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PubMed2002

Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.

Crystal structures of endopolygalacturonase from Stereum purpureum were solved in native and two galacturonic acid complex states at atomic resolution. Endopolygalacturonase catalyzes the hydrolysis of alpha-1,4-glycosidic linkage of polygalacturonate in pectin. The native structure was determined by the multiple wavelength anomalous dispersion method and was refined anisotropically with SHELXL-97, with an R factor of 11.4% and an R(free) factor of 14.0% at 0.96 A resolution. The enzyme folds into a right-handed parallel beta-helix with 10 complete turns. The crystal structures of its binary complex with one D-galacturonate and its ternary complex with two D-galacturonates were also determined to identify the substrate binding site at 1.0 and 1.15 A resolutions, respectively. In the binary complex, one beta-D-galactopyranuronate was found in the +1 subsite, thus proving the strong affinity of the +1 subsite expected from the bond cleavage frequency on oligogalacturonates. In the ternary complex, an additional beta-D-galactofuranuronate was found in the -1 subsite. In both subsites, the recognition of the galacturonate carboxy group is important in galacturonate binding. In the +1 subsite, the carboxy group interacts with three basic residues, His195, Arg226, and Lys228, which were conserved in all endopolygalacturonases. In the -1 subsite, the unique nonprolyl cis-peptide bond is believed to be involved in binding the carboxy group of the substrate. The active site architecture of the complexes provides insight into the mechanism of inverting glycosyl hydrolases and also sheds light on the basis of the differences between the family 28 and the other inverting glycosyl hydrolases.

Amino Acid Sequence↗
PubMed2005

Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum.

We have determined the crystal structure of nicotinate phosphoribosyltransferase from Themoplasma acidophilum (TaNAPRTase). The TaNAPRTase has three domains, an N-terminal domain, a central functional domain, and a unique C-terminal domain. The crystal structure revealed that the functional domain has a type II phosphoribosyltransferase fold that may be a common architecture for both nicotinic acid and quinolinic acid (QA) phosphoribosyltransferases (PRTase) despite low sequence similarity between them. Unlike QAPRTase, TaNAPRTase has a unique extra C-terminal domain containing a zinc knuckle-like motif containing 4 cysteines. The TaNAPRTase forms a trimer of dimers in the crystal. The active site pocket is formed at dimer interfaces. The complex structures with phosphoribosylpyrophosphate (PRPP) and nicotinate mononucleotide (NAMN) showed, surprisingly, that functional residues lining on the active site of TaNAPRTase are quite different from those of QAPRTase, although their substrates are quite similar to each other. The phosphate moiety of PRPP and NAMN is anchored to the phosphate-binding loops formed by backbone amides, as found in many alpha/beta barrel enzymes. The pyrophosphate moiety of PRPP is located at the entrance of the active site pocket, whereas the nicotinate moiety of NAMN is located deep inside. Interestingly, the nicotinate moiety of NAMN is intercalated between highly conserved aromatic residues Tyr(21) and Phe(138). Careful structural analyses combined with other NAPRTase sequence subfamilies reveal that TaNAPRTase represents a unique sequence subfamily of NAPRTase. The structures of TaNAPRTase also provide valuable insight for other sequence subfamilies such as pre-B cell colony-enhancing factor, known to have nicotinamide phosphoribosyltransferase activity.

Amino Acid Sequence↗
PubMed2005

Crystal structure of acetylcholine-binding protein from Bulinus truncatus reveals the conserved structural scaffold and sites of variation in nicotinic acetylcholine receptors.

The crystal structure of acetylcholine-binding protein (AChBP) from the mollusk Lymnaea stagnalis is the established model for the ligand binding domains of the ligand-gated ion channel family, which includes nicotinic acetylcholine, 5-hydroxytryptamine (5-HT3), gamma-aminobutyric acid (GABA), types A and C, and glycine receptors. Here we present the crystal structure of a remote homolog, AChBP from Bulinus truncatus, which reveals both the conserved structural scaffold and the sites of variation in this receptor family. These include rigid body movements of loops that are close to the transmembrane interface in the receptors and changes in the intermonomer contacts, which alter the pentamer stability drastically. Structural, pharmacological and mutational analysis of both AChBPs shows how 3 amino acid changes in the binding site contribute to a 5-10-fold difference in affinity for nicotinic ligands. Comparison of these structures will be valuable for improving structure-function studies of ligand-gated ion channel receptors, including signal transduction, homology modeling, and drug design.

