Structure of the Month: November 2008 [see all]

Crystal structure of a human prostaglandin reductase in complex with NADPH and nicotinamide

Tzu-Ping Ko, Yu-Hauh Wu, and Andrew H.-J. Wang
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan

Prostaglandins are a class of versatile compounds that mediate a large number of processes, and have strong physiological effects, such as pain, inflammation, and carcinogenesis. The prostaglandin reductase PTGR2 uses NADPH to reduce 15-keto-PGE2, a key step in terminal inactivation of prostaglandins and suppression of the PPARγ-mediated adipocyte differentiation. Our crystal structures feature critical conformational changes in an LID motif and a polyproline type II helix induced by NADPH binding. The LID becomes highly disordered upon indomethacin binding, suggesting plasticity of the active site. These findings can be applied to rational design of PTGR2 inhibitors.

This year, Academia Sinica is celebrating its 80th anniversary. The Institute of Biological Chemistry (IBC) is much younger. The preparatory office for IBC was established in 1970. Construction of the IBC building on the National Taiwan University campus began in 1973 and was completed in 1977. In 1995, IBC expanded to a new building in Nankang. Starting in 2000, facing new challenges in the post-genomics era, IBC has been devoted to the studies of Structural Biology and Functional Genomics.

The Rigaku MicroMax-007 HF is a bright X-ray source with intensity comparable to some synchrotron beamlines. It allows us to collect high-resolution data sets without going to the synchrotrons. The PTGR2 structure shown here (Figure 1) contains a bound NADP molecule, which triggers the protein conformational change from an open form (PDB 1VJ1, [1]) to a closed form (this work, PDB 2ZB7 [2]). The LID motif becomes visible in the presence of cofactor in the active site, whereas in the apo-enzyme it is disordered.

The electron density for the NADP (Figure 2) is very clear, allowing detailed analysis of the molecular interactions between the enzyme and the cofactor. Interestingly, the enzyme also binds to an additional ligand with a six-membered ring. It stacks with the nicotinamide moiety of the NADP, and probably is a nicotinamide molecule from the NADP solution. Because the hydride transfer occurs in this position, the extra NIC ligand can serve as a model for substrate/inhibitor binding. In the figure, the Fo-Fc omit map was calculated for the two ligands and contoured at the 3σ level.

This work was performed in the laboratory of Dr. Andrew H.-J. Wang at Academia Sinica, in the Institute of Biological Chemistry. 

Directed by Professor Andrew H.-J. Wang (now Vice President of Academia Sinica), structural biology projects were readily integrated with the original research fields. Important proteins of our interests have been solved using X-ray crystallography. In addition to the in-house MicroMax-002, we share a MicroMax-007 HF with the Institute of Molecular Biology, and have beam-time allocations throughout the year at the National Synchrotron Radiation Research Center, as well as the Photon Factory and SPring-8 in Japan.

Data collection details

Data collection details for Human prostaglandin reductase.

References

1. Levin, I., Schwarzenbacher, R., McMullan, D., Abdubek, P., Ambing, E., Biorac, T., Cambell, J., Canaves, J.M., Chiu, H.J., Dai, X., et al. (2004). Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution. Proteins 56, 629-633.
2. Wu, Y.H., Ko, T.P., Guo, R.T., Hu, S.M., Chuang, L.M., Wang, A.H.J. (2008). Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2. Structure (in press) doi:10.1016/j.str.2008.09.007.