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The crystal structure of urease from Klebsiella aerogenes has been determined at 2.2 A resolution and refined to an R factor of 18.2 percent. The enzyme contains four structural domains: three with novel folds playing structural roles, and an [(αβ).sub.8] barrel domain, which contains the bi-nickel center. The two active site nickels are 3.5 A apart. One nickel ion is coordinated by three ligands (with low occupancy of a fourth ligand) and the second is coordinated by five ligands. A carbamylated lysine provides an oxygen ligand to each nickel, explaining why carbon dioxide is required for the activation of urease apoenzyme. The structure is compatible with a catalytic mechanism whereby urea ligates Ni-1 to complete its tetrahedral coordination and a hydroxide ligand of Ni-2 attacks the carbonyl carbon. A surprisingly high structural similarity between the urease catalytic domain and that of the zinc-dependent adenosine deaminase reveals a remarkable example of active site divergence., Urease (urea amidohydrolase; E.C. 3.5.1.5), a nickel-dependent metalloenzyme, catalyzes the hydrolysis of urea to form ammonia and carbon dioxide (1) with a rate approximately [10.sup.14] times the rate of the [...]

The crystal structure of calcium-bound calmodulin (Ca sup 2+ -CaM) bound to a peptide analog of the CaM-binding region of chicken smooth muscle myosin light chain kinase has been determined and refined to a resolution of 2.4 angstroms ([Angstroms]). The structure is compact and has the shape of an ellipsoid (axial ratio 2:1). The bound CaM forms a tunnel diagonal to its long axis that engulfs the helical peptide, with the hydrophobic regions of CaM melded into a single area that closely covers the hydrophobic side of the peptide. There is a remarkably high pseudo-twofold symmetry between the closely associated domains. The central helix of the native CaM is unwound and expanded into a bend between residues 73 and 77. About 185 contacts ( 80% of this total., Calmodulin (CaM) is a 148-amino acid protein present in all eukaryotic cells that serves as the primary receptor for intracellular [Ca.sup.2t][1]. The three-dimensional structure of native CaM with four bound [...]

The x-ray structures of a murine MHC class I molecule ([H-2K.sup.b]) were determined in complex with two different viral peptides, derived from the vesicular stomatitis virus nucleoprotein(52-59) VSV-8, and the Sendai virus nucleoprotein(324-332), SEV-9. The [H-2K.sup.b] complexes were refined at 2.3 Å for VSV-8 and 2.5 Å for SEV-9. The structure of [H-2K.sup.b] exhibits a high degree of similarity with human HLA class I, although the individual domains can have slightly altered dispositions. Both peptides bind in extended conformations with most of their surfaces buried in the [H-2K.sup.b] binding groove. The nonamer peptide maintains the same amino- and carboxyl-terminal interactions as the octamer primarily by insertion of a bulge in the center of an otherwise β conformation. Most of the specific interactions are between side-chain atoms of [H-2K.sup.b] and main-chain atoms of peptide. This binding scheme accounts in large part for the enormous diversity of peptide sequences that bind with high affinity to class I molecules. Small but significant conformational changes in [H-2K.sub.b] are associated with peptide binding, and these synergistic movements may be an integral part of the T cell receptor recognition process., Molecular recognition processes are fundamental to both humoral and cellular immunity. Despite similarities in genetics and structure[1, 2], antibodies and T cell receptors (TCR's) recognize foreign antigens differently. Antibodies bind [...]

A 3.5 angstrom resolution electron density map of the HIV-1 reverse transcriptase heterodimer complexed with nevirapine, a drug with potential for treatment of AIDS, reveals an asymmetric dimer. The polymerase [...]

[C.sub.60] and liquid bromine react to form [C.sub.60 Br.sub.24], a crystalline compound isolated as a bromine solvate, [C.sub.60 Br.24(Br.sub.2).sub.x]. The x-ray crystal structure defines of a new pattern of addition to the carbon skeleton that imparts a rare high symmetry. The parent [C.sub.60] framework is recognizable in [C.sub.60 Br.sub.24], but [sp.sup.3] carbons at sites of bromination distort the surface, affecting conformations of all the hexagonal and pentagonal rings. Twenty-four bromine atoms envelop the carbon core, shielding the 18 remaining double bonds from addition. At 150 ° to 200 ° C there is effectively quantitative reversion of [C.sub.60 Br.sub.24] to [C.sub.60] and [Br.sub.2]., Early studies on fullerene carbon clusters point to an unusual chemical reactivity of this class of molecules. Of great interest are patterns that may develop on the surfaces of these [...]

