Crystal structure of the ϵ subunit of the proton-translocating ATP synthase from Escherichia coli

AbstractBackground: Proton-translocating ATP synthases convert the energy generated from photosynthesis or respiration into ATP. These enzymes, termed F0F1-ATPases, are structurally highly conserved. In Escherichia coli, F0F1-ATPase consists of a membrane portion, F0, made up of three different polypeptides (a, b and c) and an F1 portion comprising five different polypeptides in the stoichiometry α3β3γδϵ. The minor subunits γ, δ and ϵ are required for the coupling of proton translocation with ATP synthesis; the ϵ subunit is in close contact with the α, β , γ and c subunits. The structure of the ϵ subunit provides clues to its essential role in this complex enzyme.Results: The structure of the E. coli F0F1-ATPase ϵ subunit has been solved at 2.3 Å resolution by multiple isomorphous replacement. The structure, comprising residues 2–136 of the polypeptide chain and 14 water molecules, refined to an R value of 0.214 (Rfree = 0.288). The molecule has a novel fold with two domains. The N-terminal domain is a β sandwich with two five-stranded sheets. The C-terminal domain is formed from two α helices arranged in an antiparallel coiled-coil. A series of alanine residues from each helix form the central contacting residues in the helical domain and can be described as an ‘alanine zipper’. There is an extensive hydrophobic contact region between the two domains providing a stable interface. The individual domains of the crystal structure closely resemble the structures determined in solution by NMR spectroscopy.Conclusions: Sequence alignments of a number of ϵ subunits from diverse sources suggest that the C-terminal domain, which is absent in some species, is not essential for function. In the crystal the N-terminal domains of two ϵ subunits make a close hydrophobic interaction across a crystallographic twofold axis. This region has previously been proposed as the contact surface between the ϵ and γ subunits in the complete F1-ATPase complex. In the crystal structure, we observe what is apparently a stable interface between the two domains of the ϵ subunit, consistent with the fact that the crystal and solution structures are quite similar despite close crystal packing. This suggests that a gross conformational change in the ϵ subunit, to transmit the effect of proton translocation to the catalytic domain, is unlikely, but cannot be ruled out

The NYU Survey Service: Promoting Value in Undergraduate Education

New York University\u27s Data Service Studio has recently launched the NYU Survey Service, whose ultimate aim is to support the development and administration of surveys of all types. For the web-based component, we utilize a product called Qualtrics, which allows university affiliates to develop and administer web-based surveys. This article describes the process by which we at NYU came to offer the service during a time when concerns abound about the ability of libraries to support and expand services while still meeting service imperatives such as robust data services. While many considerations went into this evaluation and the ultimate conclusion to pilot the service, we emphasize those most related to data and information literacy, undergraduate instruction, learning and research, library collaborations and application administration and support

Complete Genome Sequence of Salinisphaera sp. Strain LB1, a Moderately Halo-Acidophilic Bacterium Isolated from Lake Brown, Western Australia

Salinisphaera sp. strain LB1 was isolated from Lake Brown, Western Australia, surface water enriched at pH 4.0 and with 5% (wt/vol) NaCl. The complete genome sequence is presented in this report

The structure of TTHA0988 from Thermus thermophilus, a KipI-KipA homologue incorrectly annotated as allophanate hydrolase

The Thermus thermophilus protein TTHA0988 is a protein of unknown function which represents a fusion of two proteins found almost ubiquitously across the bacterial kingdom. These two proteins perform a role regulating sporulation in Bacillus subtilis, where they are known as KipI and KipA. kipI and kipA genes are usually found immediately adjacent to each other and are often fused to produce a single polypeptide, as is the case with TTHA0988. Here, three crystal forms are reported of TTHA0988, the first structure to be solved from the family of `KipI-KipA fusion' proteins. Comparison of the three forms reveals structural flexibility which can be described as a hinge motion between the `KipI' and `KipA' components. TTHA0988 is annotated in various databases as a putative allophanate hydrolase. However, no such activity could be identified and genetic analysis across species with known allophanate hydrolases indicates that a misannotation has occurred. © 2011, Wiley-Blackwell. The definitive version is available at www3.interscience.wiley.co

Structure of the sporulation histidine kinase inhibitor Sda from Bacillus subtilis and insights into its solution state

The crystal structure of the DNA-damage checkpoint inhibitor of sporulation, Sda, from Bacillus subtilis, has been solved by the MAD technique using selenomethionine-substituted protein. The structure closely resembles that previously solved by NMR, as well as the structure of a homologue from Geobacillus stearothermophilus solved in complex with the histidine kinase KinB. The structure contains three molecules in the asymmetric unit. The unusual trimeric arrangement, which lacks simple internal symmetry, appears to be preserved in solution based on an essentially ideal fit to previously acquired scattering data for Sda in solution. This interpretation contradicts previous findings that Sda was monomeric or dimeric in solution. This study demonstrates the difficulties that can be associated with the characterization of small proteins and the value of combining multiple biophysical techniques. It also emphasizes the importance of understanding the physical principles behind these techniques and therefore their limitations

A Compact Beam Stop for a Rare Kaon Decay Experiment

We describe the development and testing of a novel beam stop for use in a rare kaon decay experiment at the Brookhaven AGS. The beam stop is located inside a dipole spectrometer magnet in close proximity to straw drift chambers and intercepts a high-intensity neutral hadron beam. The design process, involving both Monte Carlo simulations and beam tests of alternative beam-stop shielding arrangements, had the goal of minimizing the leakage of particles from the beam stop and the resulting hit rates in detectors, while preserving maximum acceptance for events of interest. The beam tests consisted of measurements of rates in drift chambers, scintilation counter hodoscopes, a gas threshold Cherenkov counter, and a lead glass array. Measurements were also made with a set of specialized detectors which were sensitive to low-energy neutrons, photons, and charged particles. Comparisons are made between these measurements and a detailed Monte Carlo simulation.Comment: 39 pages, 14 figures, submitted to Nuclear Instruments and Method