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At least 127 records · Page 7Linked to original sources
PubMed2001

A structural variation for MurB: X-ray crystal structure of Staphylococcus aureus UDP-N-acetylenolpyruvylglucosamine reductase (MurB).

The X-ray crystal structure of the substrate free form of Staphylococcus aureus UDP-N-acetylenolpyruvylglucosamine reductase (MurB) has been solved to 2.3 A resolution with an R-factor of 20.3% and a free R-factor of 22.3%. While the overall fold of the S. aureus enzyme is similar to that of the homologous Escherichia coli MurB X-ray crystal structure, notable distinctions between the S. aureus and E. coli MurB protein structures occur in residues involved in substrate binding. Analysis of available MurB sequences from other bacteria suggest that the S. aureus MurB structure is representative of a distinct structural class of UDP-N-acetylenolpyruvylglucosamine reductases including Bacillus subtilis and Helicobacter pylori that are characterized by a modified mechanism for substrate binding.

Amino Acid Sequence↗
PubMed2004

Synthesis, crystal structure from single-crystal and powder X-ray diffraction data, and thermal behavior of mixed potassium lanthanide squarates: thermal transformations of layered [Ln(H2O)6]K(H2C4O4)(C4O4)2 into pillared LnK(C4O4)2 (Ln = Y, La, Gd, Er).

A new series of mixed potassium and rare-earth squarates, [Ln(H(2)O)(6)]K(H(2)C(4)O(4))(C(4)O(4))(2) (Ln = Y, La, Gd, Er), has been synthesized and structurally characterized from single-crystal X-ray diffraction and spectroscopic analyses. The yttrium-based compound crystallizes with a monoclinic symmetry, space group C2/c [a = 8.3341(2) A, b = 37.7094(9) A, c = 11.7195(3) A, beta = 90.3959(9) degrees , V = 3683.1(2) A(3), Z = 8]. The structure is built from layers maintained together via hydrogen bonds. Within a layer, squarate ligands act as linkers between lanthanide and potassium cations. The thermal decomposition of the precursors has been studied by powder thermodiffractometry and thermal analyses. It is shown that crystalline intermediate phases are formed during the degradation. Among them, unprecedented mixed anhydrous squarates, LnK(C(4)O(4))(2), could be isolated. The crystal structure of the Y compound has been solved ab initio from X-ray powder diffraction data, using direct-space methods [a = 6.2010(5) A, c = 11.639(1) A, V = 447.55 A(3), Z = 2]. The structure consists of layers of edge-sharing YO(8) and KO(8) antiprisms, pillared by mu(8)-squarate groups. The end of the precursor decomposition is marked by the formation of cubic sesquioxides Ln(2)O(3), including lanthanum oxide.

Journal Article↗
PubMed1992

Molecular and crystal structure of konjac glucomannan in the mannan II polymorphic form.

A probable crystal structure of konjac glucomannan (mannose:glucose ratio = 1.6) is proposed based on X-ray data and constrained linked-atom least-squares model refinement. The structure crystallizes in the mannan II polymorphic form, in an orthorhombic unit-cell with a = 9.01 A, b = 16.73 A, c (fiber axis) = 10.40 A, and a probable space group I222. The backbone conformation of the chain is a two-fold helix stabilized by intramolecular O-3-O-5' hydrogen bonds, with the O-6 rotational position gt. The unit cell contains four chains with antiparallel packing polarity and eight water molecules which reside in crystallographic positions. Intermolecular hydrogen bonds occur exclusively between chains and water molecules, establishing a three-dimensional hydrogen-bond network in the crystal structure. The glucose residues replace mannoses in the structure in isomorphous fashion, although some disorder appears possible. A structure having alternating gg-gt O-6 rotational positions and conforming to space group P222 appears to describe the disorder regions of the crystal. The reliability of the structure analysis is indicated by the X-ray residuals R = 0.276 and R" = 0.223.

Carbohydrate Conformation↗
PubMed2001

Electron crystallography without limits? Crystal structure of Ti45Se16 redetermined by electron diffraction structure analysis.