The x-ray structure of T4 endonuclease V, an enzyme responsible for the first step of a pyrimidine-dimer-specific excision-repair pathway, was determined at a 1.6-angstrom resolution. The enzyme consists of a [...]

The three-dimensional structure of a specific antibody (Fab 17/9) to a peptide immunogen from influenza virus hemagglutinin [HA1(75-110)] and two independent crystal complexes of this antibody with bound peptide ( [Tyr.sup.P100]-[Leu.sup.P108]) have been determined by x-ray crystallographic techniques at 2.0[angstrems], and 3.1[angstrems] resolution, respectively. The nonapeptide antigen assumes a type I β turn in the antibody combining site and interacts primarily with the Fab hypervariable loops L3, H2, and H3. Comparison of the bound and unbound Fab structures shows that a major rearrangement in the H3 loop accompanies antigen binding. This conformational change results in the creation of a binding pocket for the β turn of the peptide, allowing [Tyr.sup.P105] to be accommodated. The conformation of the peptide bound to the antibody shows similarity to its cognate sequence in the HA1, suggesting a possible mechanism for the cross-reactivity of this Fab with monomeric hemagglutinin. The structures of the free and antigen bound antibodies demonstrate the flexibility of the antibody combining site and provide an example of induced fit as a mechanism for antibody-antigen recognition., Fundamental questions concerning the structural basis of antibody-antigen recognition are still largely unanswered. Although hydrogen bonding, van der Waals contacts, salt bridges, and buried surface area are of critical significance [...]

The integral membrane protein porin from Rhodobacter capsulatus consists of three tightly associated 16-stranded Β barrels that give rise to three distinct diffusion channels for small solutes through the outer membrane. The x-ray structure of this porin has revealed details of its shape, the residue distributions within the pore and at the membrane-facing surface, and the location of calcium sites. The electrostatic potential has been calculated and related to function. Moreover, potential calculations were found to predict the [Ca.sup.2+] sites., GRAM-NEGATIVE BACTERIA PROTECT themselves from hostile environments by an outer membrane. This membrane, however, has to be permeable to polar, low molecular mass solutes including nutrients. For this purpose it [...]

Calcium-dependent (C-type) animal lectins participate in many cell surface recognition events mediated by protein-carbohydrate interactions. The C-type lectin family includes cell adhesion molecules, endocytic receptors, and extracellular matrix proteins. Mammalian mannose-binding proteins are C-type lectins that function in antibody-independent host defense against pathogens. The crystal structure of the carbohydrate-recognition domain of a rat mannose-binding protein, determined as the holmium-substituted complex by multiwavelength anomalous dispersion (MAD) phasing, reveals an unusual fold consisting of two distinct regions, one of which contains extensive nonregular secondary structure stabilized by two holmium ions. The structure explains the conservation of 32 residues in all C-type carbohydrate-recognition domains, suggesting that the fold seen here is common to these domains. The strong anomalous scattering observed at the Ho [L.sub.III] edge demonstrates that traditional heavy atom complexes will be generally amenable to the MAD phasing method., MAMMALIAN MANNOSE-BINDING PROTEINS (MBP's) found in serum and liver mediate immunoglobulin-independent defensive reactions against pathogens. These proteins function by binding to specific cell-surface high-mannose oligosaccharides of various bacteria and fungi, [...]

TRANSMEMBRANE RECEPTORS ARE THE PROTEINS THROUGH which cells and organisms commonly receive information from the outside of a cell and transmit it for processing inside the cell. One type of [...]

RECOGNITION OF COMPLEX CARBOhydrates by lectins [1] has been implicated in important biological processes such as protein targeting to cellular compartments [2], homing of leukocytes [3], and host-pathogen interactions [1]. [...]

TRANSCRIPTION FACTORS OF THE RECENTLY IDENTIFIED bZIP class, such as C/EBP, Fos, Jun, CREB, and GCN4, regulate the expression of many differnet genes in organisms as diverse as fungi, plants, [...]

ALTHOUGH THE WELL-CHARACTERized DNA binding motifs (helix-turn-helix, zinc finger, and so forth) use stably folded units of secondary structure for recognition, flexible regions can also contribute to site-specific recognition. Unfortunately, [...]

SEVERE PROTEIN-INDUCED BENDING of DUPLEX DNA HAS been demonstrated by a variety of biochemical and biophysical techniques [1-10], including a low-resolution crystal structure of the nucleosome core particle [10]. Current [...]