Amino Acid Sequence↗
PubMed2003

Predicting crystal structures with data mining of quantum calculations.

Predicting and characterizing the crystal structure of materials is a key problem in materials research and development. It is typically addressed with highly accurate quantum mechanical computations on a small set of candidate structures, or with empirical rules that have been extracted from a large amount of experimental information, but have limited predictive power. In this Letter, we transfer the concept of heuristic rule extraction to a large library of ab initio calculated information, and we demonstrate that this can be developed into a tool for crystal structure prediction.

Journal Article↗
PubMed1983

Additional conformational data for the mapping of the progestin binding site: crystal structures of 21-(phenylseleno)progesterone and 17 alpha-(phenylseleno)progesterone.

The crystal structures of 21-(phenylseleno)progesterone (1), which binds with moderate affinity to the progestin receptor, and 17 alpha-(phenylseleno)progesterone (2), which binds hardly at all, have been studied in an attempt to explain these differences in affinity and to obtain further information on the location of the progestin receptor binding site with respect to the progesterone molecule. The crystal structures were refined by isotropic thermal approximation to R values of 0.082 for 1 and 0.084 for 2. The unusual 17 beta side-chain orientation of 2 with a C16-C17-C20-O20 torsion angle of +13 degrees compared to -7 degrees for progesterone would seem to preclude hydrogen bonding with the progestin receptor binding site and provides strong supporting evidence for the contention that this site is located above the beta face of the molecule. Any rotation of the C21 methyl group into a more appropriate position is furthermore impeded by the presence of the 17 alpha-phenylseleno substituent. On the other hand, some hydrogen bonding can occur in the case of 1 (C16-C17-C20-O20 = 31 degrees) despite the fact that the difference in torsion angle (24 degrees) with respect to progesterone is, in absolute values, greater than that for 2 (20 degrees). This is because the orientation of the 17 beta-acetyl side chain of 1 is directed above the beta face closer to the progestin binding site, as previously defined on the basis of data on a large number of molecules, and because the 21-phenylseleno substituent constitutes only limited steric hindrance to binding. Thus, the difference in affinity of these two compounds is entirely consistent with observations that the H-bond donor is located toward O20 in the beta region of C16.

Crystallization↗
PubMed2005

Structural insights for fatty acid binding in a Lys49-phospholipase A2: crystal structure of myotoxin II from Bothrops moojeni complexed with stearic acid.

The crystal structure of dimeric Lys49-phospholipase A2 myotoxin-II from Bothrops moojeni (MjTX-II) co-crystallized with stearic acid (C(18)H(36)O(2)) has been determined at a resolution of 1.8 A. The electron density maps permitted the unambiguous inclusion of six stearic acid molecules in the refinement. Two stearic acid molecules could be located in the substrate-binding cleft of each monomer in positions, which favor the interaction of their carboxyl groups with active site residues. The way of binding of stearic acids to this Lys49-PLA(2)s is analogous to phospholipids and transition state analogues to catalytically active PLA(2)s. Two additional stearic acid molecules were located at the dimer interface region, defining a hitherto unidentified acyl-binding site on the protein surface. The strictly conserved Lys122 for Lys49-PLA(2)s may play a fundamental role for stabilization of legend-protein complex. The comparison of MjTX-II/satiric acid complex with other Lys-PLA(2)s structures whose putative fatty acids were located at their active site is also analysed. Molecular details of the stearic acid/protein interactions provide insights to binding in group I/II PLA(2)s, and to the possible interactions of Lys49-PLA(2)s with target membranes.

Animals↗
PubMed2006

Crystal structures of the trifluoromethyl sulfonates M(SO3CF3)2 (M = Mg, Ca, Ba, Zn, Cu) from synchrotron X-ray powder diffraction data.

