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At least 937 records · Page 52Linked to original sources
PubMed1993

Crystal structure of phospholipase A2 from Indian cobra reveals a trimeric association.

Phospholipase A2 (PLA2) from Indian cobra venom (Naja naja naja) was crystallized from ethanol in space group P4(3)2(1)2 in the presence of Ca2+. The x-ray crystal structure was determined to 2.3-A resolution by molecular replacement techniques using a theoretical model constructed from homologous segments of the bovine pancreatic, porcine pancreatic, and rattlesnake venom crystal structures. The structure was refined to an R value of 0.174 for 17,542 reflections between 6.0- and 2.3-A resolution (F > 2 sigma), including 148 water molecules. The 119-amino acid enzyme has an overall architecture strikingly similar to the other known PLA2 structures with regions implicated in catalysis showing the greatest structural conservation. Unexpectedly, three monomers were found to occupy the asymmetric unit and are oriented with their catalytic sites facing the pseudo-threefold axis with approximately 15% of the solvent accessible surface of each monomer buried in trimer contacts. The majority of the interactions at the subunit interfaces are made by residues unique to PLA2 sequences from cobra and krait venoms. The possible relevance of this unique trimeric structure is considered.

Amino Acid Sequence↗
PubMed2003

Subtleties in crystal structure solution from powder diffraction data using simulated annealing: ranitidine hydrochloride.

Recent advances in crystallographic computing and availability of high-resolution diffraction data have made it relatively easy to solve crystal structures from powders that would have traditionally required single crystal samples. The success of direct space methods depends heavily on starting with an accurate molecular model. In this paper we address the applicability of using these methods in finding subtleties such as disorder in the molecular conformation that might not be known a priori. We use ranitidine HCl as our test sample as it is known to have a conformational disorder from single crystal structural work. We redetermine the structure from powder data using simulated annealing and show that the conformational disorder is clearly revealed by this method.

Algorithms↗
PubMed2002

Model for a helical bundle channel based on the high-resolution crystal structure of trichotoxin_A50E.

Trichotoxin_A50E is an 18-residue peptaibol antibiotic which forms multimeric transmembrane channels through self-association. The crystal structure of trichotoxin has been determined at a resolution of 0.9 A. The trichotoxin sequence contains nine helix-promoting Aib residues, which contribute to the formation of an entirely helical structure that has a central bend of 8-10 degrees located between residues 10-13. Trichotoxin is the first solved structure of the peptaibol family that is all alpha-helix as opposed to containing part or all 3(10)-helix. Gln residues in positions 6 and 17 produce a polar face, and are proposed to form the channel lumen. An octameric model channel has been constructed from the crystal structure. It has a central pore of approximately 4-5 A radius, a size sufficient to enable transport of ions, with a constricted region at one end, formed by a ring of Gln6 residues. Electrostatic calculations are consistent with it being a cationic channel.

Acetonitriles↗
PubMed2002

Novel, predicted patterns of supramolecular self-assembly, afforded by tetrameric R44(12) rings of C2 symmetry in the crystal structures of 2-hydroxy-1-cyclopentanecarboxylic acid, 2-hydroxy-1-cyclohexanecarboxylic acid and 2-hydroxy-1-cycloheptanecarboxylic acid.

Determination of the crystal structures of the homologous (1R*,2R*)-trans-2-hydroxy-1-cyclopentanecarboxylic acid (5T), (1R*,2S*)-cis-2-hydroxy-1-cyclohexanecarboxylic acid (6C) and (1R*,2S*)-cis-2-hydroxy-1-cycloheptanecarboxylic acid (7C) proved a predicted pattern of supramolecular close packing. The prediction was based on the common features observed in the crystal structures of six related 2-hydroxy-1-cyclopentanecarboxylic acids and analogous carboxamides [Kálmán et al. (2001). Acta Cryst. B57, 539-550]. This pattern is characterized by tetrameric R(4)(4)(12) rings of C(2) symmetry formed from dimeric R(2)(2)(12) rings. The C(2) symmetry of such tetramers is not common in the literature, usually they have C(i) symmetry. Both types of tetramers are formed from dimers with similar or opposite orientation. The R(2)(2)(12) dimers differ in their hydrogen bonds. In 5T the monomers are joined by a pair of O1[bond]H...O2[double bond]C bonds, whereas in 7C they are joined by a pair of O3[bond]H...O1-H bonds. In 6C 60% of the disordered R(2)(2)(12) dimers are similar to those in 7C, while 40% resemble those in 5T. Apart from these hydrogen-bonding differences and the ring-size differences, the three crystals exhibit isostructurality.

Journal Article↗
PubMed2000

The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals.

