The cytochrome b6f complex provides the electronic connection between the photosystem I and photosystem II reaction centers of oxygenic photosynthesis and generates a transmembrane electrochemical proton gradient for adenosine triphosphate synthesis. A 3.0 angstrom crystal structure of the dimeric b6f complex from the thermophilic cyanobacterium Mastigocladus laminosus reveals a large quinone exchange cavity, stabilized by lipid, in which plastoquinone, a quinone-analog inhibitor, and a novel heme are bound. The core of the b6f complex is similar to the analogous respiratory cytochrome bc1 complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. The motion of the Rieske iron-sulfur protein extrinsic domain, essential for electron transfer, must also be different in the b6f complex.

The crystal structures of three amidohydrolases have been determined recently: glutamine PRPP amidotransferase (GAT), penicillin acylase, and the proteasome. These enzymes use the side chain of the amino-terminal residue, incorporated in a beta-sheet, as the nucleophile in the catalytic attack at the carbonyl carbon. The nucleophile is cysteine in GAT, serine in penicillin acylase, and threonine in the proteasome. Here we show that all three enzymes share an unusual fold in which the nucleophile and other catalytic groups occupy equivalent sites. This fold provides both the capacity for nucleophilic attack and the possibility of autocatalytic processing. We suggest the name Ntn (N-terminal nucleophile) hydrolases for this structural superfamily of enzymes which appear to be evolutionarily related but which have diverged beyond any recognizable sequence similarity.

A three-dimensional crystal structure of the biotin-binding core of streptavidin has been determined at 3.1i-resolution. The structure was analyzed from diffraction data measured at three wavelengths from a single crystal of the selenobiotinyl complex with streptavidin. Streptavidin is a tetramer with subunits arrayed in D2 symmetry. Each protomer is an 8-stranded fl-barrel with simple up-down topology.Biotin molecules are bound at one end of each barrel. This study demonstrates the effectiveness of multiwavelength anomalous diffraction (MAD) procedures for macromolecular crystallography and provides a basis for detailed study of biotinavidin interactions.Streptavidin takes its name from the bacterial source of the protein, Streptomyces avidinii, and from hen egg-white avidin with which it shares an extraordinary ligand binding affinity (Kd -10-15M) for biotin (1). This similarity extends to many other properties (2), including a common tetrameric structure and a 33% identity in amino acid sequence between avidin and the homologous core of streptavidin (3, 4). Core streptavidin is proteolyzed naturally, but not always completely (3), at both ends of the 159-residue gene product to a 125-to 127-residue core (4) that matches quite precisely with the actual secreted avidin gene product (5). The biological functions of avidin and streptavidin are poorly understood, but they most probably involve antibiotic properties. Interest in the avidin family, however, transcends their natural biology. Their remarkable avidity for biotin motivates two types of study: (i) efforts to understand the chemical basis for the high affinity and (ii) attempts to optimize biotechnology applications that exploit this activity (6)(7)(8). We aim to examine these biophysical and biotechnological properties in refined crystallographic detail. Streptavidin has also been crystallized by others (ref. 9 and P. McLaughlin, personal communication).This structural study of streptavidin also has a second objective related to diffraction methodology. It seemed from the outset that selenobiotinyl streptavidin could be an apt subject for direct analysis from multiwavelength anomalous diffraction (MAD) data obtained with synchrotron radiation. Selenobiotin is a stable compound (10) sufficiently similar to biotin itself that the two molecules crystallize isomorphously (11). The high affinity (Kd 10-13 M) of avidin for desthiobiotin (2, 12) suggested to us that selenobiotin would also bind well. We expected anomalous diffraction ratios (13) from the four selenium atoms in the 54-kDa core streptavidin tetramer (up to 3%) that compared favorably with signals measured successfully from crambin (14) and myohemerythrin (15) and with those obtained in our lamprey hemoglobin test of MAD phasing (16,17).The theoretical basis for the MAD method and details of its implementation are presented elsewhere (13,17,18). Qualitatively, MAD experiments can be thought of as in situ multiple isomorphous replacements (MIR) generated by the variation in scattering fact...

Flaviviruses, the human pathogens responsible for dengue fever, West Nile fever, tick-borne encephalitis and yellow fever, are endemic in tropical and temperate parts of the world. The flavivirus non-structural protein 1 (NS1) functions in genome replication as an intracellular dimer and in immune system evasion as a secreted hexamer. We report crystal structures for full-length, glycosylated NS1 from West Nile and dengue viruses. The NS1 hexamer in crystal structures is similar to a solution hexamer visualized by single-particle electron microscopy. Recombinant NS1 binds to lipid bilayers and remodels large liposomes into lipoprotein nanoparticles. The NS1 structures reveal distinct domains for membrane association of the dimer and interactions with the immune system, and are a basis for elucidating the molecular mechanism of NS1 function.

Arm muscle area (AMA, cm2) is currently calculated from triceps skinfold thickness (TSF, cm), and midarm circumference (MAC, cm). In assessing the accuracy of the current equation by comparison to AMA measured by computerized axial tomography, error in each of the four approximations made was found to result in a 20 to 25% overestimate of AMA. Two correctible error sources were: a 10 to 15% overestimation caused by assuming a circular midarm muscle compartment and a 5 to 10% overestimation due to inclusion of midarm cross-sectional bone area. Corrected AMA equations for men and women were respectively: [(MAC - pi x TSF)2/4 pi] - 10, and [MAC - pi x TSF)2/4 pip] - 6.5. With two additional study groups, the overall improved accuracy of the new equations was confirmed, although the average error for a given patient was 7 to 8%; the relationship between corrected AMA and total body muscle mass was established [muscle mass (kg) = (ht, cm2) (0.0264 + 0.0029 x corrected AMA)]; and the minimal range of corrected AMA values compatible with survival (9 to 11 cm2) was defined. Bedside estimates of undernutrition severity and prognosis can therefore be calculated from two simple measurements, TSF and MAC.

SummaryThis report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by comparison with the existing database, and the now-mandatory deposition of structure factors creates new opportunities to validate the underlying diffraction data. These developments highlighted the need for a new assessment of validation criteria. The Task Force recommends that a small set of validation data be presented in an easily understood format, relative to both the full PDB and the applicable resolution class, with greater detail available to interested users. Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators.

A two-base mechanism by which the histidine and aspartic acid together catalyze dehydration and isomerization reactions is consistent with the active-site structure. The unique topology of the protein fold and the identification of the active-site components reveal features of predictive value for another enzyme, FabZ, which may be the non-specific dehydratase involved in elongation of fatty acyl chains. A positively charged area surrounding the entrance to the active site, which could interact with the negatively charged ACP, was also found.

The crystal structure of GMP synthetase serves as a prototype for two families of metabolic enzymes. The Class I glutamine amidotransferase domain of GMP synthetase is found in related enzymes of the purine, pyrimidine, tryptophan, arginine, histidine and folic acid biosynthetic pathways. This domain includes a conserved Cys-His-Glu triad and is representative of a new family of enzymes that use a catalytic triad for enzymatic hydrolysis. The structure and conserved sequence fingerprint of the nucleotide-binding site in a second domain of GMP synthetase are common to a family of ATP pyrophosphatases, including NAD synthetase, asparagine synthetase and argininosuccinate synthetase.