolyl endopeptidase by a peptidylchloromethane. Kinetics of inactivation and identification of sites of modification. PMID:2064618.

Step 1.

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Catalytic Residues Roles

Residue Roles
Tyr473A electrostatic stabiliser
Asp641A electrostatic stabiliser, modifies pKa
Ser554A proton shuttle (general acid/base)
His680A proton shuttle (general acid/base)
Ser554A covalent catalysis

Chemical Components

Step 1.

Contributors

Alex Gutteridge, Craig Porter, Gemma L. Holliday