Rational protein engineering in action: the first crystal structure of a phenylalanine tRNA synthetase from Staphylococcus haemolyticus.

In this article, we describe for the first time the high-resolution crystal structure of a phenylalanine tRNA synthetase from the pathogenic bacterium Staphylococcus haemolyticus. We demonstrate the subtle yet important structural differences between this enzyme and the previously described Thermus thermophilus ortholog. We also explain the structure-activity relationship of several recently reported inhibitors. The native enzyme crystals were of poor quality--they only diffracted X-rays to 3-5A resolution. Therefore, we have executed a rational surface mutagenesis strategy that has yielded crystals of this 2300-amino acid multidomain protein, diffracting to 2A or better. This methodology is discussed and contrasted with the more traditional domain truncation approach.

The structure of the carboxyltransferase component of acetyl-coA carboxylase reveals a zinc-binding motif unique to the bacterial enzyme.

Acetyl-coA carboxylase (ACC) is a central metabolic enzyme that catalyzes the committed step in fatty acid biosynthesis: biotin-dependent conversion of acetyl-coA to malonyl-coA. The bacterial carboxyltransferase (CT) subunit of ACC is a target for the design of novel therapeutics that combat severe, hospital-acquired infections resistant to the established classes of frontline antimicrobials. Here, we present the structures of the bacterial CT subunits from two prevalent nosocomial pathogens, Staphylococcus aureus and Escherichia coli, at a resolution of 2.0 and 3.0 A, respectively. Both structures reveal a small, independent zinc-binding domain that lacks a complement in the primary sequence or structure of the eukaryotic homologue.

Two distinct classes of CCAAT box elements that bind nuclear factor-Y/alpha-actinin-4: potential role in human CYP1A1 regulation.

A negative regulatory element (NRE1; position -794 to -774) was previously identified that mediates the downregulation of CYP1A1, including partial suppression of Ah receptor-dependent induction. The CCAAT-box binding protein, nuclear factor-Y (NF-Y), is a component of one of two protein complexes that specifically and competitively bind the CYP1A1 NRE1 in vitro with nearly equal affinity. The second complex involves an unidentified protein(s) called the negative regulatory factor (NRF). Competitive electrophoretic mobility shift assays (EMSA) revealed two distinct classes of NF-Y-binding CCAAT-box elements distinguished by their ability or inability to also bind NRF. To further explore the identity of NRE1-binding proteins, a purification scheme was developed culminating in NRE1-dependent DNA affinity chromatography and sequence analysis. An approximate 106-kDa protein was purified and shown to be alpha-actinin-4 (ACTN4), one of two ubiquitously expressed non-muscle actinins. Electrophoretic mobility shift assays combined with Western blot analysis and co-immunoprecipitation experiments suggested that ACTN4 is associated with the NF-Y complex, but not NRF. Attempts to demonstrate a role for NF-Y/ACTN4 in regulating CYP1A1 expression were unsuccessful, likely due to an inability to significantly change nuclear ACTN4 levels with phosphatidylinositol 3'-kinase agonists and antagonists. However, given ACTN4's known functions and the suspected functions of actin and actin-related proteins in chromatin remodeling and other nuclear events, ACTN4 may assist NF-Y in recruiting chromatin-remodeling complexes or may direct NF-Y/ACTN4-targeted genes to the nuclear matrix and active transcriptional complexes.