THE PRINCIPAL BIOLOGICAL ROLE OF ACETYLCHOLINE-sterase (AChE, acetylcholine hydrolase, E.C. 3.1.1.7) is termination of impulse transmission at cholinergic synapses by rapid hydrolysis of the neurotransmitter acetylcholine (ACh) (1). [CH.SUB.3.COOCH.SUB.2.CH.SUB.2.N.SUP.+.(CH.SUB.3.).SUB.3] + [...]

OLIGOSACCHARIDE EPITOPES OF bacterial and tumor cell-surface carbohydrates are important disease markers [1] and targets for therapeutic antibodies [2], but to date a crystal structure for an antibody-carbohydrate complex has [...]

NITRITE REDUCTASES (NIRs) ARE part of a denitrification pathway in which nitrate is sequentially reduced to nitrite, nitric oxide, nitrous oxide, and dinitrogen ([NO.sub.2.sup.-] → NO → [N.sub.2.O] → [N.sub.2]) [...]

THE PROBLEM OF HOW, DURING PROTEIN PHOSPHORYLATION, a targeted protein substrate is recognized by a specific protein kinase has been particularly elusive because the determinants for peptide recognition are widely [...]

PROTEIN PHOSPHORYLATION AS A MECHANISM FOR REGULATING protein activity was first recognized with glycogen phosphorylase [1,2]. Now after over three decades, it is clear that this mechanism for the reversible [...]

IN AN ACCOMPANYING REPORT [1], THE function of FKBP [2, 3] was discussed, and its structure, determined by nuclear Overhauser effect (NOE)-restrained molecular dynamics, was described. After this structure had [...]

The x-ray crystal structure of recombinant human interferon- [Gamma] has been determined with the use of multiple-isomorphous-replacement techniques. Interferon- [Gamma], which is dimeric in solution, crystallizes with two dinners related [...]

An ab initio approach to the phase problem in macromolecular x-ray crystallography is described. A random gas of hard-sphere point scatterers is allowed to condense under the constraint of the [...]

FIBROBLAST GROWTH FACTORS (FGFs) are members of a protein family that induce mitogenic, chemotactic, and angiogenic activity in a variety of cells of epithelial, mesenchymal, and neural origins (1). As [...]

The crystal structure of a complex between a phosphonate transition-state analogue and the phospholipase [A.sub.2] ([PLA.sub.2]) from Naja naja atra venom has been solved and refined to a resolution of [...]

To Eva Pebay-Peyroula and other x-ray crystallographers, bacteriorhodopsin has brought 20 years of frustration. Beginning in the mid-1970s, researchers managed to coax this large protein (which helps convert sunlight to [...]

The conformation of the immunosuprressive drug cyclosporin A (CsA) in a complex with a Fab molecule has been established by crystallographic analysis to 2.65 angstrom resolution. This conformation of CsA is similar to that recently observed in the complex with the rotamase cyclophilin, its binding protein in vivo, and totally different from it conformation in an isolated form as determined from x-ray and nuclear magnetic resonance analysis. Because the surfaces of CsA interacting with cyclophilin or with the Fab are not identical, these results suggest that the conformation of CsA observed in the bound form preexists in aqueous solution and is not produced by interaction with the proteins., Cyclosporin A (CsA), an immunosuppressive drug that acts as inhibitor of T cell activation[1], forms a complex in vivo with cyclophilin (CYP)[2], a cis-trans isomerase, and can inhibit its activity [...]

THE RECENTLY DEVELOPED LARGE-scale production [1, 2] and separation [3] methods for the all-carbon molecules [C.sub.60], [C.sub.70], [C.sub.76/78], [C.sub.84], and [C.sub.94] (fullerenes) have opened up new vistas in organic and [...]

A MATERIALS FABRICATION TECHnique has been developed that provides the ability to draw ultrafine metallic filaments. Previously, very fine wires of metals could be drawn at a temperature at which [...]

