Crystal structure of Cd,Zn metallothionein

The anomalous scattering data from five Cd in the native protein were used to determine the crystal structure of cadmium, zinc (Cd,Zn) metallothionein isoform II from rat liver. The structure of a 4-Cd cluster was solved by direct methods. A 2.3 A resolution electron density map was calculated by iterative single-wavelength anomalous scattering. The structure is folded into two domains. The amino terminal domain (beta) of residues 1 to 29 enfolds a three-metal cluster of one Cd and two Zn atoms coordinated by six terminal cysteine thiolate ligands and three bridging cysteine thiolates. The carboxyl terminal domain (alpha) of residues 30 to 61 enfolds a 4-Cd cluster coordinated by six terminal and five bridging cysteine thiolates. All seven metal sites have tetrahedral coordination geometry. The domains are roughly spherical, and the diameter is 15 to 20 A; there is limited contact between domains. The folding of alpha and beta is topologically similar but with opposite chirality. Redundant, short cysteine-containing sequences have similar roles in cluster formation in both alpha and beta.     

Possible biochemical implications of the crystal structure of biotin

An examination of the molecular architecture of biotin, as determined by x-ray crystallographic analysis, has indicated that biotin may be capable of forming an intramolecular hydrogen bond in solution. A review of various chemical analogs of the vitamin has shown a close correlation between the possibility of forming such a hydrogen bond and biotin-like activity.     

Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization

Defensins (molecular weight 3500 to 4000) act in the mammalian immune response by permeabilizing the plasma membranes of a broad spectrum of target organisms, including bacteria, fungi, and enveloped viruses. The high-resolution crystal structure of defensin HNP-3 (1.9 angstrom resolution, R factor 0.19) reveals a dimeric beta sheet that has an architecture very different from other lytic peptides. The dimeric assembly suggests mechanisms by which defensins might bind to and permeabilize the lipid bilayer.     

Crystal structure of L-N-acetylhistidine monohydrate: an open and closed case

L-N-Acetylhistidine crystallizes from aqueous solution as the monohydrate. The crystals are triclinic, space group P1, with two formula units per cell. The structural solution was accomplished by direct methods. The two independent molecules have very different conformations, one open and one closed. These two conformations are compared with those found in other histidine structures.     

Crystal structure of an ancient protein: evolution by conformational epistasis

The structural mechanisms by which proteins have evolved new functions are known only indirectly. We report x-ray crystal structures of a resurrected ancestral protein-the approximately 450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. "Permissive" mutations-substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes-played a major role in determining GR's evolutionary trajectory.     

Crystal structure of serotonin picrate, a donor-acceptor complex

The crystal structure of the red picric acid salt of serotonin was determined by x-ray diffraction methods. The structure consists of parallel hydroxyindole and picrate planes which are intimately stacked with an interplanar separation of 3.3 to 3.4 angstroms. The stacking interaction appears to be of the donor-acceptor (charge-transfer) type, involving specific contacts between picrate nitro groups and atoms of the hydroxyindole moieties. Similar interactions might mediate biological processes involving serotonin.     

Purification of an allene oxide synthase and identification of the enzyme as a cytochrome P-450

Fatty acid hydroperoxides (lipoxygenase products) are metabolized to allene oxides by a type of dehydrase that has been detected in plants, corals, and starfish oocytes. The allene oxides are unstable epoxide precursors of more complex products such as jasmonic acid, the plant growth hormone. Characterization of the dehydrase enzyme of flaxseed revealed that it is a 55-kilodalton hemoprotein. The spectral characteristics of this dehydrase revealed it to be a cytochrome P-450. It operates with the remarkable activity of greater than or equal to 1000 turnovers per second. The results establish a new catalytic activity for a cytochrome P-450 and illustrate the cooperation of different oxygenases in pathways of fatty acid metabolism.     

Crystal structure of an early protein-RNA assembly complex of the signal recognition particle

The signal recognition particle (SRP) is a universally conserved ribonucleoprotein complex that mediates the cotranslational targeting of secretory and membrane proteins to cellular membranes. A crucial early step in SRP assembly in archaea and eukarya is the binding of protein SRP19 to specific sites on SRP RNA. Here we report the 1.8 angstrom resolution crystal structure of human SRP19 in complex with its primary binding site on helix 6 of SRP RNA, which consists of a stem-loop structure closed by an unusual GGAG tetraloop. Protein-RNA interactions are mediated by the specific recognition of a widened major groove and the tetraloop without any direct protein-base contacts and include a complex network of highly ordered water molecules. A model of the assembly of the SRP core comprising SRP19, SRP54, and SRP RNA based on crystallographic and biochemical data is proposed.     

Crystal structure of an initiation factor bound to the 30S ribosomal subunit

Initiation of translation at the correct position on messenger RNA is essential for accurate protein synthesis. In prokaryotes, this process requires three initiation factors: IF1, IF2, and IF3. Here we report the crystal structure of a complex of IF1 and the 30S ribosomal subunit. Binding of IF1 occludes the ribosomal A site and flips out the functionally important bases A1492 and A1493 from helix 44 of 16S RNA, burying them in pockets in IF1. The binding of IF1 causes long-range changes in the conformation of H44 and leads to movement of the domains of 30S with respect to each other. The structure explains how localized changes at the ribosomal A site lead to global alterations in the conformation of the 30S subunit.     

