Prolyl aminopeptidase

 

Proline iminopeptidases belong to serine peptidase family S33. They catalyse the removal of an N-terminal proline residue from peptides with high specificity.

The bacterial Xanthomonas citri enzyme is thought to be involved in proline metabolism and sensitivity to ascamycin (has ascamycin dealanylating activity).

The archaeal Tricorn> protease interacting factor 1 (F1) from is responsible for the cleavage of hydrophobic peptides which are generated by tricorn peptidase. It cleaves H-Pro-AMC as well as a wide spectrum of amino acid substrates and including several peptide substrates without a proline at the N-terminus.

The mechanism of the serine proteases is commonly believed to be among the best understood of all enzymes. As their name suggests, they are involved in hydrolysis of proteins using a serine nucleophile.

 

Reference Protein and Structure

Sequence
P52279 UniProt (3.4.11.5) IPR002410 (Sequence Homologues) (PDB Homologues)
Biological species
Xanthomonas citri (Bacteria) Uniprot
PDB
1azw - PROLINE IMINOPEPTIDASE FROM XANTHOMONAS CAMPESTRIS PV. CITRI (2.7 Å) PDBe PDBsum 1azw
Catalytic CATH Domains
3.40.50.1820 CATHdb (see all for 1azw)
Click To Show Structure

Enzyme Reaction (EC:3.4.11.5)

Dipeptide (Xaa-Pro)
CHEBI:4635ChEBI
+
water
CHEBI:15377ChEBI
→
proline
CHEBI:26271ChEBI
+
alpha-amino acid
CHEBI:33704ChEBI
Alternative enzyme names: Pro-X aminopeptidase, Cytosol aminopeptidase V, Proline aminopeptidase, Proline iminopeptidase,

Enzyme Mechanism

Introduction

The key feature of the mechanism is the presence of the catalytic triad of serine, histidine and aspartate. Serine, having been deprotonated by histidine, attacks the carbonyl of the substrate. The negatively charged tetrahedral intermediate is stabilised by the oxyanion hole, while the positive charge on histidine is stabilised by the aspartate residue. When the tetrahedral intermediate collapses, the amide bond of the substrate is broken. The acylenzyme intermediate is hydrolysed by a water molecule, activated by histidine, to release the product and restore the enzyme to its active state.

Catalytic Residues Roles

UniProt PDB* (1azw)
Asp266 Asp266A Forms part of the catalytic triad. Stabilises the positive charge on histidine. electrostatic stabiliser
His294 His294A Forms part of the catalytic triad. Deprotonates serine to activate it as a nucleophile, and is stabilised by hydrogen bonding interactions with aspartate. In the deacylation step, deprotonates a water molecule to activate it as a nucleophile. proton shuttle (general acid/base), electrostatic stabiliser
Ser110 Ser110A When activated by histidine, serine is the nucleophile which attacks the substrate carbonyl, forming a covalent intermediate. covalent catalysis, proton shuttle (general acid/base)
Trp111 (main-N), Gly43 (main-N) Trp111A (main-N), Gly43A (main-N) Forms part of the oxyanion hole which stabilises the negatively charged oxygen in the transition state. 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. Medrano FJ et al. (1998), EMBO J, 17, 1-9. Structure of proline iminopeptidase from Xanthomonas campestris pv. citri: a prototype for the prolyl oligopeptidase family. DOI:10.1093/emboj/17.1.1. PMID:9427736.
  2. Jing Z et al. (2015), Protein J, 34, 173-180. Studies on the Molecular Docking and Amino Acid Residues Involving in Recognition of Substrate in Proline Iminopeptidase by Site-Directed Mutagenesis. DOI:10.1007/s10930-015-9611-4. PMID:25957260.
  3. Goettig P et al. (2005), J Biol Chem, 280, 33387-33396. X-ray Snapshots of Peptide Processing in Mutants of Tricorn-interacting Factor F1 from Thermoplasma acidophilum. DOI:10.1074/jbc.m505030200. PMID:15994304.
  4. Topf M et al. (2002), Proteins, 47, 357-369. Molecular dynamics simulations of the acyl-enzyme and the tetrahedral intermediate in the deacylation step of serine proteases. DOI:10.1002/prot.10097. PMID:11948789.
  5. Goettig P et al. (2002), EMBO J, 21, 5343-5352. Structures of the tricorn-interacting aminopeptidase F1 with different ligands explain its catalytic mechanism. DOI:10.1093/emboj/cdf552. PMID:12374735.
  6. Yoshimoto T et al. (1999), J Biochem, 126, 559-565. Crystal Structure of Prolyl Aminopeptidase from Serratia marcescens. DOI:10.1093/oxfordjournals.jbchem.a022486. PMID:10467172.
  7. Tamura T et al. (1996), FEBS Lett, 398, 101-105. Tricorn protease (TRI) interacting factor 1 fromThermoplasma acidophilumis a proline iminopeptidase. DOI:10.1016/s0014-5793(96)01163-5. PMID:8946961.

Step 1.

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Catalytic Residues Roles

Residue Roles
Gly43A (main-N) electrostatic stabiliser
Trp111A (main-N) electrostatic stabiliser
Asp266A electrostatic stabiliser
His294A electrostatic stabiliser, proton shuttle (general acid/base)
Ser110A covalent catalysis, proton shuttle (general acid/base)

Chemical Components

Step 1.

Contributors

Alex Gutteridge, Craig Porter, Ellie Wright, Gemma L. Holliday