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Structural Comparison (structural + comparison)
Selected AbstractsChelate [2-(Iminoethyl)pyridine N -oxide]metal Complexes , Synthesis and Structural Comparison with Their Chemically Related 2-(Iminoethyl)pyridine-Derived SystemsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 2 2006Katrin Nienkemper Abstract The N,O-chelate ligands 2-(iminoethyl)pyridine N -oxide (2a) and 2-(iminoethyl)-6-isopropylpyridine N -oxide (2b) were prepared by conventional synthetic routes, the latter involving a variant of the Reissert,Henze reaction. Treatment of 2a with FeCl2 resulted in a deoxygenation reaction of the ligand and formation of the salt [bis{2-(iminoethyl)pyridine}FeCl]+[FeCl4], (18a). In contrast, the reaction of 2a with PdCl2 or CoCl2 cleanly furnished the six-membered chelate [,N,O -2(iminoethyl)pyridine N -oxide]MCl2 complexes (19a, M = Pd) or (20a, M = Co), respectively, which were both characterised by X-ray diffraction. Treatment of 2b with [NiBr2(dme)], followed by crystallisation from THF, gave the complex [(,N,O - 2b)NiBr2(THF)] (21b), which features a distorted trigonal-bipyramidal coordination geometry of the central metal atom. The reaction of 2a with [NiBr2(dme)] gave the structurally related complex [(,N,O - 2a)NiBr2(,O - 2a)] (21a). The N,O-chelate Pd complex 19a was shown to be an active catalyst for the Suzuki coupling reaction. The ligand systems 2a,b and their related 2-(iminoethyl)pyridines 3a,b and a variety of metal complexes of ligands 3 were also prepared and characterised for comparison by X-ray diffraction. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Crystal structure of archaeal highly thermostable L -aspartate dehydrogenase/NAD/citrate ternary complexFEBS JOURNAL, Issue 16 2007Kazunari Yoneda The crystal structure of the highly thermostable l -aspartate dehydrogenase (l -aspDH; EC 1.4.1.21) from the hyperthermophilic archaeon Archaeoglobus fulgidus was determined in the presence of NAD and a substrate analog, citrate. The dimeric structure of A. fulgidusl -aspDH was refined at a resolution of 1.9 Å with a crystallographic R -factor of 21.7% (Rfree = 22.6%). The structure indicates that each subunit consists of two domains separated by a deep cleft containing an active site. Structural comparison of the A. fulgidusl -aspDH/NAD/citrate ternary complex and the Thermotoga maritimal -aspDH/NAD binary complex showed that A. fulgidusl -aspDH assumes a closed conformation and that a large movement of the two loops takes place during substrate binding. Like T. maritimal -aspDH, the A. fulgidus enzyme is highly thermostable. But whereas a large number of inter- and intrasubunit ion pairs are responsible for the stability of A. fulgidusl -aspDH, a large number of inter- and intrasubunit aromatic pairs stabilize the T. maritima enzyme. Thus stabilization of these two l -aspDHs appears to be achieved in different ways. This is the first detailed description of substrate and coenzyme binding to l -aspDH and of the molecular basis of the high thermostability of a hyperthermophilic l -aspDH. [source] Solution structure of the region 51,160 of human KIN17 reveals an atypical winged helix domainPROTEIN SCIENCE, Issue 12 2007Ludovic Carlier Abstract Human KIN17 is a 45-kDa eukaryotic DNA- and RNA-binding protein that plays an important role in nuclear metabolism and in particular in the general response to genotoxics. Its amino acids sequence contains a zinc finger motif (residues 28,50) within a 30-kDa N-terminal region conserved from yeast to human, and a 15-kDa C-terminal tandem of SH3-like subdomains (residues 268,393) only found in higher eukaryotes. Here we report the solution structure of the region 51,160 of human KIN17. We show that this fragment folds into a three-,-helix bundle packed against a three-stranded ,-sheet. It belongs to the winged helix (WH) family. Structural comparison with analogous WH domains reveals that KIN17 WH module presents an additional and highly conserved 310 -helix. Moreover, KIN17 WH helix H3 is not positively charged as in classical DNA-binding WH domains. Thus, human KIN17 region 51,160 might rather be involved in protein,protein interaction through its conserved surface centered on the 310 -helix. [source] Crystal structure of the Streptococcus pneumoniae mevalonate kinase in complex with diphosphomevalonatePROTEIN SCIENCE, Issue 5 2007John L. Andreassi II Abstract Streptococcuspneumoniae, a ubiquitous gram-positive pathogen with an alarming, steadily evolving resistance to frontline antimicrobials, poses a severe global health threat both in the community and in the clinic. The recent discovery that diphosphomevalonate (DPM), an essential intermediate in the isoprenoid biosynthetic pathway, potently and allosterically inhibits S. pneumoniae mevalonate kinase (SpMK) without affecting the human isozyme established a new target and lead compound for antimicrobial design. Here we present the crystal structure of the first S. pneumoniae mevalonate kinase, at a resolution of 2.5 Å and in complex with DPM·Mg2+ in the active-site cleft. Structural comparison of SpMK with other members of the GHMP kinase family reveals that DPM functions as a partial bisubstrate analog (mevalonate linked to the pyrophosphoryl moiety of ATP) in that it elicits a ternary-complexlike form of the enzyme, except for localized disordering