We have re-determined the crystal structure of yeast tRNA(Phe) to 2. 0 A resolution using 15 year old crystals. The accuracy of the new structure, due both to higher resolution data and formerly unavailable refinement methods, consolidates the previous structural information, but also reveals novel details. In particular, the water structure around the tightly bound Mg(2+) is now clearly resolved, and hence provides more accurate information on the geometry of the magnesium-binding sites and the role of water molecules in coordinating the metal ions to the tRNA. We have assigned a total of ten magnesium ions and identified a partly conserved geometry for high-affinity Mg(2+ )binding. In the electron density map there is also clear density for a spermine molecule binding in the major groove of the TPsiC arm and also contacting a symmetry-related tRNA molecule. Interestingly, we have also found that two specific regions of the tRNA in the crystals are partially cleaved. The sites of hydrolysis are within the D and anticodon loops in the vicinity of Mg(2+).

Base Sequence↗
PubMed1976

Crystal structures of synthetic analgetics. V. Dextromoramide.

The molecular and crystal structure of dextromoramide has been determined by X-ray methods. The crystals are orthorhombic, space group P212121 with unit cell dimensions a = 9.720(4) A; b = 12.226(3) A; c = 18.381(3) A. The structure was determined by direct methods and the model refined to an R-value of 0.036 for 1788 observed reflections. The mean e.s.d.'s in bond lengths and angles are 0.004 A and 0.3, respectively. The morpholine moiety is nearly in antiposition relative to the quaternary carbon atom C6, the pertinent angle C6 - C7 - C9 - N2 being - 159.4. This conformation is similar to that previously reported for the bitartrate of the title compound. The pyrrolidine ring has the envelope conformation and the amide group is strictly planar. The conformation of some acyclic analgetics are discussed.

Dextromoramide↗
PubMed2003

Comparison of the four anhydrous polymorphs of carbamazepine and the crystal structure of form I.

For decades, carbamazepine (CBZ) has served as a model compound for groups engaged in the study of crystal polymorphism. Despite considerable effort, crystal structures for only three of its four anhydrous forms have previously been determined. Herein, we report the first single crystal X-ray structure of the high temperature modification of CBZ (form I). Form I crystallizes in a triclinic cell (P-1) having four inequivalent molecules with the following lattice parameters: a = 5.1705(6), b = 20.574(2), c = 22.245(2) A, alpha = 84.12(4), beta = 88.01(4), and gamma = 85.19(4) degrees. Furthermore, we compare the physical properties of the four anhydrous polymorphs of CBZ, including the first comprehensive characterization of form IV. Substantial differences are seen among these forms by powder X-ray diffraction, infrared spectroscopy, thermomicroscopy, and differential scanning calorimetry. These data are correlated to their respective crystal structures for the first time. We have found that all polymorphs possess identical strong hydrogen bonding patterns, similar molecular conformations, and stabilities that are within 0.7 kcal/mol of each other.

Calorimetry, Differential Scanning↗
PubMed2003

Crystal structure of the homolog of the oncoprotein gankyrin, an interactor of Rb and CDK4/6.

The oncoprotein gankyrin plays a central role in tumorigenesis and cell proliferation. Gankyrin interacts with the retinoblastoma tumor suppressor (Rb) and cyclin-dependent kinase 4/6 (CDK4/6), increases phosphorylation at specific residues of Rb by CDK4/6 in vivo, and promotes tumorigenesis. The phosphorylation of Rb by CDK4/6 leads to the deregulation of the cell cycle during G1/S transition. Although how phosphorylation occurs on Rb has been studied extensively, the mechanism of site-specific phosphorylation of Rb remains unclear due to a lack of information on the structural arrangement of Rb and CDK4/6. Here, we have determined and refined to 2.3-A resolution the crystal structure of a gankyrin homolog, the non-ATPase subunit 6 (Nas6p) of the proteasome from yeast. The crystal structure reveals that Nas6p contains seven ankyrin repeats. The number of the repeats is different from that predicted from the primary structure. Nas6p also possesses an unusual curved structure with two acidic regions at the N- and C-terminal regions separated by one basic region, suggesting that it has at least two functional surfaces. The tertiary structure of Nas6p, together with the previous biochemical studies, indicates that the CDK4/6 and Rb binding surfaces of gankyrin are located at the N- and C-terminal regions, respectively, and face the same side of gankyrin. These observations suggest that gankyrin brings Rb and CDK4/6 together through gankyrin-Rb and gankyrin-CDK4/6 interactions and determines the relative positioning of the substrate (Rb) and the enzyme (CDK4/6). Our findings provide mechanistic insight into site-specific phosphorylation of Rb caused by CDK4/6.

Amino Acid Sequence↗
PubMed1995

Refined crystal structures of unligated adenylosuccinate synthetase from Escherichia coli.

