Credit: © 2010 ACS

Some enzymes that carry out multiple reaction steps are known to contain tunnels that are used to direct the transport of reactive intermediates. One such enzyme is carbamoyl phosphate synthetase from Escherichia coli, which catalyses the production of carbamoyl phosphate — an intermediate in nucleotide and arginine synthesis. An important step in this synthesis is the transport of carbamate, after its formation, through a ∼40-Å-long tunnel within the enzyme to another active site where it is phosphorylated to give the final product.

Now Frank Raushel, Yi Qin Gao and colleagues from Texas A&M University have used molecular dynamics simulations to reveal that the tunnel is composed of three pockets filled with water connected by two narrow passages (pictured; J. Am. Chem. Soc. 132, 3870–3878; 2010). To understand the factors that influence carbamate transport, they also calculated the potential energy of the system under different substrate–product binding conditions with carbamate at different positions along the tunnel.

The researchers found that phosphate, a by-product from the carbamate-forming reaction step, must be released from that active site before the carbamate can enter the tunnel. This release causes the rotation of an arginine residue within the enzyme that unblocks the tunnel entrance, and also shields the carbamate from undesirable electrostatic interactions with three glutamate residues within the tunnel.

The original version of this story first appeared on the Research Highlights section of the Nature Chemistry website.