in a region that would otherwise interact with the missing portion of the nucleotide. Features of the SpMK-binding pockets are discussed in the context of established mechanistic findings and inherited human diseases linked to MK deficiency. [source] Structural comparison of three N -(4-halogenophenyl)- N,-[1-(2-pyridyl)ethylidene]hydrazine hydrochloridesACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2010Julia Heilmann-Brohl 2-{1-[(4-Chloroanilino)methylidene]ethyl}pyridinium chloride methanol solvate, C13H13ClN3+·Cl,·CH3OH, (I), crystallizes as discrete cations and anions, with one molecule of methanol as solvent in the asymmetric unit. The N,C,C,N torsion angle in the cation indicates a cis conformation. The cations are located parallel to the (02) plane and are connected through hydrogen bonds by a methanol solvent molecule and a chloride anion, forming zigzag chains in the direction of the b axis. The crystal structure of 2-{1-[(4-fluoroanilino)methylidene]ethyl}pyridinium chloride, C13H13FN3+·Cl,, (II), contains just one anion and one cation in the asymmetric unit but no solvent. In contrast with (I), the N,C,C,N torsion angle in the cation corresponds with a trans conformation. The cations are located parallel to the (100) plane and are connected by hydrogen bonds to the chloride anions, forming zigzag chains in the direction of the b axis. In addition, the crystal packing is stabilized by weak ,,, interactions between the pyridinium and benzene rings. The crystal of (II) is a nonmerohedral monoclinic twin which emulates an orthorhombic diffraction pattern. Twinning occurs via a twofold rotation about the c axis and the fractional contribution of the minor twin component refined to 0.324,(3). 2-{1-[(4-Fluoroanilino)methylidene]ethyl}pyridinium chloride methanol disolvate, C13H13FN3+·Cl,·2CH3OH, (III), is a pseudopolymorph of (II). It crystallizes with two anions, two cations and four molecules of methanol in the asymmetric unit. Two symmetry-equivalent cations are connected by hydrogen bonds to a chloride anion and a methanol solvent molecule, forming a centrosymmetric dimer. A further methanol molecule is hydrogen bonded to each chloride anion. These aggregates are connected by C,H...O contacts to form infinite chains. It is remarkable that the geometric structures of two compounds having two different formula units in their asymmetric units are essentially the same. [source] Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotidesACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2010Matthias Haffke The human ATP-binding cassette (ABC) transporter ABCB6 is involved in haem-precursor transport across the mitochondrial membrane. The crystal structure of its nucleotide-binding domain (NBD) has been determined in the apo form and in complexes with ADP, with ADP and Mg2+ and with ATP at high resolution. The overall structure is L-shaped and consists of two lobes, consistent with other reported NBD structures. Nucleotide binding is mediated by the highly conserved Tyr599 and the Walker A motif, and induces notable structural changes. Structural comparison with other structurally characterized NBDs and full-length ABC transporters gives the first insight into the possible catalytic mechanism of ABCB6 and the role of the N-terminal helix ,1 in full-length ABCB6. [source] Structure of Arabidopsis chloroplastic monothiol glutaredoxin AtGRXcpACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2010Lenong Li Monothiol glutaredoxins (Grxs) play important roles in maintaining redox homeostasis in living cells and are conserved across species. Arabidopsis thaliana monothiol glutaredoxin AtGRXcp is critical for protection from oxidative stress in chloroplasts. The crystal structure of AtGRXcp has been determined at 2.4,Å resolution. AtGRXcp has a glutaredoxin/thioredoxin-like fold with distinct structural features that differ from those of dithiol Grxs. The structure reveals that the putative active-site motif CGFS is well defined and is located on the molecular surface and that a long groove extends to both sides of the catalytic Cys97. Structural comparison and molecular modeling suggest that glutathione can bind in this groove and form extensive interactions with conserved charged residues including Lys89, Arg126 and Asp152. Further comparative studies reveal that a unique loop with five additional residues adjacent to the active-site motif may be a key structural feature of monothiol Grxs and may influence their function. This study provides the first structural information on plant CGFS-type monothiol Grxs, allowing a better understanding of the redox-regulation mechanism mediated by these plant Grxs. [source] Conservation of a conformational switch in RadA recombinase from Methanococcus maripaludisACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Yang Li Archaeal RadAs are close homologues of eukaryal Rad51s (,40% sequence identity). These recombinases promote ATP hydrolysis and a hallmark strand-exchange reaction between homologous single-stranded and double-stranded DNA substrates. Pairing of the 3,-overhangs located at the damaged DNA with a homologous double-stranded DNA enables the re-synthesis of the damaged region using the homologous DNA as the template. In recent studies, conformational changes in the DNA-interacting regions of Methanococcus voltae RadA have been correlated with the presence