CO2 migration pathways in oxalate decarboxylase and clues about its active site.
Oxalate decarboxylase catalyzes the decarboxylation of oxalate to formate and CO2 in the presence of molecular oxygen. This enzyme has two domains, each containing a Mn(II) ion coordinated with three histidine residues. The specific domain in which the decarboxylation process takes place is still a matter of investigation. Herein, the transport of the product, i.e., CO2, from the reaction center to the surface of the enzyme is studied using atomistic molecular dynamics simulations. The specific pathway for the migration of the molecule as well as its microscopic interactions with the amino acid residues lining the path is delineated. Further, the transport of CO2 is shown to occur in a facile manner from only domain I and not from domain II, indicating that the former is likely to be the active site of the enzyme.
Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India.
Tarak
T
Karmakar
Ganga
G
Periyasamy
Sundaram
S
Balasubramanian
D055162:Biocatalysis; D002245:Carbon Dioxide / Q000378:metabolism*; D002262:Carboxy-Lyases / Q000737:chemistry* / Q000378:metabolism*; D020134:Catalytic Domain; D005561:Formates / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010070:Oxalates / Q000737:chemistry / Q000378:metabolism; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism; D013499:Surface Properties
D005561:Formates; D010070:Oxalates; C030544:formic acid; D002245:Carbon Dioxide; D002262:Carboxy-Lyases; C021915:oxalate decarboxylase; D010100:Oxygen