Assignment 4: Finalized Protein Summary

Rex-family repressors fine-tune the expression of genes involved in respiration in response to oxygen levels. These redox-sensing repressors are found in Gram-positive bacterial species like streptococcus and staphylococcus (Reference 1). T-Rex is isolated from thermus aquaticus, a type of bacteria that can withstand high temperatures and was first discovered in the hot springs of Yellowstone National Park (Reference 2).

Figure 1: Thermus Aquaticus Rex colored by secondary structure, with DNA attached. PDB file (1XCB), edited by author on PyMol software.

The geometry of T-Rex is specific to both NAD and DNA. Molecule binding of NAD occurs in the large cleft between each subunit, and up to 2 NAD molecules can bind at a time at this domain. The two protruding bumps on T-Rex are the DNA binding domain (Figure 1). The two domains for NAD and DNA, respectively, are connected by an alpha helical arm, which reaches between domains and locks the subunits of the T-Rex complex together (Reference 3). Figure 2 offers a cross-sectional view of T-Rex, exposing the NAD binding domain that can bind two NAD molecules with the alpha-helical arm and the DNA in its domain. 

Figure 2: Geometric domains of T-Rex. PDB file (1XCB), edited by author on PyMol software and with PowerPoint.

T-Rex represses respiratory gene expression until a limited oxygen supply raises the ratio of intracellular NADH: NAD+. Both NAD+ and NADH bind to T-Rex, evoking different reactions. Elevated NADH levels indicate that oxygen is unavailable, and that the expression of genes required in respiration are needed. With NADH bound the NAD domain in T-Rex, the two DNA binding domains are located so closely that the shape of DNA cannot fit and match the domains, and transcription of DNA continues. Increased NAD+ indicate a restoration of oxygen levels and no need for continued respiration. The binding of NAD+ induces a conformational shift of the entire T-Rex complex, opening the DNA domains like a scissors. In this form, DNA can bind to T-Rex, thus suppressing transcription activity. Figure 3 shows T-Rex with a) NAD+ bound state and open domains allowing for DNA binding, and b) NADH bound, inducing a rotation of the repressor and a contraction of the DNA binding domain disallowing for DNA to bind (Reference 4).

Figure 3: T-Rex with a) NAD+ bound state and open DNA binding domains and b) NADH bound and closed state. Figure from McLaughlin paper, reference 3. 

In summary, the intracellular ratio of NADH: NAD+ is a sensitive indicator of the redox state and whether oxygen is present or not. T-Rex facilitates this oxygen responsiveness as a signaling method for gene transcription. It is one of the first well-characterized structures responsible for allosteric gene regulation by the reduction of NADH to oxidized NAD+.

Don’t you just love T-Rex?

Figure 4: PDB file (1XCB), edited by author on PyMol software.

References:
1. Sickmier, E. A. "X-Ray Structure of a Rex Family Repressor/NADH Complex from Thermus Aquaticus." RCSB Protein Data Bank. Dec. 2005. Web.
2. Shapiro, Leo. "Thermus Aquaticus." Encyclopedia of Life. Web. 
3. Goodsell, David S. "T-Rex." Protein Structure Initiative. Sept. 2008. Web.
4. McLaughlin, Krystle J. "Structural Basis for NADH/NAD+ Redox Sensing." Molecular Cell. 38 (2011): 563-75. Web.