Crystal structure of human enterovirus 71

Enterovirus 71 is a picornavirus associated with fatal neurological illness in infants and young children. Here, we report the crystal structure of enterovirus 71 and show that, unlike in other enteroviruses, the "pocket factor," a small molecule that stabilizes the virus, is partly exposed on the floor of the "canyon." Thus, the structure of antiviral compounds may require a hydrophilic head group designed to interact with residues at the entrance of the pocket.     

Crystal structure of the zeolite paulingite

Paulingite, a zeolite, has a framework structure consisting of 2016 atoms (672 silicon or aluminum and 1344 oxygen) which are in a cubic cell with an edge of length 35.093 A. The framework has several features in common with the synthetic zeolites Linde A and ZK-5; the main channels are of similar size. We have also located most of the cations and water molecules inside the frame-work.     

Crystal structure of the eukaryotic ribosome

Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation.     

Crystal and molecular structure of adenosine 3',5'-cyclic phosphate

The structure of adenosine 3',5'-cyclic phosphate has been determined by single-crystal x-ray diffraction. The two molecules in the asymmetric unit show different conformation about the glycosidic bond, while other structural details are essentially the same. The furanose rings are puckered with the C(4') atom out of the best four-atom plane. The bond lengths and angles appear to be normal.     

Crystal structure of Escherichia coli MscS,a voltage-modulated and mechanosensitive channel

The mechanosensitive channel of small conductance (MscS) responds both to stretching of the cell membrane and to membrane depolarization. The crystal structure at 3.9 angstroms resolution demonstrates that Escherichia coli MscS folds as a membrane-spanning heptamer with a large cytoplasmic region. Each subunit contains three transmembrane helices (TM1, -2, and -3), with the TM3 helices lining the pore, while TM1 and TM2, with membrane-embedded arginines, are likely candidates for the tension and voltage sensors. The transmembrane pore, apparently captured in an open state, connects to a large chamber, formed within the cytoplasmic region, that connects to the cytoplasm through openings that may function as molecular filters. Although MscS is likely to be structurally distinct from other ion channels, similarities in gating mechanisms suggest common structural elements.     

Crystal structure of ethylene di-11-bromoundecanoate

Ethylene di-11-bromoundecanoate, C(24)H(44)Br(2)O(4), was synthesized as a model for the hydrophobic moiety of saturated phospholipids. The crystals are monoclinic, space group P2(1)/a, with two molecules per unit cell. Unlike folded configurations proposed for phospholipids in biological membranes, the hydrocarbon chains of this diester are fully extended in the crystalline state.     

Crystal structure of the dynein motor domain

Dyneins are microtubule-based motor proteins that power ciliary beating, transport intracellular cargos, and help to construct the mitotic spindle. Evolved from ring-shaped hexameric AAA-family adenosine triphosphatases (ATPases), dynein's large size and complexity have posed challenges for understanding its structure and mechanism. Here, we present a 6 angstrom crystal structure of a functional dimer of two ~300-kilodalton motor domains of yeast cytoplasmic dynein. The structure reveals an unusual asymmetric arrangement of ATPase domains in the ring-shaped motor domain, the manner in which the mechanical element interacts with the ATPase ring, and an unexpected interaction between two coiled coils that create a base for the microtubule binding domain. The arrangement of these elements provides clues as to how adenosine triphosphate-driven conformational changes might be transmitted across the motor domain.     

Crystal and molecular structure of acetylselenocholine iodide

The structure of acetylselenocholine iodide has been determined by x-ray crystallographic analysis. The molecule is in the trans conformation about the C-C bond of the choline residue. This conformation appears to explain the molecule's inability to give a positive cholinergic response when added to an electroplax preparation.     

Crystal structure of human ZAG, a fat-depleting factor related to MHC molecules

Zn-alpha2-glycoprotein (ZAG) is a soluble protein that is present in serum and other body fluids. ZAG stimulates lipid degradation in adipocytes and causes the extensive fat losses associated with some advanced cancers. The 2.8 angstrom crystal structure of ZAG resembles a class I major histocompatibility complex (MHC) heavy chain, but ZAG does not bind the class I light chain beta2-microglobulin. The ZAG structure includes a large groove analogous to class I MHC peptide binding grooves. Instead of a peptide, the ZAG groove contains a nonpeptidic compound that may be implicated in lipid catabolism under normal or pathological conditions.     

Crystal and molecular structure of a pentagonal dodecahedrane

The successful synthesis of a pentagonal dodecahedrane molecule has been achieved. Obtained by a sequence of 20 stereochemically controlled steps beginning with the readily available cyclopentadienide anion, the 1,16-dimethyl derivative has D(3d) symmetry and unusual physical properties. The x-ray crystal structure shows that the alkyl groups cause only small distortions from pure dodecahedral symmetry.