The crystal structures of divalent metal salts of trifluoromethyl sulfonic acid ("trifluoromethyl sulfonates") M(SO(3)CF(3))(2) (M = Mg, Ca, Ba, Zn, Cu) were determined from high-resolution X-ray powder diffraction data. Magnesium, calcium and zinc trifluoromethyl sulfonate crystallize in the rhombohedral space group R(bar)3. Barium trifluoromethyl sulfonate crystallizes in the monoclinic space group I2/a(C2/c) and copper trifluoromethyl sulfonate crystallizes in the triclinic group P(bar)1. Within the crystal structures the trifluoromethyl sulfonate anions are arranged in double layers with the apolar CF(3) groups pointing towards each other. The cations are located next to the SO(3) groups. The symmetry relations between the different crystal structures have been analysed.

Journal Article↗
PubMed2004

Analysis of the class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99A resolution.

The crystal structure of the bacterial (Escherichia coli) class I 2-deoxyribose-5-phosphate aldolase (DERA) has been determined by Se-Met multiple anomalous dispersion (MAD) methods at 0.99A resolution. This structure represents the highest-resolution X-ray structure of an aldolase determined to date and enables a true atomic view of the enzyme. The crystal structure shows the ubiquitous TIM alpha/beta barrel fold. The enzyme contains two lysine residues in the active site. Lys167 forms the Schiff base intermediate, whereas Lys201, which is in close vicinity to the reactive lysine residue, is responsible for the perturbed pK(a) of Lys167 and, hence, also a key residue in the reaction mechanism. DERA is the only known aldolase that is able to use aldehydes as both aldol donor and acceptor molecules in the aldol reaction and is, therefore, of particular interest as a biocatalyst in synthetic organic chemistry. The uncomplexed DERA structure enables a detailed comparison with the substrate complexes and highlights a conformational change in the phosphate-binding site. Knowledge of the enzyme active-site environment has been the basis for exploration of catalysis of non-natural substrates and of mutagenesis of the phosphate-binding site to expand substrate specificity. Detailed comparison with other class I aldolase enzymes and DERA enzymes from different organisms reveals a similar geometric arrangement of key residues and implies a potential role for water as a general base in the catalytic mechanism.

Aldehyde-Lyases↗
PubMed2006

Crystal structure of the trigonal form of isotactic polypropylene as an example of density-driven polymer structure.

Propene-hexene copolymers crystallize in a new polymorphic form of isotactic polypropylene when the concentration of hexene is higher than nearly 10-15 mol %. The hexene units are included in the crystals, inducing an increase of density that allows crystallization of 3-fold helical chains in a trigonal unit cell according to the space group R3c or Rc, where the helical symmetry of the chains is maintained in the crystal lattice. The structure of this new form is similar to those of isotactic polybutene and polystyrene and does not crystallize in polypropylene homopolymer because it would have too low density. The crystal structure of isotactic polypropylene is therefore no longer an exception to the principles of polymer crystallography, but the new structure represents the fulfillment of these principles and indicates that the packing of polymer molecules is mainly driven by density.

Journal Article↗
PubMed1994

Refined crystal structure of mitochondrial malate dehydrogenase from porcine heart and the consensus structure for dicarboxylic acid oxidoreductases.

The crystal structure of mitochondrial malate dehydrogenase from porcine heart contains four identical subunits in the asymmetric unit of a monoclinic cell. Although the molecule functions as a dimer in solution, it exists as a tetramer with 222 point symmetry in the crystal. The crystallographic refinement was facilitated in the early stages by using weak symmetry restraints and molecular dynamics. The R-factor including X-ray data to 1.83-A resolution was 21.1%. The final root mean square deviation from canonical values is 0.015 A for bond lengths and 3.2 degrees for bond angles. The resulting model of the tetramer includes independent coordinates for each of the four subunits allowing an internal check on the accuracy of the model. The crystalline mitochondrial malate dehydrogenase tetramer has been analyzed to determine the surface areas lost at different subunit-subunit interfaces. The results show that the interface with the largest surface area is the same one found in cytosolic malate dehydrogenase. Each of the subunits contains a bound citrate molecule in the active site permitting the elaboration of a model for substrate binding which agrees with that found for the crystalline enzyme from Escherichia coli. The environment of the N-terminal region of the crystallographic model has been studied because the functional protein is produced from a precursor. This precursor form has an additional 24 residues which are involved in mitochondrial targeting and, possibly, translocation. The crystallographic model of mitochondrial malate dehydrogenase has been compared with its cytosolic counterpart from porcine heart and two prokaryotic enzymes. Small but significant differences have been found in the polar versus nonpolar accessible surface areas between the mitochondrial and cytosolic enzymes. Using least squares methods, four different malate dehydrogenases have been superimposed and their consensus structure has been determined. An amino acid sequence alignment based on the crystallographic structures describes all the conserved positions. The consensus active site of these dicarboxylic acid dehydrogenases is derived from the least squares comparison.

