featured system 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.
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.
DcpS Scavenger Decapping Enzyme (PDB entry 3bla)
The DcpS enzyme is a dimer of identical subunits. In this Jmol image, the N-terminal domains are colored blue and the C-terminal domains are colored magenta. One subunit is in bright colors and the other is in pastel colors. Notice that the N-terminal domain is rocked to one side, binding tightly around one of the bound inhibitors (shown in green). Also notice the large domain-swapped portions in the N-terminal domains.
(2005) X-ray structure of a Rex-family repressor/NADH complex: insights into the mechanism of redox sensing. Structure 13, 43-54. E. A. Sickmier, D. Brekasis, S. Paranawithana, J. B. Bonanno, M. S. B. Paget, S. K. Burley and C. L. Kielkopf