The ability of the cell to respond to its environment depends on the effective coordination and/or integration of metabolic pathways. For those pathways that involve the biosynthesis of lipophilic signaling molecules, their coordination may be exceptionally challenging in terms of substrate acquisition and specificity, as hydrophobic compounds will partition into the membrane phase, and active sites that recognize bulky hydrophobic substrates might be inherently promiscuous. In order to understand how specificity is achieved in the context of the cell, and how the channeling of intermediates might enhance specificity, we have focused our recent efforts on the structural biology of enzymes involved in the biosynthesis of compounds derived from arachidonic acid released from the membrane by the action of phospholipases. These compounds serve as the precursor for prostaglandins, leukotrienes, thromboxanes, and other biologically active eicosanoids, and the enzymes involved in their biosynthesis represent drug targets, or avenues for the preparation of related compounds for pharmacological uses. In our laboratory we address questions of the regio- and stereo- specificity of these biosynthetic enzymes, as well as how soluble enzymes in this pathway acquire insoluble substrates. Naturally occurring fusion proteins provide us with a system with which to address the structural basis for regio- and stereo- specificity of animal lipoxygenases and their regulation by Ca++, as well as aspects of channeling of intermediates in eicosanoid biosynthetic pathways and protein-protein recognition.
Bilder, P. W., Ding, H. & Newcomer, M. E. (2004). Crystal structure of the ancient, Fe-S scaffold IscA reveals a novel protein fold. Biochemistry 43, 133-9.
Bordelon, T., Montegudo, S. K., Pakhomova, S., Oldham, M. L. & Newcomer, M. E. (2004). A disorder to order transition accompanies catalysis in retinaldehyde dehydrogenase type II. J Biol Chem 279, 43085-91.
Pakhomova, S., Buck, J. & Newcomer, M. E. (2005). The structures of the unique sulfotransferase retinol dehydratase with product and inhibitors provide insight into enzyme mechanism and inhibition. Protein Sci 14, 176-82.
Oldham, M. L., Brash, A. R. & Newcomer, M. E. (2005). Insights from the X-ray Crystal Structure of Coral 8R-Lipoxygenase: CALCIUM ACTIVATION VIA A C2-LIKE DOMAIN AND A STRUCTURAL BASIS OF PRODUCT CHIRALITY. J Biol Chem 280, 39545-52.
Oldham, M. L., Brash, A. R. & Newcomer, M. E. (2005). The structure of coral allene oxide synthase reveals a catalase adapted for metabolism of a fatty acid hydroperoxide. Proc Natl Acad Sci U S A 102, 297-302.
Vander Kooi, C. W., Ohi, M. D., Rosenberg, J. A., Oldham, M. L., Newcomer, M. E., Gould, K. L., and Chazin, W. J. (2006). The Prp19 U-box Crystal Structure Suggests a Common Dimeric Architecture for a Class of Oligomeric E3 Ubiquitin Ligases. Biochemistry 45, 121-130.
Bilder, P. W., Lightle, S., Ohren, J., Bainbridge, G., Finzel, B., Sun, F., Holly, S., Al-Kassim, L., Spessard, C., Melnick, M., Newcomer, M. E. & Waldrop, G. L. (2006). The Structure of the Carboxyltransferase Component of Acetyl-CoA Carboxylase Reveals a Zinc-binding Motif Unique to the Bacterial Enzyme. Biochemistry 45, 1712-1722.
Bordelon, T., Wilkinson, S. P., Grove, A. & Newcomer, M. E. (submitted). The crystal structure of the transcriptional regulator HucR from Deinococcus radiodurans reveals a repressor preconfigured for DNA binding. J. Mol. Biol. In press.