Amino Acid Sequence↗
PubMed2006

The use of biophysical methods increases success in obtaining liganded crystal structures.

In attempts to determine the crystal structure of small molecule-protein complexes, a common frustration is the absence of ligand binding once the protein structure has been solved. While the first structure, even with no ligand bound (apo), can be a cause for celebration, the solution of dozens of apo structures can give an unwanted sense of déjà vu. Much time and material is wasted on unsuccessful experiments, which can have a serious impact on productivity and morale. There are many reasons for the lack of observed binding in crystals and this paper highlights some of these. Biophysical methods may be used to confirm and optimize solution conditions to increase the success rate of crystallizing protein-ligand complexes. As there are an overwhelming number of biophysical methods available, some of the factors that need to be considered when choosing the most appropriate technique for a given system are discussed. Finally, a few illustrative examples where biophysical methods have proven helpful in real systems are given.

Amino Acid Sequence↗
PubMed1995

Crystal structure of a theta-class glutathione transferase.

Glutathione S-transferases (GSTs) are a family of enzymes involved in the cellular detoxification of xenotoxins. Cytosolic GSTs have been grouped into four evolutionary classes for which there are representative crystal structures of three of them. Here we report the first crystal structure of a theta-class GST. So far, all available GST crystal structures suggest that a strictly conserved tyrosine near the N-terminus plays a critical role in the reaction mechanism and such a role has been convincingly demonstrated by site-directed mutagenesis. Surprisingly, the equivalent residue in the theta-class structure is not in the active site, but its role appears to have been replaced by either a nearby serine or by another tyrosine residue located in the C-terminal domain of the enzyme.

Amino Acid Sequence↗
PubMed2006

Predicting crystal structure by merging data mining with quantum mechanics.

Modern methods of quantum mechanics have proved to be effective tools to understand and even predict materials properties. An essential element of the materials design process, relevant to both new materials and the optimization of existing ones, is knowing which crystal structures will form in an alloy system. Crystal structure can only be predicted effectively with quantum mechanics if an algorithm to direct the search through the large space of possible structures is found. We present a new approach to the prediction of structure that rigorously mines correlations embodied within experimental data and uses them to direct quantum mechanical techniques efficiently towards the stable crystal structure of materials.

Journal Article↗
PubMed1992

Molecular interactions in binary solids: crystal structure of a cholesteryl ester solid solution.

The x-ray crystal structure analysis of a cholesteryl ester solid solution, cholesteryl undecanoate/cholesteryl laurate in a molar ratio 0.52/0.48, is described. The unit cell is monoclinic with a = 13.005(2) A, b = 9.005(1) A, c = 31.421(3) A, and beta = 90.82(1) degrees and the space group P2(1) with Z = 4 (two molecules per asymmetric unit). Thus, the d001 spacing is almost the value predicted by Vegard's law from the values for the pure compounds. The room-temperature crystal structure is very much like that of cholesteryl laurate monolayer I packing, in the form where the esterified fatty acid chains are fully extended, with no salient sign of conformational disorder seen in this binary solid. The final R factor for 6571 observed reflections is 0.097.

Cholesterol Esters↗
PubMed2005

Crystal structure of a bacterial ribonuclease P RNA.