of activity-stimulating potassium or calcium ions in the ATPase centre. The series of crystal structures of M. maripaludis RadA presented here further suggest the conservation of an allosteric switch in the ATPase centre which controls the conformational status of DNA-interacting loops. Structural comparison with the distant Escherichia coli RecA homologue supports the notion that the conserved Lys248 and Lys250 residues in RecA play a role similar to that of cations in RadA. The conservation of a cationic bridge between the DNA-interacting L2 region and the terminal phosphate of ATP, together with the apparent stability of the nucleoprotein filament, suggests a gap-displacement model which may explain the advantage of ATP hydrolysis for DNA-strand exchange. [source] Structure of OsmC from Escherichia coli: a salt-shock-induced proteinACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2004Dong Hae Shin The crystal structure of an osmotically inducible protein (OsmC) from Escherichia coli has been determined at 2.4,Å resolution. OsmC is a representative protein of the OsmC sequence family, which is composed of three sequence subfamilies. The structure of OsmC provides a view of a salt-shock-induced protein. Two identical monomers form a cylindrically shaped dimer in which six helices are located on the inside and two six-stranded ,-sheets wrap around these helices. Structural comparison suggests that the OsmC sequence family has a peroxiredoxin function and has a unique structure compared with other peroxiredoxin families. A detailed analysis of structures and sequence comparisons in the OsmC sequence family revealed that each subfamily has unique motifs. In addition, the molecular function of the OsmC sequence family is discussed based on structural comparisons among the subfamily members. [source] Structural comparison of Escherichia colil -asparaginase in two monoclinic space groupsACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2003Mario Sanches The functional l -asparaginase from Escherichia coli is a homotetramer with a molecular weight of about 142,kDa. The X-ray structure of the enzyme, crystallized in a new form (space group C2) and refined to 1.95,Å resolution, is compared with that of the previously determined crystal form (space group P21). The asymmetric unit of the new crystal form contains an l -asparaginase dimer instead of the tetramer found in the previous crystal form. It is found that crystal contacts practically do not affect the conformation of the protein. It is shown that subunit C of the tetrameric form is in a conformation which is systematically different from that of all other subunits in both crystal forms. Major conformational differences are confined to the lid loop (residues 14,27). In addition, the stability of this globular protein is analyzed in terms of the interactions between hydrophobic parts of the subunits. [source] Structures of hypoxanthine-guanine phosphoribosyltransferase (TTHA0220) from Thermus thermophilus HB8ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2010Mayumi Kanagawa Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase), which is a key enzyme in the purine-salvage pathway, catalyzes the synthesis of IMP or GMP from ,- d -phosphoribosyl-1-pyrophosphate and hypoxanthine or guanine, respectively. Structures of HGPRTase from Thermus thermophilus HB8 in the unliganded form, in complex with IMP and in complex with GMP have been determined at 2.1, 1.9 and 2.2,Å resolution, respectively. The overall fold of the IMP complex was similar to that of the unliganded form, but the main-chain and side-chain atoms of the active site moved to accommodate IMP. The overall folds of the IMP and GMP complexes were almost identical to each other. Structural comparison of the T. thermophilus HB8 enzyme with 6-oxopurine PRTases for which structures have been determined showed that these enzymes can be tentatively divided into groups I and II and that the T. thermophilus HB8 enzyme belongs to group I. The group II enzymes are characterized by an N-terminal extension with additional secondary elements and a long loop connecting the second ,-helix and ,-strand compared with the group I enzymes. [source] The structure of PhaZ7 at atomic (1.2,Å) resolution reveals details of the active site and suggests a substrate-binding modeACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2010Sachin Wakadkar Poly-(R)-hydroxyalkanoates (PHAs) are bacterial polyesters that are degraded by a group of enzymes known as PHA depolymerases. Paucimonas lemoignei PhaZ7 depolymerase is the only extracellular depolymerase that has been described as being active towards amorphous PHAs. A previously determined crystal structure of PhaZ7 revealed an ,/,-hydrolase fold and a Ser-His-Asp catalytic triad. In order to address questions regarding the catalytic mechanism and substrate binding, the atomic resolution structure of PhaZ7 was determined after cocrystallization with the protease inhibitor PMSF. The reported structure has the highest resolution (1.2,Å) of currently known depolymerase structures and shows a sulfur dioxide molecule covalently attached to the active-site residue Ser136. Structural comparison with the free PhaZ7 structure (1.45,Å resolution) revealed no major changes in the active site, suggesting a preformed catalytic triad. The oxyanion hole was found to be formed by the amide