The crystal structure of the metal-rich compound Ti(45)Se(16) was redetermined from selected-area electron diffraction film data. The structure was solved by quasi-automatic direct methods using a data set of quantified h0l electron diffraction intensities. Improved atomic coordinates were obtained from a subsequent least-squares refinement on the basis of the kinematical approximation. The compound crystallizes in the monoclinic space group C2/m with lattice parameters a = 36.534, b = 3.453, c = 16.984 A, beta = 91.73 degrees. The structure contains 23 titanium and 8 selenium atoms per asymmetric part of the unit cell. The refined atomic coordinates agree on average within 0.18 A with the previously determined structure from high-resolution electron-microscopy images. The precision of the determined atomic coordinates obtained in this study is better than 0.05 A. The structure of Ti(45)Se(16) is the eighth metal-rich structure that has been solved by direct methods from two-dimensional selected-area electron diffraction data using the quasi-kinematical approximation. The present investigation proves again that direct methods with electron diffraction data work extremely reliably provided that the structure in question is composed of elements of nearly equal scattering power and that data covering the most significant parts of the unit-cell transform up to atomic resolution are available. Moreover, a method was developed that allows the estimation of the average crystal thickness from the effective atomic potential in the refined structure.

Journal Article↗
PubMed1992

Comparison of the NMR solution structure and the x-ray crystal structure of rat metallothionein-2.

Metallothioneins are small cysteine-rich proteins capable of binding heavy metal ions such as Zn2+ and Cd2+. They are ubiquitous tissue components in higher organisms, which tentatively have been attributed both unspecific protective functions against toxic metal ions and highly specific roles in fundamental zinc-regulated cellular processes. In this paper a detailed comparison of the NMR solution structure [Schultze, P., Wörgötter, E., Braun, W., Wagner, G., Vasák, M., Kägi, J. H. R. & Wüthrich, K. (1988) J. Mol. Biol. 203, 251-268] and a recent x-ray crystal structure [Robbins, A. H., McRee, D. E., Williamson, M., Collett, S. A., Xoung, N. H., Furey, W. F., Wang, B. C. & Stout, C. D. (1991) J. Mol. Biol. 221, 1269-1293] of rat metallothionein-2 shows that the metallothionein structures in crystals and in solution have identical molecular architectures. The structures obtained with both techniques now present a reliable basis for discussions on structure-function correlations in this class of metalloproteins.

Amino Acid Sequence↗
PubMed1987

The crystal structures of octyl alpha-D-glucopyranoside monohydrate and hemihydrate: mesogenic structures with interdigitizing alkyl chains.

The crystal structure of octyl alpha-D-glucopyranoside monohydrate, C14H28O6.H2O, is monoclinic, C2, with Z = 4, a = 17.896(2), b = 5.154(1), c = 18.303(2) A, beta = 90.30(1) degrees. The hemihydrate, C14H28O6.0.5 H2O, is also monoclinic, C2, with Z = 4, a = 15.190(5), b = 5.136(3), c = 19.944(7), beta = 92.74(3) degrees. The crystal structures were solved using SHELXTL and refined to R values of 0.037 and 0.052 for 1224 and 1231 observed structure amplitudes, respectively. The crystal structures have bilayer head-to-head molecular packing with interdigitizing alkyl chains similar to those observed in other long-chain alkyl pyranosides. The carbohydrate moieties are hydrogen-bonded in infinite chains which exclude the ring and glycosidic oxygen atoms. Both crystal structures transform to a smectic A liquid crystal at 72.3 degrees, which has a clearing point at 116.5 degrees.

Carbohydrate Conformation↗
PubMed2003

Determinants of enzymatic specificity in the Cys-Met-metabolism PLP-dependent enzymes family: crystal structure of cystathionine gamma-lyase from yeast and intrafamiliar structure comparison.

The crystal structure of cystathionine gamma-lyase (CGL) from yeast has been solved by molecular replacement at a resolution of 2.6 A. The molecule consists of 393 amino acid residues and one PLP moiety and is arranged in the crystal as a tetramer with D2 symmetry as in other related enzymes of the Cys-Met-metabolism PLP-dependent family like cystathionine beta-lyase (CBL). A structure comparison with other family members revealed surprising insights into the tuning of enzymatic specificity between the different family members. CGLs from yeast or human are virtually identical at their active sites to cystathionine gamma-synthase (CGS) from E. coli. Both CGLs and bacterial CGSs exhibit gamma-synthase and gamma-lyase activities depending on their position in the metabolic pathway and the available substrates. This group of enzymes has a glutamate (E333 in yeast CGL) which binds to the distal group of cystathionine (CTT) or the amino group of cysteine. Plant CGSs use homoserine phosphate instead of O-succinyl-homoserine as one substrate. This is reflected by a partially different active site structure in plant CGSs. In CGL and CBL the pseudosymmetric substrate must dock at the active site in different orientations, with S in gamma-position (CBL) or in delta-position (CGL). The conserved glutamate steers the substrate as seen in other CGLs. In CBLs this position is occupied by either tyrosine or hydrophobic residues directing binding of CTT such that S is in the in gamma-position. In methionine gamma-lyase a hydrophic patch operates as recognition site for the methyl group of the methionine substrate.

