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Both LPC and CSU can be accessed through the PDB and are integrated in the 3DB Atlas page of all PDB files. For any given file, the tools can also be accessed at http://www.pdb.bnl. gov/pdb-bin/lpc?PDB_ID= and http://www.pdb.bnl. gov/pdb-bin/csu?PDB_ID= with the four-letter PDB code added at the end in each case. Finally, LPC and CSU can be accessed at: http://sgedg.weizmann.ac.il/lpc and http://sgedg.weizmann.ac.il/csu.

Despite their functional and structural diversity, G protein-coupled receptors (GPCRs) share a common mechanism of signal transduction via conformational changes in the seven-transmembrane (7TM) helical domain. New major insights into this mechanism come from the recent crystallographic discoveries of a partially hydrated sodium ion that is specifically bound in the middle of the 7TM bundle of multiple class A GPCRs. This review discusses the remarkable structural conservation and distinct features of the Na+ pocket in this most populous GPCR class, as well as the conformational collapse of the pocket on receptor activation. New insights help to explain allosteric effects of sodium on GPCR agonist binding and activation, and sodium’s role as a potential co-factor in class A GPCR function.

The Protein Data Bank (PDB) at Brookhaven National Laboratory, is a database containing experimentally determined three-dimensional structures of proteins, nucleic acids and other biological macromolecules, with approximately 8000 entries. Data are easily submitted via PDB's WWW-based tool AutoDep, in either mmCIF or PDB format, and are most conveniently examined via PDB's WWW-based tool 3DB Browser.

With the recent breakthroughs in G protein-coupled receptor structure, one can now compare experimentally determined structures with the most recent modeling and docking methods. A community-wide blind prediction experiment (GPCR Dock 2008) was conducted in coordination with the publication of the human adenosine A 2A receptor bound to the ligand ZM241385 crystal structure (Science 322, 1211(Science 322, (2008). Twenty-nine participating groups submitted 206 models that were evaluated for the accuracy of the ligand binding mode and the overall receptor model. Several new insights emerged including the critical importance of disulfide bonds in the extracellular loops, helix residue registry, and domain knowledge.

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We have recently observed promising success in a mouse model at treating the metabolic disorder phenylketonuria (PKU) with phenylalanine ammonia lyase (PAL) from R. toruloides and A. variabilis. Both molecules, however, required further optimization in order to overcome problems with protease susceptibility, thermal stability and aggregation. We reduced aggregation of the A. variabilis PAL by mutating two surface cysteine residues (C503 and C565) to serines. Here we report the structural and biochemical characterization of the A. variabilis PAL C503S/C565S double mutant. Unlike previously published PAL structures, significant electron density is observed for the two active site loops in the A. variabilis C503S/C565S double mutant, yielding a complete view of the active site. Docking studies and NHS-biotin binding studies support a proposed mechanism in which the amino group of the phenylalanine substrate is attacked directly by the 4-methylideneimidazole-5-one (MIO) prosthetic group. We propose a helix-to-loop conformational switch in the helices flanking the inner active site loop that regulates accessibility of the active site. Differences in loop stability among PAL homologs may explain the observed variation in enzyme efficiency despite the highly conserved structure of the active site. A. variabilis C503S/C565S PAL is shown to be both more thermally stable and more resistant to proteolytic cleavage than R. toruloides PAL. Additional increases in thermal stability and protease resistance upon ligand binding may be due to enhanced interactions among the residues of the active site, possibly locking the active site structure in place and stabilizing the tetramer. Examination of the A. variabilis C503S/C565S PAL structure combined with analysis of its physical properties provides a structural basis for further engineering of residues that could result in a better therapeutic molecule.