Methionyl aminopeptidase

 

Methionine aminopeptidase (MAP) catalyses the hydrolytic cleavage of the N-terminal methionine from newly synthesised polypeptides. These enzymes have a requirement for a divalent metal which has been shown to be feasible with multiple different metal ions including Co(II), Mn(II), Fe(II) and Zn(II) with Zinc showing to be the lowest activation energy .

 

Reference Protein and Structure

Sequence
P56218 UniProt (3.4.11.18) IPR028595 (Sequence Homologues) (PDB Homologues)
Biological species
Pyrococcus furiosus DSM 3638 (Archaea) Uniprot
PDB
1xgm - METHIONINE AMINOPEPTIDASE FROM HYPERTHERMOPHILE PYROCOCCUS FURIOSUS (2.8 Å) PDBe PDBsum 1xgm
Catalytic CATH Domains
3.90.230.10 CATHdb (see all for 1xgm)
Cofactors
Zinc(2+) (2)
Click To Show Structure

Enzyme Reaction (EC:3.4.11.18)

water
CHEBI:15377ChEBI
+
Met-Ala
CHEBI:73610ChEBI
→
L-alanine
CHEBI:16977ChEBI
+
L-methionine
CHEBI:16643ChEBI
Alternative enzyme names: L-methionine aminopeptidase, MAP, Methionine aminopeptidase, Peptidase M,

Enzyme Mechanism

Introduction

Water is polarised by coordinating to Zinc which is a strong Lewis acid as a result Glu 187 can more easily abstract a proton from the activated water molecule. The activated hydroxide can then nucleophilically attack the carbon of the scissille peptide bond and produce an oxyanion intermediate which is stabilised by coordination to zinc and hydrogen bonding to His 161. The oxyanion will then initiate an elimination which results in the cleavage of the peptide bond releasing the terminal Methionine. The N-terminal product then accepts a proton from Glu 187.

Catalytic Residues Roles

UniProt PDB* (1xgm)
His161 His161A Forms an oxyanion hole with Zinc to stabilise the negative charge on the oxyanion intermediate. electrostatic stabiliser
Asp82, His153, Asp93, Glu280, Glu187 Asp82A, His153A, Asp93A, Glu280A, Glu187A Forms part of the catalytic metal binding site. metal ligand
Glu187 Glu187A Acts as a general acid/base by at first accepting a proton from Zinc activated water and then donating a proton to the N-terminal amino group. metal ligand, proton acceptor, proton donor
*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

proton transfer, overall reactant used, bimolecular nucleophilic addition, intermediate formation, rate-determining step, unimolecular elimination by the conjugate base, intermediate collapse, overall product formed, native state of enzyme regenerated

References

  1. Copik AJ et al. (2005), Biochemistry, 44, 121-129. EPR and X-ray crystallographic characterization of the product-bound form of the MnII-loaded methionyl aminopeptidase from Pyrococcus furiosus. DOI:10.1021/bi048123+. PMID:15628852.
  2. Mitra S et al. (2008), FEBS J, 275, 6248-6259. Analyzing the catalytic role of Asp97 in the methionine aminopeptidase from Escherichia coli. DOI:10.1111/j.1742-4658.2008.06749.x. PMID:19019076.
  3. Leopoldini M et al. (2007), J Am Chem Soc, 129, 7776-7784. Which one among Zn(II), Co(II), Mn(II), and Fe(II) is the most efficient ion for the methionine aminopeptidase catalyzed reaction? DOI:10.1021/ja068168t. PMID:17523636.
  4. Meng L et al. (2002), Biochemistry, 41, 7199-7208. Overexpression and divalent metal binding properties of the methionyl aminopeptidase from Pyrococcus furiosus. PMID:12044150.
  5. Tahirov TH et al. (1998), J Mol Biol, 284, 101-124. Crystal structure of methionine aminopeptidase from hyperthermophile, Pyrococcus furiosus. DOI:10.1006/jmbi.1998.2146. PMID:9811545.

Step 1. Glu187 deprotonates the Iron activated water.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp93A metal ligand
His153A metal ligand
Glu187A metal ligand
Glu280A metal ligand
Asp82A metal ligand
His161A electrostatic stabiliser
Glu187A proton acceptor

Chemical Components

proton transfer, overall reactant used

Step 2. The activated hydroxide attacks the peptide carbonyl in a nucleophilic addition producing an oxyanion intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp82A metal ligand
Asp93A metal ligand
His153A metal ligand
Glu187A metal ligand
Glu280A metal ligand
His161A electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic addition, intermediate formation, overall reactant used, rate-determining step

Step 3. The oxyanion initiates an elimination which results in the cleavage of the peptide bond. The N-terminal amino group accepts a proton from Glu187.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp82A metal ligand
Asp93A metal ligand
His153A metal ligand
Glu187A metal ligand
Glu280A metal ligand
His161A electrostatic stabiliser
Glu187A proton donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer, intermediate collapse, overall product formed, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Glu187 deprotonates the Iron activated water.

Step 2. The activated hydroxide attacks the peptide carbonyl in a nucleophilic addition producing an oxyanion intermediate.

Step 3. The oxyanion initiates an elimination which results in the cleavage of the peptide bond. The N-terminal amino group accepts a proton from Glu187.

Products.

Contributors

Christian Drew, Craig Porter, Gemma L. Holliday, Charity Hornby