groups of Met137 and Asn49. Nine well ordered water molecules were located in the active site. Manual docking of a substrate trimer showed that the positions of these water molecules coincide well with the substrate atoms. It is proposed that these water molecules are displaced upon binding of the substrate. Furthermore, conformational changes were identified after comparison with a previously determined PhaZ7 dimer structure in a different space group. The changes were located in surface loops involved in dimer formation, indicating some flexibility of these loops and their possible involvement in polyester binding. [source] Structure of the complex of porcine pancreatic elastase with a trimacrocyclic peptide inhibitor FR901451ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2005Takayoshi Kinoshita Porcine pancreatic elastase (PPE) resembles the attractive drug target leukocyte elastase, which has the ability to degrade connective tissue in the body. The crystal structure of PPE complexed with a novel trimacrocyclic peptide inhibitor, FR901451, was solved at 1.9,Å resolution. The inhibitor occupied the subsites S3 through S3, of PPE and induced conformational changes in the side chains of Arg64 and Arg226, which are located at the edges of the substrate-binding cleft. Structural comparison of five PPE,inhibitor complexes, including the FR901451 complex and non-ligated PPE, reveals that the residues forming the S2, S1, S1, and S2, subsites in the cleft are rigid, but the two arginine residues playing a part in the S3 and S3, subsites are flexible. Structural comparison of PPE with human leukocyte elastase (HLE) implies that the inhibitor binds to HLE in a similar manner to the FR901451,PPE complex. This structural insight may help in the design of potent elastase inhibitors. [source] Structural and electrical characterization of a -plane GaN grown on a -plane SiCPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 7 2003M. D. Craven Abstract Planar nonpolar () a -plane GaN thin films were grown on () a -plane 6H-SiC substrates via metalorganic chemical vapor deposition by depositing a high temperature AlN buffer layer prior to the epitaxial GaN growth. The orientation of the GaN film and AlN buffer layer directly match that of the SiC substrate, as determined by on- and off-axis X-ray diffraction measurements. The morphological evolution of GaN grown on the AlN buffer layers was investigated using atomic force microscopy. Microstructural characterization of the coalesced a -plane GaN films provided by plan-view transmission electron microscopy revealed threading dislocation and stacking fault densities of ,3 × 1010 cm,2 and ,7 × 105 cm,1, respectively. Structural comparisons to a -plane GaN films grown on r -plane sapphire substrates are presented. Si-doped films were grown with a variety of Si/Ga ratios and electrically characterized using Hall effect measurements. A maximum Hall mobility of 109 cm2/Vs was attained at a carrier concentration of 1.8 × 1019 cm,3. [source] Methyl ,-allolactoside [methyl ,- d -galactopyranosyl-(1,6)-,- d -glucopyranoside] monohydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2009Thomas E. Klepach Methyl ,-allolactoside [methyl ,- d -galactopyranosyl-(1,6)-,- d -glucopyranoside], (II), was crystallized from water as a monohydrate, C13H24O11·H2O. The ,Galp and ,Glcp residues in (II) assume distorted 4C1 chair conformations, with the former more distorted than the latter. Linkage conformation is characterized by ,, (C2Gal,C1Gal,O1Gal,C6Glc), ,, (C1Gal,O1Gal,C6Glc,C5Glc) and , (C4Glc,C5Glc,C6Glc,O1Gal) torsion angles of 172.9,(2), ,117.9,(3) and ,176.2,(2)°, respectively. The ,, and , values differ significantly from those found in the crystal structure of ,-gentiobiose, (III) [Rohrer et al. (1980). Acta Cryst. B36, 650,654]. Structural comparisons of (II) with related disaccharides bound to a mutant ,-galactosidase reveal significant differences in hydroxymethyl conformation and in the degree of ring distortion of the ,Glcp residue. Structural comparisons of (II) with a DFT-optimized structure, (IIC), suggest a link between hydrogen bonding, pyranosyl ring deformation and linkage conformation. [source] Structural comparisons between methylated and unmethylated nitrophenyl lophinesACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2009Diana Yanover The lophine derivative 2-(2-nitrophenyl)-4,5-diphenyl-1H -imidazole, C21H15N3O2, (I), crystallized from ethanol as a solvent-free crystal and from acetonitrile as the monosolvate, C21H15N3O2·C2H3N, (II). Crystallization of 2-(4-nitrophenyl)-4,5-diphenyl-1H -imidazole from methanol yielded the methanol monosolvate, C21H15N3O2·CH4O, (III). Three lophine derivatives of methylated imidazole, namely, 1-methyl-2-(2-nitrophenyl)-4,5-diphenyl-1H -imidazole methanol solvate, C22H17N3O2·CH4O, (IV), 1-methyl-2-(3-nitrophenyl)-4,5-diphenyl-1H -imidazole, C22H17N3O2, (V), and 1-methyl-2-(4-nitrophenyl)-4,5-diphenyl-1H -imidazole, C22H17N3O2, (VI), were recrystallized from methanol, acetonitrile and ethanol, respectively, but only (IV) produced a solvate. Compounds (III) and (IV) each crystallize with two independent molecules in the asymmetric unit. Five imidazole molecules in the six crystals differ in their molecular conformations by rotation of the aromatic rings with respect to the central imidazole ring. In the absence of a methyl group