Binding Sites↗
PubMed1996

Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme.

Using site-directed mutagenesis, X-ray crystallography, and titration calorimetry, we have examined the structural and thermodynamic consequences of removing specific hydrogen bonds in an antigen-antibody interface. Crystal structures of three antibody FvD1.3 mutants, VLTyr50Ser (VLY50S), VHTyr32Ala (VHY32A), and VHTyr101Phe (VHY101F), bound to hen egg white lysozyme (HEL) have been determined at resolutions ranging from 1.85 to 2.10 A. In the wild-type (WT) FvD1.3-HEL complex, the hydroxyl groups of VLTyr50, VHTyr32, and VHTyr101 each form at least one hydrogen bond with the lysozyme antigen. Thermodynamic parameters for antibody-antigen association have been measured using isothermal titration calorimetry, giving equilibrium binding constants Kb (M-1) of 2.6 x 10(7) (VLY50S), 7.0 x 10(7) (VHY32A), and 4.0 x 10(6) (VHY101F). For the WT complex, Kb is 2.7 x 10(8) M-1; thus, the affinities of the mutant Fv fragments for HEL are 10-, 4-, and 70-fold lower than that of the original antibody, respectively. In all three cases entropy compensation results in an affinity loss that would otherwise be larger. Comparison of the three mutant crystal structures with the WT structure demonstrates that the removal of direct antigen-antibody hydrogen bonds results in minimal shifts in the positions of the remaining protein atoms. These observations show that this complex is considerably tolerant, both structurally and thermodynamically, to the truncation of antibody side chains that form hydrogen bonds with the antigen. Alterations in interface solvent structure for two of the mutant complexes (VLY50S and VHY32A) appear to compensate for the unfavorable enthalpy changes when protein-protein interactions are removed. These changes in solvent structure, along with the increased mobility of side chains near the mutation site, probably contribute to the observed entropy compensation. For the VHY101F complex, the nature of the large entropy compensation is not evident from a structural comparison of the WT and mutant complexes. Differences in the local structure and dynamics of the uncomplexed Fv molecules may account for the entropic discrepancy in this case.

Antigen-Antibody Complex↗
PubMedDate not supplied

Crystal structures of cephaibols.

The crystal structures of the peptaibol antibiotics cephaibol A, cephaibol B and cephaibol C have been determined at ca. 0.9 A resolution. All three adopt a helical conformation with a sharp bend (of about 55 degrees) at the central hydroxyproline. All isovalines were found to possess the D configuration, superposition of all four models (there are two independent molecules in the cephaibol B structure) shows that the N-terminal helix is rigid and the C-terminus is flexible. There are differences in the hydrogen bonding patterns for the three structures that crystallize in different space groups despite relatively similar unit cell dimensions, but only in the case of cephaibol C does the packing emulate the formation of a membrane channel believed to be important for their biological function.

Anti-Bacterial Agents↗
PubMed2004

Structural evidence for guanidine-protein side chain interactions: crystal structure of CutA from Pyrococcus horikoshii in 3 M guanidine hydrochloride.