Structures of 70S ribosome complexes containing messenger RNA and transfer RNA (tRNA), or tRNA analogs, have been solved by x-ray crystallography at up to 7.8 angstrom resolution. Many details of the interactions between tRNA and the ribosome, and of the packing arrangements of ribosomal RNA (rRNA) helices in and between the ribosomal subunits, can be seen. Numerous contacts are made between the 305 subunit and the P-tRNA anticodon stem-loop; in contrast, the anticodon region of A-tRNA is much more exposed. A complex network of molecular interactions suggestive of a functional relay is centered around the long penultimate stem of 16S rRNA at the subunit interface, including interactions involving the 'switch' helix and decoding site of 165 rRNA, and RNA bridges from the 505 subunit., Translation of the RNA-encoded genetic message into the polypeptide chain of a protein links genotype to phenotype. It is carried out by the ribosome, an ancient ribonucleo-protein particle whose structural [...]

Three-Dimensional Structure of an Oncogene Protein: Catalytic Domain of Human c-H-ras p21 The crystal structure at 2.7 A resolution of the normal human c-H-ras oncogene protein lacking a flexible carboxyl-terminal [...]

Replacements of Pro.sup.86 in Phage T4 Lysonzyme Extend an α-Helix But do Not Alter Protein Stability A MAJOR PROBLEM IN UNDERSTANDING the physical basis of protein stability is to quantitate [...]

Mechanism of the Body-Centered Cubic-Hexagonal Close-Packed Phase Transition in Iron AT ROOM TEMPERATURE AND ATMOSPHERIC pressure, iron has the bodycentered cubic (bcc) structure. The bcc phase of iron undergoes a [...]

Protein, DNA, and Virus Crystallography with a Focused Imaging Proportional Counter THE MOST EFFICIENT METHOD OF collecting x-ray diffraction data is to record at one time with a photon counting [...]

If one picture is worth a thousand words, recent advances in x-ray crystallography methods are providing the equivalent of the Encyclopedia Britannica. Crystallographers are now churning out the three-dimensional (3D) [...]

Urease has a long and distinguished history in the development of enzymology. This enzyme catalyzes the hydrolysis of urea, an abundant end product of metabolism (humans release 10 kilograms per [...]

In large families, the oldest child and the youngest often get most of their parent's attention, while the middle children seemingly get lost in the crowd. Until lately, such has [...]

CHOLERA SOUNDS LIKE A 19TH-CENTURY DISease--something the heroine of an Emily Bronte novel dies of. But it's not. The debilitating diarrhea caused by the Vibrio cholerae bacterium, which has created [...]

An x-ray crystal structure that confirms the soccer ball-shaped carbon framework of [C.sub.60] (buckminsterfullerene) is reported. An osmyl unit was added to [C.sub.60] in order to break its pseudospherical symmetry [...]

Bulk Superconductivity at 122 K in TI(Ba,Ca).sub.2.Ca.sub.3.Cu.sub.4.O.sub.10.5+δ with Four Consecutive Copper Layers THE 'SECOND-GENERATION' SUPER-conducting cuprates containing thallium or bismuth are layered compounds with the general formula (B.sup.III).sub.y.sub.- (A.sup.II).sub.2.Ca.sub.n.-1.Cu.sub.n.O.sub.z., where [...]

Genetic and Crystallographic Studies of the 3',5'-Exonucleolytic Site of DNA Polymerase I THE LARGE PROTEOLYTIC FRAGMENT (Klenow fragment) of Escherichia coli DNA polymerase I is the only DNA-synthesizing enzyme for [...]

A three-dimensional structure for the monomeric iron-containing hydrogenase (CpI) from Clostridium pasteurianum was determined to 1.8 angstrom resolution by x-ray crystallography using multiwavelength anomalous dispersion (MAD) phasing. CpI, an enzyme that catalyzes the two-electron reduction of two protons to yield dihydrogen, was found to contain 20 gram atoms of iron per mole of protein, arranged into five distinct [Fe-S] dusters. The probable active-site duster, previously termed the H-duster, was found to be an unexpected arrangement of six iron atoms existing as a [4Fe-4S] cubane subcluster covalent[y bridged by a cysteinate thiol to a [2Fe] subcluster. The iron atoms of the [2Fe] subcluster both exist with an octahedral coordination geometry and are bridged to each other by three non-protein atoms, assigned as two sulfide atoms and one carbonyl or cyanide molecule. This structure provides insights into the mechanism of biological hydrogen activation and has broader implications for [Fe-S] duster structure and function in biological systems., The activation of molecular hydrogen constitutes a central reaction in the global biological energy cycle. This reaction is found among a diverse group of microorganisms where both the reduction of [...]

Industrial chemists have long wished they could mimic the action of a bacterial enzyme known as nitrogenase. The active component of nitrogen-fixing bacteria, nitrogenase somehow manages to convert atmospheric nitrogen [...]