Enzymology
Do FeS clusters rule bacterial iron regulation?
For decades, the bacterial ferric uptake regulator (Fur) has been thought to respond to ferrous iron to transcriptionally regulate genes required for balancing iron uptake, storage, and utilization. Because iron binding to Fur has never been confirmed in vivo, the physiological iron-sensing mechanism remains an open question. Fontenot et al. now show that Fur purified from Escherichia coli binds an all-Cys-coordinated [2Fe-2S] cluster. This finding opens the exciting possibility that Fur may join numerous well-studied bacterial, fungal, and mammalian proteins that use FeS clusters for cellular iron regulation.To cut or not to cut: New rules for proteolytic shedding of membrane proteins
Sheddases are specialized proteases that control the abundance and function of membrane proteins by cleaving their substrate's extracellular domain (ectodomain), a process known as shedding. Hundreds of shedding substrates have been identified, but little is known about the mechanisms that govern ectodomain shedding. Iwagishi et al. now report that negatively charged amino acids in the membrane-proximal juxtamembrane domain of substrates make them resistant to shedding by the metalloprotease ADAM17.Solving a furan fatty acid biosynthesis puzzle
Furan fatty acids (FuFAs), characterized by a central furan moiety, are widely dispersed in nature, but their biosynthetic origins are not clear. A new study from Lemke et al. employs a full court press of genetics, genomics, biochemical, and advanced analytical techniques to dissect the biosynthetic pathway of mono- and dimethyl FuFAs and their intermediates in two related bacteria. These findings lay the foundation both for detailed study of these novel enzymes and for gaining further insights into FuFA functions.Keep a lid on it: A troika in kinase allostery
The malaria parasite Plasmodium falciparum encodes a cGMP-dependent protein kinase G (PfPKG) that is critical for its life cycle. Specific cGMP analogs are able to act as partial agonists of PfPKG. Using the exquisite diagnostic power of NMR chemical shifts, Byun et al. demonstrate that the extent of agonism by these cGMP derivatives relates to the degree of stabilization of a unique inactive conformation that shares structural features with both the ligand-free, inactive and the cGMP-bound, active states.How a tailor achieves the perfect fit
Most antigenic peptides that bind stably to a major histocompatibility complex (MHC) I molecule for display to the immune system are approximately the same length, thanks in part to the expert trimming done by endoplasmic reticulum aminopeptidases (ERAPs), the final peptidases in the antigen-presentation pathway. An open question is whether ERAPs edit peptides to this optimal length while they are bound to MHC I molecules (using the latter as a pattern of sorts) or by free hand. Mavridis et al. present multiple lines of evidence that this trimming cannot readily occur on MHC I molecules, but rather only in solution, suggesting that ERAPs work alone to tailor the perfect fit for the immunopeptidome.A moonlighting nuclease puts CRISPR in its place
Integration of spacers into CRISPR loci requires the Cas1/Cas2 integrase complex, frequently in combination with Cas4 exonuclease. However, several CRISPR-Cas systems lack Cas4. Whether Cas4-like activity is dispensable in these systems or provided by an unidentified actor was not known. In this issue of the Journal of Biological Chemistry, Ramachandran et al. show that in subtype I-E systems, Cas4-like activity is supplied by DnaQ-superfamily exonucleases, providing a beautiful example of cellular machinery moonlighting in support of CRISPR-Cas adaptive immunity.Deoxyribonucleotide salvage falls short in whole animals
Ribonucleotide reductase (RNR) catalyzes the first committed reaction in DNA synthesis. Most of what we know about RNR regulation comes from studies with cultured cells and with purified proteins. In this study, Tran et al. use Cre-Lox technology to inactivate RNR large subunit expression in heart and skeletal muscle of mouse embryos. Analysis of these mutants paints a picture of dNTP regulation in whole animals quite different from that seen in studies of purified proteins and cultured cells.How a purine salvage enzyme singles out the right base
Two phosphoribosyltransferases in the purine salvage pathway exhibit exquisite substrate specificity despite the chemical similarity of their distinct substrates, but the basis for this discrimination was not fully understood. Ozeir et al. now employ a complementary biochemical, structural, and computational approach to deduce the chemical constraints governing binding and propose a distinct mechanism for catalysis in one of these enzymes, adenine phosphoribosyltransferase. These insights, built on data from an unexpected finding, finally provide direct answers to key questions regarding these enzymes and substrate recognition more generally.Surprise! A hidden B12 cofactor catalyzes a radical methylation
Radical S-adenosylmethionine (SAM) (RS) methylases perform methylation reactions at unactivated carbon and phosphorus atoms. RS enzymes typically abstract a hydrogen from their substrates, generating a substrate-centered radical; class B RS methylases catalyze methyl transfer from SAM to cobalamin and then to a substrate-centered carbon or phosphorus radical. Radle et al. now show that Mmp10, an RS enzyme implicated in the methylation of Arg-285 in methyl coenzyme M reductase, binds a methylcobalamin cofactor required for methyl transfer from SAM to a peptide substrate.Chloride to the rescue
On the fiftieth anniversary of the discovery of the Ser-His-Asp catalytic triad, perhaps the most unusual variation on the textbook classic is described: An incomplete catalytic triad in a hydrolase is rescued by a chloride ion (Fig. 1). Structural and functional data provide compelling evidence that the active site of a phospholipase from Vibrio vulnificus employs the anion in place of the commonly observed Asp, reminding us that even well-trodden scientific ground has surprises in store.On the trail of steroid aromatase: The work of Kenneth J. Ryan
The sexes in humans and other animals typically display numerous differences. This belies the fact that the two major hormone classes responsible for these differences, androgens and estrogens, differ only subtly in their chemical backbones. Androgens have a six-carbon nonaromatic ring—the “A ring” (Fig. 1)—in their steroid skeleton, whereas estrogens have an aromatic A ring. Remarkably, a single protein, steroid aromatase (also called estrogen synthase), is the only known enzyme capable of “aromatizing” the A ring in androgens such as testosterone and androstenedione to produce estrogens such as estradiol and estrone.Masochistic Enzymology: Dennis Vance's Work on Phosphatidylcholine
Purification of Phosphatidylethanolamine N-Methyltransferase from Rat LiverImproving on Nature: James Travis' Work on Recombinant Human α1-Proteinase Inhibitor: Isolation and Properties of Recombinant DNA Produced Variants of Human α -Proteinase Inhibitor
In 1985, when recombinant DNA technology was still in its infancy, James Travis at the University of Georgia and colleagues developed a nonoxidizable form of a protein critical for preventing emphysema. Emphysema is an obstructive lung disease caused by progressive destruction of the lung tissue. The researchers synthesized the natural and variant forms of the protein through a partnership with the biotechnology firm Chiron and then tested it in rabbits to see if it could be used to supplement the protein in patients.