on the imidazole [compounds (I),(III)], the rotation angles are not strongly affected by the position of the nitro group [44.8,(2) and 45.5,(1)° in (I) and (II), respectively, and 15.7,(2) and 31.5,(1)° in the two molecules of (III)]. However, the rotation angle is strongly affected by the presence of a methyl group on the imidazole [compounds (IV),(VI)], and the position of the nitro group (ortho, meta or para) on a neighbouring benzene ring; values of the rotation angle range from 26.0,(1) [in (VI)] to 85.2,(1)° [in (IV)]. This group repulsion also affects the outer N,C,N bond angle. The packing of the molecules in (I), (II) and (III) is determined by hydrogen bonding. In (I) and (II), molecules form extended chains through N,H...N hydrogen bonds [with an N...N distance of 2.944,(5),Å in (I) and 2.920,(3),Å in (II)], while in (III) the chain is formed with a methanol solvent molecule as the mediator between two imidazole rings, with O...N distances of 2.788,(4),2.819,(4),Å. In the absence of the imidazole N,H H-atom donor, the packing of molecules (IV),(VI) is determined by weaker intermolecular interactions. The methanol solvent molecule in (IV) is hydrogen bonded to imidazole [O...N = 2.823,(4),Å] but has no effect on the packing of molecules in the unit cell. [source] Atomic resolution studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnelsACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2010A. Stsiapanava The haloalkane dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 is a bacterial enzyme that shows catalytic activity for the hydrolytic degradation of the highly toxic industrial pollutant 1,2,3-trichloropropane (TCP). Mutagenesis focused on the access tunnels of DhaA produced protein variants with significantly improved activity towards TCP. Three mutants of DhaA named DhaA04 (C176Y), DhaA14 (I135F) and DhaA15 (C176Y + I135F) were constructed in order to study the functional relevance of the tunnels connecting the buried active site of the protein with the surrounding solvent. All three protein variants were crystallized using the sitting-drop vapour-diffusion technique. The crystals of DhaA04 belonged to the orthorhombic space group P212121, while the crystals of DhaA14 and DhaA15 had triclinic symmetry in space group P1. The crystal structures of DhaA04, DhaA14 and DhaA15 with ligands present in the active site were solved and refined using diffraction data to 1.23, 0.95 and 1.22,Å, resolution, respectively. Structural comparisons of the wild type and the three mutants suggest that the tunnels play a key role in the processes of ligand exchange between the buried active site and the surrounding solvent. [source] pH-dependent structural changes in haemoglobin component V from the midge larva Propsilocerus akamusi (Orthocladiinae, Diptera)ACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2010Takao Kuwada Haemoglobin component V (Hb,V) from the midge larva Propsilocerus akamusi exhibits oxygen affinity despite the replacement of HisE7 and a pH-dependence of its functional properties. In order to understand the contribution of the distal residue to the ligand-binding properties and the pH-dependent structural changes in this insect Hb, the crystal structure of Hb,V was determined under five different pH conditions. Structural comparisons of these Hb structures indicated that at neutral pH ArgE10 contributes to the stabilization of the haem-bound ligand molecule as a functional substitute for the nonpolar E7 residue. However, ArgE10 does not contribute to stabilization at acidic and alkaline pH because of the swinging movement of the Arg side chain under these conditions. This pH-dependent behaviour of Arg results in significant differences in the hydrogen-bond network on the distal side of the haem in the Hb,V structures at different pH values. Furthermore, the change in pH results in a partial movement of the F helix, considering that coupled movements of ArgE10 and the F helix determine the haem location at each pH. These results suggested that Hb,V retains its functional properties by adapting to the structural changes caused by amino-acid replacements. [source] Structures of human deoxycytidine kinase product complexesACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2007Erika V. Soriano Human deoxycytidine kinase (dCK) is involved in the nucleotide-biosynthesis salvage pathway and has also been shown to phosphorylate several antitumor and antiviral prodrugs. The structures of dCK alone and the dead-end complex of dCK with substrate nucleoside and product ADP or UDP have previously been reported; however, there is currently no structure available for a substrate or product complex. Here, the structures of dCK complexes with the products dCMP, UDP and Mg2+ ion, and with dAMP, UDP and Mg2+ ion are reported. Structural comparisons show that the product complexes with UDP and a dead-end complex with substrate and UDP have similar active-site conformations. [source] Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2001Jason W. O'Neill The three-dimensional structure of a tryptophan-containing variant of the IgG-binding B1 domain of protein L has been solved in two crystal forms to 1.7 and 1.8,Å resolution. In one of the crystal forms, the entire N-terminal histidine-tag region was immobilized through the coordination of zinc ions and its structural conformation along with the zinc