This study was carried out to investigate the structural perturbation of the protein's local structure by the denaturants under non-denaturing conditions. Crystal structure of CutA from an archaeon Pyrococcus horikosii (PhoCutA), a heavy-metal binding protein, was determined at 1.6-angstroms resolution in the presence of 3 M guanidine HCl (GdnHCl). Native PhoCutA has a large number of short intramolecular hydrogen bonds and salt bridges on the protein surface, of which greater than 90% of hydrogen bonds and all salt bridges were retained in 3 M GdnHCl. Hydrogen bonds that disappeared in the GdnHCl crystal structure were mainly located on the protein surface, especially around the structurally perturbed loop, suggesting interactions between peptide groups and GdnHCl. Only a few GdnH+ ions were observed in the crystal structure, although none at the surface, of the protein. Two GdnH+ ions were observed in the center of the trimeric structure, replacing water molecules, and were hydrogen bonded with Asp84 and Asp86 of each chain. The exterior loop from Tyr39 to Lys44, including Trp40-Trp41, was perturbed structurally. Decreases in temperature factors were observed in beta strand 5 and the N terminus of helix 3. These results suggest the specific bindings of GdnH+ with some acidic residues and the non-specific bindings around Trp residues and peptide groups on the protein surface and that binding of GdnHCl to the native protein is limited, resulting in local structural perturbation.

Archaeal Proteins↗
PubMed2006

Molecular pair analysis: C-H...F interactions in the crystal structure of fluorobenzene? And related matters.

The crystal structure of fluorobenzene is compared with isomorphous crystal structures of molecules of roughly similar shape. The lowest-energy fluorobenzene dimers are identified by theoretical calculations. Molecular pair analysis of the crystal structure of fluorobenzene and of an isomorphous virtual low-energy polymorph of benzene suggests that the important intermolecular interactions in the two structures are closely similar. In particular, the intermolecular C-H...F interactions in the fluorobenzene crystal have approximately the same structure-directing ability and influence on the intermolecular energy as the corresponding C-H...H interactions in benzene. Molecular pair analysis of the isomorphous crystal structures of benzonitrile, alloxan, and cyclopentene-1,2,3-trione indicates that essentially the same crystal structure can be adopted with quite different patterns of pair energies and atom-atom interactions. The question as to whether the packing radius of organic fluorine is larger or smaller than that of hydrogen, is addressed, but not answered.

Journal Article↗
PubMed1998

Use of papain as a model for the structure-based design of cathepsin K inhibitors: crystal structures of two papain-inhibitor complexes demonstrate binding to S'-subsites.

Papain has been used as a surrogate enzyme in a drug design effort to obtain potent and selective inhibitors of cathepsin K, a new member of the papain superfamily of cysteine proteases that is selectively and highly expressed in osteoclasts and is implicated in bone resorption. Here we report the crystal structures of two papain-inhibitor complexes and the rational design of novel cathepsin K inhibitors. Unlike previously known crystal structures of papain-inhibitor complexes, our papain structures show ligand binding extending deep within the S'-subsites. The two inhibitor complexes, carbobenzyloxyleucinyl-leucinyl-leucinal and carbobenzyloxy-L-leucinyl-L-leucinyl methoxymethyl ketone, were refined to 2.2- and 2.5-A resolution with R-factors of 0.190 and 0. 217, respectively. The S'-subsite interactions with the inhibitors are dominated by an aromatic-aromatic stacking and an oxygen-aromatic ring edge interaction. The knowledge of S'-subsite interactions led to a design strategy for an inhibitor spanning both subsites and yielded a novel, symmetric inhibitor selective for cathepsin K. Simultaneous exploitation of both S- and S'-sites provides a general strategy for the design of cysteine protease inhibitors having high specificity to their target enzymes.

Binding Sites↗
PubMed2000

The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited.

The crystal structure of the monoclinic form of yeast phenylalanine tRNA has been redetermined at a resolution of 1.93 A. The structure of yeast tRNAphe described here is more accurate than its predecessors not only because it incorporates higher resolution data, but also because it has been refined using techniques that had not been developed when its predecessors were determined more than 20 years ago. The 1.93 A resolution version of this structure differs interestingly from its predecessors in its details. In loop regions particularly, the backbone torsion angles in the new structure are not the same as those reported earlier. Several new divalent cation binding sites have been identified, and the water structure that has emerged is also different.

Base Sequence↗
PubMed2003

The crystal structure of a novel, inactive, lysine 49 PLA2 from Agkistrodon acutus venom: an ultrahigh resolution, AB initio structure determination.

