Leucyl aminopeptidase

 

Bovine lens leucine aminopeptidase (blLAP) is a widespread bizinc exopeptidase, whose function is to remove the N-terminal residue in a peptide chain. It plays a key role in the degradation and modification of proteins in the metabolism of mammals and has even been implicated in human HIV pathophysiology. blLAP has a hexameric structure, in which each monomer functions independently of the others. The active site (one per monomer) is sitting on the edge of two water channels: a large one for the substrate located below the two metal ions and a much smaller one located above Zn1.

 

Reference Protein and Structure

Sequence
P00727 UniProt (3.4.11.1, 3.4.11.5, 3.4.13.23) IPR023042 (Sequence Homologues) (PDB Homologues)
Biological species
Bos taurus (Cattle) Uniprot
PDB
1lam - LEUCINE AMINOPEPTIDASE (UNLIGATED) (1.6 Å) PDBe PDBsum 1lam
Catalytic CATH Domains
3.40.630.10 CATHdb (see all for 1lam)
Cofactors
Carbonate (1), Zinc(2+) (2)
Click To Show Structure

Enzyme Reaction (EC:3.4.11.1)

Leu-Gly
CHEBI:74534ChEBI
+
water
CHEBI:15377ChEBI
→
glycine zwitterion
CHEBI:57305ChEBI
+
L-leucine zwitterion
CHEBI:57427ChEBI
Alternative enzyme names: L-leucine aminopeptidase, FTBL proteins, Aminopeptidase I, Aminopeptidase II, Aminopeptidase III, Cathepsin III, Cytosol aminopeptidase, Leucinamide aminopeptidase, Leucinaminopeptidase, Leucine aminopeptidase, Leucyl peptidase, Peptidase S, Proteinates FTBL,

Enzyme Mechanism

Introduction

Bicarbonate ion acts as a general base to deprotonate a water molecule bound by the two active site zinc ions, creating a hydroxide nucleophile. Zinc1 (Zinc488) and a hydrogen bond from Lys262 polarises the carbonyl group of the substrate, to increase its electrophilicity. In concert with the bicarbonate ion deprotonating the water molecule, it nucleophilically attacks the polarised carbonyl group to form a tetrahedral gem-diolate intermediate. The negative charge is subsequently stabilised by the Lys262 and Zinc1. Collapse of the tetrahedral intermediate leads to protonation of the amine leaving group by the bicarbonate ion, which shuttles the proton from water to it. Arg336 provides a positively charged pocket for the bicarbonate ion.

Catalytic Residues Roles

UniProt PDB* (1lam)
Lys294 Lys262A Acts to polarise the carbonyl side to chain to activate it to nucleophilic attack. Stabilises the gem-diolate intermediate via hydrogen bonding. electrostatic stabiliser
Arg368 Arg336A Forms a positive pocket for the bicarbonate ion. 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. Sträter N et al. (1999), Proc Natl Acad Sci U S A, 96, 11151-11155. A bicarbonate ion as a general base in the mechanism of peptide hydrolysis by dizinc leucine aminopeptidase. DOI:10.1073/pnas.96.20.11151. PMID:10500145.
  2. Sträter N et al. (1995), Biochemistry, 34, 14792-14800. Two-Metal Ion Mechanism of Bovine Lens Leucine Aminopeptidase: Active Site Solvent Structure and Binding Mode of L-Leucinal, a gem-Diolate Transition State Analog, by X-ray Crystallography. DOI:10.1021/bi00045a021. PMID:7578088.

Step 1.

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Catalytic Residues Roles

Residue Roles
Lys262A electrostatic stabiliser
Arg336A electrostatic stabiliser

Chemical Components

Step 1.

Contributors

Anna Waters, Craig Porter, Gemma L. Holliday