Polyamine oxidase (propane-1,3-diamine-forming)

 

Polyamine oxidase is able to catalyse the oxidation of the secondary amino groups of polyamines to their corresponding imino forms, using FAD as a cofactor coupled to eventual reduction of H2O2 to form water. The product of the reaction depends on the initial starting material; for example mammalian polyamine oxidase can convert spermidine to putrescine. Polyamines bind DNA and regulate transcription and translation, thus play roles in cell differentiation and multiplication, causing them to be implicated in the development of certain forms of cancer. As a result the enzyme is of interest as a drug target. Despite different physiological roles, mammalian, plant and bacterial forms of the enzyme show significant sequence and structural homology, and polyamine oxidases also show homology to monoamine oxidases, suggesting a common catalytic mechanism.

 

Reference Protein and Structure

Sequence
O64411 UniProt (1.5.3.14, 1.5.3.15) IPR001613 (Sequence Homologues) (PDB Homologues)
Biological species
Zea mays (Maize) Uniprot
PDB
1b5q - A 30 ANGSTROM U-SHAPED CATALYTIC TUNNEL IN THE CRYSTAL STRUCTURE OF POLYAMINE OXIDASE (1.9 Å) PDBe PDBsum 1b5q
Catalytic CATH Domains
3.50.50.60 CATHdb (see all for 1b5q)
Cofactors
Fadh2(2-) (1)
Click To Show Structure

Enzyme Reaction (EC:1.5.3.14)

water
CHEBI:15377ChEBI
+
dioxygen
CHEBI:15379ChEBI
+
spermidine(3+)
CHEBI:57834ChEBI
→
4-ammoniobutanal
CHEBI:58264ChEBI
+
hydrogen peroxide
CHEBI:16240ChEBI
+
trimethylenediaminium
CHEBI:57484ChEBI
Alternative enzyme names: MPAO, Maize PAO,

Enzyme Mechanism

Introduction

The reaction is believed to proceed through nucleophilic attack from the amino group, deprotonated by Glu 62, on the C4a of FAD. This leads to a covalent adduct which collapses, assisted by proton transfer from the alpha carbon to the N5 of FAD via a water molecule, to give the product imine.

Catalytic Residues Roles

UniProt PDB* (1b5q)
Glu90 Glu62C Acts as general base to remove proton from the nucleophilic amino group of the substrate. 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, bimolecular nucleophilic addition, intermediate formation, elimination (not covered by the Ingold mechanisms), intermediate collapse, inferred reaction step, overall product formed, native state of enzyme regenerated

References

  1. Royo M et al. (2005), Biochemistry, 44, 7079-7084. Mechanistic Studies of Mouse Polyamine Oxidase with N1,N12-Bisethylspermine as a Substrate†. DOI:10.1021/bi050347k. PMID:15865452.
  2. Binda C et al. (2001), Biochemistry, 40, 2766-2776. Structural Bases for Inhibitor Binding and Catalysis in Polyamine Oxidase†,‡. DOI:10.1021/bi002751j. PMID:11258887.
  3. Binda C et al. (1999), Structure, 7, 265-276. A 30 Å long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase. DOI:10.1016/S0969-2126(99)80037-9.

Step 1. Glu62 deprotonates the secondary amine nitrogen of the reactant.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu62C proton acceptor

Chemical Components

proton transfer

Step 2. Nucleophilic attack of the secondary amine on C4 of FAD is accompanied by proton transfer to N5 of FAD, forming a covalent intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer, intermediate formation

Step 3. The reactant-FAD bond is cleaved, forming FADH- and an imine intermediate. FADH- is reoxidised by molecular oxygen.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

elimination (not covered by the Ingold mechanisms), intermediate formation

Step 4. The water molecule that is H bonded to the flavin N5 atom is well positioned to perform the hydrolytic attack on the imino compound.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

ingold: bimolecular nucleophilic addition, intermediate formation

Step 5. Proton transfer between the hydroxyl group and secondary amine occurs prior to this step. The amine is then eliminated, forming the aldehyde product.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

elimination (not covered by the Ingold mechanisms), intermediate collapse, inferred reaction step, overall product formed

Step 6. Glu62 is deprotonated to regenerate the active site.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu62C proton donor

Chemical Components

proton transfer, inferred reaction step, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Glu62 deprotonates the secondary amine nitrogen of the reactant.

Step 2. Nucleophilic attack of the secondary amine on C4 of FAD is accompanied by proton transfer to N5 of FAD, forming a covalent intermediate.

Step 3. The reactant-FAD bond is cleaved, forming FADH- and an imine intermediate. FADH- is reoxidised by molecular oxygen.

Step 4. The water molecule that is H bonded to the flavin N5 atom is well positioned to perform the hydrolytic attack on the imino compound.

Step 5. Proton transfer between the hydroxyl group and secondary amine occurs prior to this step. The amine is then eliminated, forming the aldehyde product.

Step 6. Glu62 is deprotonated to regenerate the active site.

Products.

Contributors

Peter Sarkies, Gemma L. Holliday, Amelia Brasnett