The crystal structure of acutohaemolysin, a lysine 49 phospholipase A2 protein with 1010 non-hydrogen protein atoms and 232 water molecules, has been determined ab initio using the program SnB at an ultrahigh resolution of 0.8 A. The lack of catalytic activity appears to be related to the presence of Phe102, which prevents the access of substrate to the active site. The substitution of tryptophan for leucine at residue 10 interferes with dimer formation and may be responsible for the additional loss of hemolytic activity. The ultrahigh resolution of the experimental diffraction data permits alternative conformations to be modeled for disordered residues, many hydrogen atoms to be located, the protonation of the Nepsilon2 atom in the catalytic residue His48 to be observed experimentally, and the density of the bonding electrons to be analyzed in detail.

Agkistrodon↗
PubMed2000

Structure of the zinc-binding site in the crystal structure of a zinc endoprotease from Streptomyces caespitosus at 1 A resolution.

A zinc endoprotease produced by Streptomyces caespitosus (ScNP) contains a H83E84TGH87VLG90LPD93-Met103 sequence. Except for D93, this amino acid sequence is the same as a characteristic consensus HEXXHXXGXXH-M motif found in one class of zinc endoprotease called 'metzincins'. We analyzed the structural and functional role of the consensus sequence located around a catalytically essential zinc ion based on the crystal structure of ScNP. The structure was determined at the highest level on resolution (1 A resolution) and accuracy among crystal structures of zinc endoproteases ever determined. The zinc ion of ScNP is tetrahedrally coordinated by three amino acid side-chains (H83, H87 and D93) and a water molecule. The distances between the zinc ion and the coordinating atoms are 2.01, 2.01 and 1.95 A for H83N epsilon, H87N epsilon and D93O delta, respectively. These distances agree very well with those normally found in crystal structures of zinc-containing small molecules in the Cambridge Structural Database. On the other hand, the distance between the zinc ion and the coordinating water molecule (1.93 A) is slightly shorter than the typical value (2.01 A) found in the database. In addition, E84O epsilon makes a short hydrogen bond to this water molecule with the distance of 2.54 A. Two hydrogen bonds (H83N delta-L102O, H87N delta-L91O) and van der Waals interactions between the side-chain of M103 and the two imidazole rings of H83 and H87 are also observed. These interactions are probably important for the imidazole rings to construct the tetrahedral coordination arrangement toward the zinc ion.

Amino Acid Motifs↗
PubMed2000

Crystal structure of recombinant native SDF-1alpha with additional mutagenesis studies: an attempt at a more comprehensive interpretation of accumulated structure-activity relationship data.

Crystal structures, forms 1 and 2, of recombinant native stromal cell-derived factor-1alpha (SDF-1alpha), expressed using the Sendai virus expression vector system, have been determined by x-ray crystallography at 2.0 A resolution. The crystal of form 1 is almost isomorphous with that used in the previous crystal structure analysis of the synthetic [N33A] mutant of SDF-1alpha (Dealwis, C., et al. Proc. Natl. Acad. Sci. USA 1998;95, 6941-6946). However, the present structure analysis led to considerably better refinement statistics, revealing an error in the structural assignment of N-terminal residues in the previous report. Comparison of the solution structure, as previously determined by nuclear magnetic resonance (NMR) spectroscopy, and the present structure, with two monomers in the asymmetric unit, reveals several local conformational differences. Alanine scan mutagenesis studies for each residue in the so-called RFFESH motif revealed that only the first residue, Arg12, is effective in enhancing receptor binding (and successive activation). A new notion that steric restraint between Arg8 and Arg12 is favorable (if not vital) for retaining SDF activities appears to explain more consistently the structure-activity relationship data accumulated to date. Four guiding principles are presented that may be useful for designing potent therapeutic compounds interfering with HIV-1 infection through competition at the CXCR4 coreceptor.

Amino Acid Motifs↗
PubMed2002

Structure prediction as a tool for solution of the crystal structures of metallo-organic complexes using powder X-ray diffraction data.

A simulated-annealing direct-space approach has been applied to predict the crystal structures of a series of metallo-organic complexes containing Zn, Cu and Ni. The prediction methodology generates a set of energetically reasonable crystal structures among which the actual structure is present, but it is not always possible to specify unambiguously the known crystal structure solely on the basis of energy. In each case, however, the ambiguity may be resolved by recourse to laboratory powder X-ray diffraction (PXRD) data. In this manner, structure prediction is shown to be a powerful tool for structure solution using PXRD data, with the additional advantage that indexing of the PXRD profile is not required at the outset.

Journal Article↗