Ornithine cyclodeaminase

 

Ornithine cyclodeaminase (OCD) from Pseudomonas putida belongs to the mu-crystallin protein family. It catalyses the conversion of L-ornithine to L-proline by an NAD+ dependent hydride transfer reaction. The precise function of this protein is still unknown, but it may have a regulatory function in the use of amino acids as neurotransmitters.

 

Reference Protein and Structure

Sequence
Q88H32 UniProt (4.3.1.12) IPR003462 (Sequence Homologues) (PDB Homologues)
Biological species
Pseudomonas putida KT2440 (Bacteria) Uniprot
PDB
1x7d - Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms (1.6 Å) PDBe PDBsum 1x7d
Catalytic CATH Domains
3.30.1780.10 CATHdb 3.40.50.720 CATHdb (see all for 1x7d)
Cofactors
Nadph(4-) (1)
Click To Show Structure

Enzyme Reaction (EC:4.3.1.12)

L-ornithinium(1+)
CHEBI:46911ChEBI
→
L-proline zwitterion
CHEBI:60039ChEBI
+
ammonium
CHEBI:28938ChEBI
Alternative enzyme names: Ornithine cyclase, Ornithine cyclase (deaminating), OCD, L-ornithine ammonia-lyase (cyclizing),

Enzyme Mechanism

Introduction

Asp 228 abstracts a proton from the alpha-amino nitrogen, which causes a hydride to be transferred from the alpha-carbon to the re face of NAD+. Glu 56 acts as a general base by deprotonating the nitrogen atom of the delta-amino group, activating it for nucleophilic attack on the alpha-carbon atom. This results in the double bond between the alpha-carbon and nitrogen breaking, and the alpha-nitrogen being protonated by Asp 228. Asp 228 then deprotonates the delta-nitrogen, causing it to nucleophilically attack the alpha-carbon again, forming a double bond and eliminating ammonia. This results in an electrophilic C2 centre which then accepts a hydride from NADH, breaking the C=N to form L-proline and reforming NAD+.

Catalytic Residues Roles

UniProt PDB* (1x7d)
Glu56 Glu56A Acts as a general base, deprotonating the nitrogen atom of the delta-amino group, activating it for nucleophilic attack on the alpha-carbon. increase nucleophilicity, proton acceptor, proton donor
Asp228 Asp228A Acts as an acid/base to the substrate by deprotonating the alpha-amino nitrogen, activating it for nucleophilic attack. It then donates this proton back to the alpha-nitrogen once nucleophilic attack has taken place. Asp 228 then deprotonates the delta-nitrogen, activating it for nucleophilic attack. 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, hydride transfer, cofactor used, overall reactant used, intramolecular nucleophilic addition, cyclisation, bimolecular elimination, native state of cofactor regenerated, overall product formed, bimolecular nucleophilic addition

References

  1. Goodman JL et al. (2004), Biochemistry, 43, 13883-13891. Ornithine Cyclodeaminase:  Structure, Mechanism of Action, and Implications for the μ-Crystallin Family†,‡. DOI:10.1021/bi048207i. PMID:15518536.

Step 1. Asp 228 abstracts a proton from the alpha-amino nitrogen, which causes a hydride to be transferred from the alpha-carbon to the re face of NAD+

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp228A proton acceptor

Chemical Components

proton transfer, hydride transfer, cofactor used, overall reactant used

Step 2. Glu 56 acts as a general base by deprotonating the nitrogen atom of the delta-amino group, activating it for nucleophilic attack on the alpha-carbon atom. This results in the double bond between the alpha-carbon and nitrogen breaking, and the alpha-nitrogen being protonated by Asp 228.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu56A increase nucleophilicity
Asp228A proton donor
Glu56A proton acceptor

Chemical Components

proton transfer, ingold: intramolecular nucleophilic addition, cyclisation

Step 3. Asp 228, which loses a proton to an unknown base between the previous step and this one then deprotonates the delta-nitrogen, causing it to nucleophilically attack the alpha-carbon again, forming a double bond and eliminating ammonia.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp228A proton acceptor
Glu56A proton donor

Chemical Components

ingold: bimolecular elimination, proton transfer

Step 4. The electrophilic C2 centre then accepts a hydride from NADH, breaking the C=N to form L-proline and reforming NAD+.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

native state of cofactor regenerated, overall product formed, ingold: bimolecular nucleophilic addition, hydride transfer
Download: Image, Marvin File

Step 1. Asp 228 abstracts a proton from the alpha-amino nitrogen, which causes a hydride to be transferred from the alpha-carbon to the re face of NAD+

Step 2. Glu 56 acts as a general base by deprotonating the nitrogen atom of the delta-amino group, activating it for nucleophilic attack on the alpha-carbon atom. This results in the double bond between the alpha-carbon and nitrogen breaking, and the alpha-nitrogen being protonated by Asp 228.

Step 3. Asp 228, which loses a proton to an unknown base between the previous step and this one then deprotonates the delta-nitrogen, causing it to nucleophilically attack the alpha-carbon again, forming a double bond and eliminating ammonia.

Step 4. The electrophilic C2 centre then accepts a hydride from NADH, breaking the C=N to form L-proline and reforming NAD+.

Products.

Contributors

Ellie Wright, Gemma L. Holliday, James Willey