coordination scheme were determined. However, the ordering of the histidine tag by zinc does not affect the overall structure of the rest of the protein. Structural comparisons of the tryptophan-containing variant with an NMR-derived wild-type structure, which contains a tyrosine at position 47, reveals a common fold, although the overall backbone root-mean-square difference is 1.5,Å. The Y47W substitution only caused local rearrangement of several side chains, the most prominent of which is the rotation of the Tyr34 side chain, resulting in a 6,Å displacement of its hydroxyl group. A small methyl-sized cavity bounded by ,-strands 1, 2 and 4 and the ,-helix was found in the structures of the Y47W-substituted protein L B1 domain. This cavity may be created as the result of subsequent side-chain rearrangements caused by the Y47W substitution. These high-resolution structures of the tryptophan-containing variant provide a reference frame for the analysis of thermodynamic and kinetic data derived from a series of mutational studies of the protein L B1 domain. [source] Structure of a fibronectin type III-like module from Clostridium thermocellumACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2010Markus Alahuhta The 1.6,Å resolution structure of a fibronectin type III-like module from Clostridium thermocellum (PDB code 3mpc) with two molecules in the asymmetric unit is reported. The crystals used for data collection belonged to space group P212121, with unit-cell parameters a = 35.43, b = 45.73, c = 107.72,Å, and the structure was refined to an R factor of 0.166. Structural comparisons found over 800 similar structures in the Protein Data Bank. The broad range of different proteins or protein domains with high structural similarity makes it especially demanding to classify these proteins. Previous studies of fibronectin type III-like modules have indicated that they might function as ligand-binding modules, as a compact form of peptide linkers or spacers between other domains, as cellulose-disrupting modules or as proteins that help large enzyme complexes remain soluble. [source] Structure of human factor VIIa/tissue factor in complex with a peptide-mimetic inhibitor: high selectivity against thrombin by introducing two charged groups in P2 and P4ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2005Shojiro Kadono The crystal structure of human factor VIIa/soluble tissue factor (FVIIa/sTF) in complex with a highly selective peptide-mimetic FVIIa inhibitor which shows 1670-fold selectivity against thrombin inhibition has been solved at 2.6,Å resolution. The inhibitor is bound to FVIIa/sTF at the S1, S2 and S3 sites and at the additional S1 subsite. Two charged groups, the amidino group in P2 and the carboxylate group in P4, form ionic interactions with Asp60 and Lys192 of FVIIa, respectively. Structural comparisons between factor VIIa and thrombin show that thrombin has oppositely charged residues, Lys60F and Glu192, in the S2 site and the S1 subsites, respectively. These data suggest that the utilization of the differences of charge distribution in the S2 site and the S1 subsites between FVIIa and thrombin is critical for achieving high selectivity against thrombin inhibition. These results will provide valuable information for the structure-based drug design of specific inhibitors for FVIIa/TF. [source] Highly Ordered Interstitial Water Observed in Bone by Nuclear Magnetic Resonance,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 4 2005Erin E Wilson Abstract NMR was used to study the nanostructure of bone tissue. Distance measurements show that the first water layer at the surface of the mineral in cortical bone is structured. This water may serve to couple the mineral to the organic matrix and may play a role in deformation. Introduction: The unique mechanical characteristics of bone tissue have not yet been satisfactorily connected to the exact molecular architecture of this complex composite material. Recently developed solid-state nuclear magnetic resonance (NMR) techniques are applied here to the mineral component to provide new structural distance constraints at the subnanometer scale. Materials and Methods: NMR dipolar couplings between structural protons (OH, and H2O) and phosphorus (PO4) or carbon (CO3) were measured using the 2D Lee-Goldburg Cross-Polarization under Magic-Angle Spinning (2D LG-CPMAS) pulse sequence, which simultaneously suppresses the much stronger proton-proton dipolar interactions. The NMR dipolar couplings measured provide accurate distances between atoms, e.g., OH and PO4 in apatites. Excised and powdered femoral cortical bone was used for these experiments. Synthetic carbonate (,2-4 wt%)-substituted hydroxyapatite was also studied for structural comparison. Results: In synthetic apatite, the hydroxide ions are strongly hydrogen bonded to adjacent carbonate or phosphate ions, with hydrogen bond (O-H) distances of ,1.96 Å observed. The bone tissue sample, in contrast, shows little evidence of ordered hydroxide. Instead, a very ordered (structural) layer of water molecules is identified, which hydrates the small bioapatite crystallites through very close arrangements. Water protons are ,2.3-2.55 Å from surface phosphorus atoms. Conclusions: In synthetic carbonated apatite, strong hydrogen bonds were observed between the hydroxide ions and structural phosphate and carbonate units