The x-ray crystal structure of a 417-nt ribonuclease P RNA from Bacillus stearothermophilus was solved to 3.3-A resolution. This RNA enzyme is constructed from a number of coaxially stacked helical domains joined together by local and long-range interactions. These helical domains are arranged to form a remarkably flat surface, which is implicated by a wealth of biochemical data in the binding and cleavage of the precursors of transfer RNA substrate. Previous photoaffinity crosslinking data are used to position the substrate on the crystal structure and to identify the chemically active site of the ribozyme. This site is located in a highly conserved core structure formed by intricately interlaced long-range interactions between interhelical sequences.

Bacterial Proteins↗
PubMed1996

The crystal structure of human cyclin H.

The crystal structure of human cyclin H has been solved at 2.6 A resolution by the MIR method and refined to an R-factor of 23.1%. The core of the molecule consists of two helical repeats adopting the canonical cyclin fold already observed in the structures of cyclin A [Brown et al. (1995) Structure 3, 1235-1247; Jeffrey et al. (1995) Nature 376, 313-320; Russo et al. (1996) Nature 382, 325-331] and TFIIB [Nikoilov et al. (1995) Nature 377, 119-128]. The N-terminal and C-terminal residues form a new domain built on two long helices interacting essentially with the first repeat of the molecule.

Crystallization↗
PubMed2000

Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase.

BACKGROUND: Methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr), catalyzes a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation. It transfers the N5-methyl group from methyltetrahydrofolate (CH3-H4folate) to a cob(I)amide center in another protein, the corrinoid iron-sulfur protein. MeTr is a member of a family of proteins that includes methionine synthase and methanogenic enzymes that activate the methyl group of methyltetra-hydromethano(or -sarcino)pterin. We report the first structure of a protein in this family. RESULTS: We determined the crystal structure of MeTr from Clostridium thermoaceticum at 2.2 A resolution using multiwavelength anomalous diffraction methods. The overall architecture presents a new functional class of the versatile triose phosphate isomerase (TIM) barrel fold. The MeTr tertiary structure is surprisingly similar to the crystal structures of dihydropteroate synthetases despite sharing less than 20% sequence identity. This homology permitted the methyl-H4folate binding site to be modeled. The model suggests extensive conservation of the pterin ring binding residues in the polar active sites of the methyltransferases and dihydropteroate synthetases. The most significant structural difference between these enzymes is in a loop structure above the active site. It is quite open in MeTr, where it can be modeled as the cobalamin binding site. CONCLUSIONS: The MeTr structure consists of a TIM barrel that embeds methyl-H4folate and cobamide. All related methyltransferases are predicted to fold into a similar TIM barrel pattern and have a similar pterin and cobamide binding site. The observed structure is consistent with either a 'front' (N5) or 'back' (C8a) side protonation of CH3-H4folate, a key step that enhances the electrophilic character of the methyl group, activating it for nucleophilic attack by Co(I).

Amino Acid Sequence↗
PubMed2002

Crystal structure studies on rubrerythrin: enzymatic activity in relation to the zinc movement.

Rubrerythrin (Rr) is a non-heme iron protein isolated from anaerobic sulfate-reducing bacteria. Rr is a dimeric molecule, each monomer contains a Fe(SCys)(4) center in the C-terminal domain and a binuclear metal center in the N-terminal domain. Rr structures with different protein sources and/or preparation procedures have been studied. Two Rr crystal structures have been solved with significant differences in their binuclear metal centers. The first structure, which was obtained from expressed protein under aerobic conditions, has a diiron-oxo center. The second structure, which was obtained from native protein of Desulfovibrio vulgaris under aerobic conditions, has an Fe-Zn center with the zinc position differing from the corresponding iron position in the former structure by approximately 2 A. The crystal structures of Rr isolated from D. vulgaris (Hildenborough, NCIB 8303), the same as the second structured but prepared under anaerobic conditions, are reported in this paper. The binuclear metal center in these structures is an Fe-Zn center. When the crystal was exposed to air, the zinc atom moved gradually, approximately 2 A, accompanied by the entrance of a water molecule (or hydroxyl group) and changes in the binuclear metal center microenvironment. This finding can explain the differences between the two different structures. The results suggest that the zinc movement may be related to the enzymatic activity of Rr.

Bacterial Proteins↗