September 2008

The repressor protein T-Rex has the difficult job of distinguishing the difference between NAD+ and NADH. It monitors the level of NADH in Gram-positive bacteria, which is normally quite low. If the level begins to rise, the repressor binds to NADH and drops off the DNA. This allows the production of enzymes that use alternative electron acceptors, such as a cytochrome bd terminal oxidase variant. Together, these enzymes work to bring the NADH level back to normal.

T-Rex Up Close

Researchers at the New York Structural GenomiX Research Consortium have taken a closer look at the structural basis of this recognition. The T-Rex protein is composed of two identical subunits, shown here from PDB entry 1xcb. Two molecules of NAD bind in a large cleft in the interface between the two subunits (only one NADH molecule is seen in this view, in red). Notice that the adenine ring (at upper left here) is bound in a deep pocket, and the molecule snakes down to bury the nicotinamide ring between the two subunits. The NAD-binding domain is connected to a DNA-binding domain, at the bottom here. A domain-swapped alpha helical arm threads through the gap between the two domains, reaching from one subunit to the other and forming a locked grip that holds the complex together.

Redox Sensing

T-Rex binds to both NAD+ and NADH, but only the NAD+ complex can bind to the DNA operator and block transcription. In this structure, the two DNA-binding domains are too close to each other to bind comfortably to DNA. Binding of NAD+ presumably shifts the entire complex, scissoring the DNA-binding domains apart to match the shape of DNA. The state of the nicotinamide ring is probed by a collection of hydrophobic amino acids, as shown in the Jmol image below, which includes a phenylalanine (in turquoise) that binds between the two nicotinamides and tyrosines (in magenta) that stack against the carbon atom that is reduced in NADH.

T-Rex (PDB entry 1xcb)

T-Rex can distinguish the small chemical difference between NAD+ and NADH. In this Jmol image, two NADH molecules are in spacefilling spheres. The nicotinamide rings are close together at the center with a phenylalanine (in turquoise) bound in between. The nicotinamides are surrounded by hydrophobic amino acids, including a key tyrosine (in magenta) that interacts with the nicotinamide carbon atom that is reduced. Notice that the binding site is asymmetric, with one of the phenylalanines bound between the nicotinamides and the similar phenylalanine from the other subunit folded back towards the protein.


  1. E. A. Sickmier, D. Brekasis, S. Paranawithana, J. B. Bonanno, M. S. B. Paget, S. K. Burley and C. L. Kielkopf (2005) X-ray structure of a Rex-family repressor/NADH complex: insights into the mechanism of redox sensing. Structure 13, 43-54.