in the apatite crystal lattice. These hydrogen bonding interactions may contribute to the long-range stability of this mineral structure. The biological apatite in cortical bone tissue shows evidence of hydrogen bonding with an ordered surface water layer at the faces of the mineral particles. This structural water layer has been inferred, but direct spectroscopic evidence of this interstitial water is given here. An ordered structural water layer sandwiched between the mineral and the organic collagen fibers may affect the biomechanical properties of this complex composite material. [source] Varicella-zoster virus isolates, but not the vaccine strain OKA, induce sensitivity to alpha-1 and beta-1 adrenergic stimulation of sensory neurones in cultureJOURNAL OF MEDICAL VIROLOGY, Issue S1 2003Michaela Schmidt Abstract The reactivation of varicella-zoster virus (VZV) from its persistent state in sensory neurones causes shingles and induces severe, long-lasting pain and hyperalgesia that often lead to postherpetic neuralgia. To investigate the VZV-induced neuropathic changes, we established conditions for the active infection of sensory neurones from rat dorsal root ganglia in vitro. After 2 days of culture, up to 50% of the cells expressed viral antigens of the immediate-early and late replication phase. The intracellular calcium ion concentration was monitored in individual cells by microfluorimetry. Whereas the calcium response to capsaicin was preserved, the VZV-infected neurones gained an unusual sensitivity to noradrenaline stimulation in contrast to non-infected cells. The adrenergic agonists phenylephrine and isoproterenol had a similar efficacy demonstrating that both ,1 - and ,1 -adrenoreceptors were involved. The sensitivity to adrenergic stimulation was observed after infection with different wildtype isolates, but not with the attenuated vaccine strain OKA. The lack of noradrenaline sensitivity of vaccine-infected neurones demands a structural comparison of wildtype and vaccine viruses with and without phenotype. A partial sequence evaluation (26 kb) of the European OKA vaccine strain surprisingly revealed a series of nucleotide exchanges in comparison to presumably identical OKA strains from other sources, although VZV is generally considered genetically stable. In summary, we report that the infection with wildtype VZV isolates, but not with the vaccine strain, induces noradrenaline sensitivity in sensory neurones, which correlates with clinical and experimental observations of adrenergic effects involved in VZV-induced neuralgia. J. Med. Virol. 70:S82,S89, 2003. © 2003 Wiley-Liss, Inc. [source] Three monophyletic superfamilies account for the majority of the known glycosyltransferasesPROTEIN SCIENCE, Issue 7 2003Jing Liu Abstract Sixty-five families of glycosyltransferases (EC 2.4.x.y) have been recognized on the basis of high-sequence similarity to a founding member with experimentally demonstrated enzymatic activity. Although distant sequence relationships between some of these families have been reported, the natural history of glycosyltransferases is poorly understood. We used iterative searches of sequence databases, motif extraction, structural comparison, and analysis of completely sequenced genomes to track the origins of modern-type glycosyltransferases. We show that >75% of recognized glycosyltransferase families belong to one of only three monophyletic superfamilies of proteins, namely, (1) a recently described GPGTF/GT-B superfamily; (2) a nucleoside-diphosphosugar transferase (GT-A) superfamily, which is characterized by a DxD sequence signature and also includes nucleotidyltransferases; and (3) a GT-C superfamily of integral membrane glycosyltransferases with a modified DxD signature in the first extracellular loop. Several developmental regulators in Metazoans, including Fringe and Egghead homologs, belong to the second superfamily. Interestingly, Tout-velu/Exostosin family of developmental proteins found in all multicellular eukaryotes, contains separate domains belonging to the first and the second superfamilies, explaining multiple glycosyltransferase activities in one protein. [source] Linkage isomeric oxamate chelates: rac -bis(ethane-1,2-diamine)oxamatocobalt(III) bis(trifluoromethanesulfonate) dihydrate and ,(+)578 -bis(ethane-1,2-diamine)[oxamato(2,)]cobalt(III) trifluoromethanesulfonateACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2009Anders Hammershøi The structures of rac -bis(ethane-1,2-diamine)(oxamato-,2O1,O2)cobalt(III) bis(trifluoromethanesulfonate) dihydrate, [Co(C2H2NO3)(C2H8N2)2](CF3SO3)2·2H2O, (I), and ,(+)578 -bis(ethane-1,2-diamine)[oxamato(2,)-,2N,O1]cobalt(III) trifluoromethanesulfonate, [Co(C2HNO3)(C2H8N2)2]CF3SO3, (II), are compared. Together, the two complexes constitute the first pair of linkage isomers of bidentate oxamate available for structural comparison. [source] 3,4-Diethyl-2,5-dihydro-1H -pyrrole-2,5-dioneACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2007Frédérique Brégier In the crystal structure of the title compound, C8H11NO2, three distinct molecules are present in the asymmetric unit. The molecules are organized in two different hydrogen-bonded tapes, which form a complex layered structure. A structural comparison with the crystal structures of related maleimide derivatives unravels a stepwise evolution of morphological complexity with