Iron–sulfur (Fe/S) clusters are essential protein cofactors crucial for many cellular functions including DNA maintenance, protein translation, and energy conversion. De novo Fe/S cluster synthesis occurs on the mitochondrial scaffold protein ISCU and requires cysteine desulfurase NFS1, ferredoxin, frataxin, and the small factors ISD11 and ACP (acyl carrier protein). Both the mechanism of Fe/S cluster synthesis and function of ISD11-ACP are poorly understood. Here, we present crystal structures of three different NFS1-ISD11-ACP complexes with and without ISCU, and we use SAXS analyses to define the 3D architecture of the complete mitochondrial Fe/S cluster biosynthetic complex. Our structural and biochemical studies provide mechanistic insights into Fe/S cluster synthesis at the catalytic center defined by the active-site Cys of NFS1 and conserved Cys, Asp, and His residues of ISCU. We assign specific regulatory rather than catalytic roles to ISD11-ACP that link Fe/S cluster synthesis with mitochondrial lipid synthesis and cellular energy status.

Mycoplasma parasites escape host immune responses via mechanisms that depend on remarkable phenotypic plasticity. Identification of these mechanisms is of great current interest. The aminoacyl-tRNA synthetases (AARSs) attach amino acids to their cognate tRNAs, but occasionally make errors that substitute closely similar amino acids. AARS editing pathways clear errors to avoid mistranslation during protein synthesis. We show here that AARSs in Mycoplasma parasites have point mutations and deletions in their respective editing domains. The deleterious effect on editing was confirmed with a specific example studied in vitro. In vivo mistranslation was determined by mass spectrometric analysis of proteins produced in the parasite. These mistranslations are uniform cases where the predicted closely similar amino acid replaced the correct one. Thus, natural AARS editing-domain mutations in Mycoplasma parasites cause mistranslation. We raise the possibility that these mutations evolved as a mechanism for antigen diversity to escape host defense systems.amino acid editing | fidelity | quality control | statistical proteins | host-pathogen interactions

Mistranslation is toxic to bacterial and mammalian cells and can lead to neurodegeneration in the mouse. Mistranslation is caused by the attachment of the wrong amino acid to a specific tRNA. Many aminoacyl-tRNA synthetases have an editing activity that deacylates the mischarged amino acid before capture by the elongation factor and transport to the ribosome. For class I tRNA synthetases, the editing activity is encoded by the CP1 domain, which is distinct from the active site for aminoacylation. What is not clear is whether the enzymes also have an editing activity that is separable from CP1. A point mutation in CP1 of class I leucyl-tRNA synthetase inactivates deacylase activity and produces misacylated tRNA. In contrast, although deletion of the entire CP1 domain also disabled the deacylase activity, the deletion-bearing enzyme produced no mischarged tRNA. Further investigation showed that a second tRNA-dependent activity prevented misacylation and is intrinsic to the active site for aminoacylation.amino acid editing ͉ fidelity ͉ protein synthesis

Intracellular pathogenic bacteria evade the immune response by replicating within host cells. Legionella pneumophila, the causative agent of Legionnaires’ Disease, makes use of numerous effector proteins to construct a niche supportive of its replication within phagocytic cells. The L. pneumophila effector SidK was identified in a screen for proteins that reduce the activity of the proton pumping vacuolar-type ATPases (V-ATPases) when expressed in the yeast Saccharomyces cerevisae. SidK is secreted by L. pneumophila in the early stages of infection and by binding to and inhibiting the V-ATPase, SidK reduces phagosomal acidification and promotes survival of the bacterium inside macrophages. We determined crystal structures of the N-terminal region of SidK at 2.3 Å resolution and used single particle electron cryomicroscopy (cryo-EM) to determine structures of V-ATPase:SidK complexes at ~6.8 Å resolution. SidK is a flexible and elongated protein composed of an α-helical region that interacts with subunit A of the V-ATPase and a second region of unknown function that is flexibly-tethered to the first. SidK binds V-ATPase strongly by interacting via two α-helical bundles at its N terminus with subunit A. In vitro activity assays show that SidK does not inhibit the V-ATPase completely, but reduces its activity by ~40%, consistent with the partial V-ATPase deficiency phenotype its expression causes in yeast. The cryo-EM analysis shows that SidK reduces the flexibility of the A-subunit that is in the ‘open’ conformation. Fluorescence experiments indicate that SidK binding decreases the affinity of V-ATPase for a fluorescent analogue of ATP. Together, these results reveal the structural basis for the fine-tuning of V-ATPase activity by SidK.

a b s t r a c tThe fidelity of tRNA aminoacylation is dependent in part on amino acid editing mechanisms. A hydrolytic activity that clears mischarged tRNAs typically resides in an active site on the tRNA synthetase that is distinct from its synthetic aminoacylation active site. A second pre-transfer editing pathway that hydrolyzes the tRNA synthetase aminoacyl adenylate intermediate can also be activated. Pre-and post-transfer editing activities can co-exist within a single tRNA synthetase resulting in a redundancy of fidelity mechanisms. However, in most cases one pathway appears to dominate, but when compromised, the secondary pathway can be activated to suppress tRNA synthetase infidelities.Ó 2009 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.The aminoacyl-tRNA synthetases (aaRSs) are responsible for committing amino acid-tRNA pairs in the first step of protein synthesis. Once the amino acid is linked to its cognate tRNA isoacceptor, it is passed from the aaRS to an elongation factor and then ultimately to the ribosome for incorporation into the nascent polypeptide chain. Decades of experimental and theoretical studies have emphasized that the synthetases and other tRNA partners are exquisitely adapted to ensure fidelity. Indeed, compromised fidelity results in amino acid toxicities that cause cell death in microbes [1] and neurological disease in mammals [2].Even before the tRNA aminoacylation reaction was discovered in 1956 [3], Linus Pauling predicted that proteins would lack the discriminatory power to fully distinguish isosteric substrates such as amino acids that differed by a single methyl group ([4] i.e. alanine and glycine). Yet early in vivo studies using chick ovalbumin extractions indicated that the fidelity of protein synthesis was quite high [5]. Subsequently, Alan Fersht proposed a double sieve model for the aaRSs to account for this high fidelity [6]. In essence, he hypothesized that when one enzyme active site cannot adequately discriminate between pairs of structurally related amino acids, two active sites with two different strategies for amino acid recognition could increase fidelity for protein synthesis to the threshold levels that are required by the physiology of the cell.Since the double sieve model was first proposed [6] biochemistry and structural biology investigations have revealed that about half of the aaRSs contain a wholly separate domain with a hydrolytic active site for amino acid editing [7]. Thus, only those aaRSs where amino acid discrimination is sufficiently threatened have evolved to meet the fidelity demands of the cell. In addition, independent hydrolytic tRNA deacylases aid in clearing mischarged tRNAs, and in some cases provide a third auxiliary sieve to ensure fidelity [8,9]. These editing active sites of the aaRS and the tRNA deacylases must be crafted to eliminate binding or translocation of the activated cognate amino acid, so that it can bypass the hydrolysis pathway and allows correctly charged tRNA to be efficient...