increasing molecular complexity for this class of compounds. [source] Structure of Helicobacter pyloril -asparaginase at 1.4,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2009Prathusha Dhavala Bacterial l -asparaginases have been used in the treatment of childhood acute lymphoblastic leukaemia for over 30,years. Their therapeutic effect is based on their ability to catalyze the conversion of l -asparagine, an essential amino acid in certain tumours, to l -aspartic acid and ammonia. Two l -asparaginases, one from Escherichia coli and the other from Erwinia chrysanthemi, have been widely employed in clinical practice as anti-leukaemia drugs. However, l -asparaginases are also able to cause severe side effects owing to their intrinsic glutaminase activity. Helicobacter pyloril -asparaginase (HpA) has been reported to have negligible glutaminase activity. To gain insight into the properties of HpA, its crystal structure in the presence of l -aspartate was determined to 1.4,Å resolution, which is one of the highest resolutions obtained for an l -asparaginase structure. The final structure has an Rcryst of 12.6% (Rfree = 16.9%) with good stereochemistry. A detailed analysis of the active site showed major differences in the active-site flexible loop and in the 286,297 loop from the second subunit, which is involved in active-site formation. Accordingly, Glu289, Asn255 and Gln63 are suggested to play roles in modulating the accessibility of the active site. Overall, the structural comparison revealed that HpA has greater structural similarity to E. colil -asparaginase than to any other l -asparaginase, including Er. carotovoral -asparaginase, despite the fact that the latter is also characterized by low glutaminase activity. [source] A structural comparison of three isoforms of anionic trypsin from chum salmon (Oncorhynchus keta)ACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2009Eiko Toyota Three anionic salmon trypsin isoforms (CST-1, CST-2 and CST-3) were isolated from the pyloric caeca of chum salmon (Oncorhynchus keta). The order of catalytic efficiency (Km/kcat) of the isoforms during BAPA hydrolysis was CST-2 > CST-1 > CST-3. In order to find a structural rationalization for the observed difference in catalytic efficiency, the X-ray crystallographic structures of the three isoforms were compared in detail. Some structural differences were observed in the C-terminal ,-helix, interdomain loop and active-site region. From the results of the detailed comparison, it appears that the structural flexibility of the C-terminal ,-helix, which interacts with the N-terminal domain, and the substrate-binding pocket in CST-3 are lower than those in CST-1 and CST-2. In addition, the conformation of the catalytic triad (His57, Asp102 and Ser195) differs among the three isoforms. The imidazole N atom of His57 in CST-1 and CST-2 forms a hydrogen bond to the hydroxyl O atom of Ser195, but the distance between the imidazole N atom of His57 and the hydroxyl O atom of Ser195 in CST-3 is too great (3.8,Å) for the formation of a hydrogen bond. Thus, the nucleophilicity of the hydroxyl group of Ser195 in CST-3 is weaker than that in CST-1 or CST-2. Furthermore, the electrostatic potential of the substrate-binding pocket in CST-2 is markedly lower than those in CST-1 and CST-3 owing to the negative charges of Asp150, Asp153 and Glu221B that arise from the long-range effect. These results may explain the higher catalytic efficiency of CST-2 compared with CST-1 and CST-3. [source] Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodonsACTA CRYSTALLOGRAPHICA SECTION D, Issue 10 2007Yoshiteru Sato In protein synthesis, 20 types of aminoacyl-tRNA synthetase (aaRS) are generally required in order to distinguish between the 20 types of amino acid so that each achieves strict recognition of the cognate amino acid and the cognate tRNA. In the crenarchaeon Sulfolobus tokodaii strain 7 (St), however, asparaginyl-tRNA synthetase (AsnRS) is missing. It is believed that AspRS instead produces Asp-tRNAAsn in addition to Asp-tRNAAsp. In order to reveal the recognition mechanism for the two anticodons, GUC for aspartate and GUU for asparagine, the crystal structure of St -AspRS (nondiscriminating type) has been determined at 2.3,Å resolution as the first example of the nondiscriminating type of AspRS from crenarchaea. A structural comparison with structures of discriminating AspRSs indicates that the structures are similar to each other overall and that the catalytic domain is highly conserved as expected. In the N-terminal domain, however, the binding site for the third anticodon nucleotide is modified to accept two pyrimidine bases, C and U, but not purine bases. The C base can bind to form a hydrogen bond to the surrounding main-chain amide group in the discriminating AspRS, while in the nondiscriminating AspRS the corresponding amino-acid residue is replaced by proline, which has no amide H atom for hydrogen-bond formation, thus allowing the U base to be accommodated in this site. In addition, the residues that cover the base plane are missing in the nondiscriminating AspRS. These amino-acid changes make it possible for both C and U to be accepted by the nondiscriminating AspRS. It is speculated that this type of nondiscriminating AspRS has been introduced into Thermus thermophilus through horizontal gene transfer. [source] | |||||||||||||