Crystal structures of unligated adenylosuccinate synthetase from Escherichia coli in space groups P2(1) and P2(1)2(1)2(1) have been refined to R-factors of 0.199 and 0.206 against data to 2.0 and 2.5 A, respectively. Bond lengths and angles deviate from expected values by 0.011 A and 1.7 degrees for the P2(1) crystal form and by 0.015 A and 1.7 degrees for the P2(1)2(1)2(1) crystal form. The fold of the polypeptide chain is dominated by a central beta-sheet, which is composed of nine parallel strands and a tenth antiparallel strand. Extending off from this central beta-sheet are four subdomains. The four subdomains contribute loops of residues that are disordered or have high thermal parameters. At least three of these loops (residues 42 to 52, 120 to 131 and 298 to 304) contribute essential residues to the putative active site of the synthetase. In the absence of ligands, much of the active site of the synthetase exists in an ill-defined conformational state. Two, nearly independent regions contribute residues to the interface between polypeptide chains of the synthetase dimer. A pair of helices (H4 and H5) interact with their symmetry-equivalent mates by way of residues that are not conserved amongst the known sequences of the synthetase. The second interface region involves conserved residues belonging to structural elements that connect strands of the central beta-sheet. Residues putatively involved in the binding of IMP lie at or near the interface between polypeptide chains of the dimer. Of the four sequence elements putatively common to all GTP hydrolases, the synthetase has only the guanine recognition element and a glycine-rich loop (P-loop). Although the base recognition element is essentially identical with those of the p21 ras and G alpha proteins, the P-loop of the synthetase is extended in size relative to the P-loops of other GTP hydrolases. The P-loop has two acid residues (Asp13 and Glu14), which are found in the P-loops of only the synthetase family. Glu14 may be involved in the stabilization of the enlarged P-loop of the synthetase, whereas Asp13 may play a role in catalysis and in the coordination of Mg2+. The structural elements of the p21 ras and G alpha proteins responsible for binding Mg2+ are either absent from the synthetase or unavailable for the coordination of metal cations.

Adenylosuccinate Synthase↗
PubMed1990

Crystal structure of two covalent nucleoside derivatives of ribonuclease A.

Crystal structures of two forms of ribonuclease A with deoxynucleosides covalently bound to respectively His 12 and His 119 have been solved. One form, T-H12-RNase, has a deoxythymidine bound to N epsilon 2 of His 12, while the other one, U-H119-RNase, has a deoxyuridine bound to N delta 1 of His 119. The two crystal forms are nearly isomorphous, with two molecules in the asymmetric unit. However, the modified ribonucleases differ both in their enzymatic activities and in the conformation of the catalytic site and of the deoxynucleoside-histidine moiety. T-H12-RNase is characterized by complete loss of enzymatic activity; in this form the deoxynucleoside completely blocks the catalytic site and forms intramolecular contacts with residues associated with both the B1 and B2 sites. U-H119-RNase retains 1% of the activity of the unmodified enzyme, and in this form His 119 adopts a different orientation, corresponding to the alternate conformation reported for this residue; the deoxynucleoside-histidine moiety points out of the active site and does not form any contacts with the rest of the protein, thus allowing partial access to the catalytic site. On the basis of these structures, we propose possible mechanisms for the reactions of bromoacetamido nucleosides with ribonuclease A.

Binding Sites↗
PubMed2005

Crystal structure of cone arrestin at 2.3A: evolution of receptor specificity.

Arrestins play a fundamental role in the regulation and signal transduction of G protein-coupled receptors. Here we describe the crystal structure of cone arrestin at 2.3A resolution. The overall structure of cone visual arrestin is similar to the crystal structures of rod visual and the non-visual arrestin-2, consisting of two domains, each containing ten beta-sheets. However, at the tertiary structure level, there are two major differences, in particular on the concave surfaces of the two domains implicated in receptor binding and in the loop between beta-strands I and II. Functional analysis shows that cone arrestin, in sharp contrast to its rod counterpart, bound cone pigments and non-visual receptors. Conversely, non-visual arrestin-2 bound cone pigments, suggesting that it may also regulate phototransduction and/or photopigment trafficking in cone photoreceptors. These findings indicate that cone arrestin displays structural and functional features intermediate between the specialized rod arrestin and the non-visual arrestins, which have broad receptor specificity. A unique functional feature of cone arrestin was the low affinity for its cognate receptor, resulting in an unusually rapid dissociation of the complex. Transient arrestin binding to the photopigment in cones may be responsible for the extremely rapid regeneration and reuse of the photopigment that is essential for cone function at high levels of illumination.

Alanine↗
PubMed1994

DNA recognition by beta-sheets in the Arc repressor-operator crystal structure.

Transcription of the ant gene during lytic growth of bacteriophage P22 (ref. 1) is regulated by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Here we report the co-crystal structure of this Arc tetramer-operator complex at 2.6 A resolution. As expected from genetic and structural studies and from the co-crystal structure of the homologous Escherichia coli MetJ repressor, each Arc dimer uses an antiparallel beta-sheet to recognize bases in the major groove. However, the Arc and MetJ complexes differ in several important ways: the beta-sheet-DNA interactions of Arc are far less symmetrical; DNA binding by Arc is accompanied by important conformational changes in the beta-sheet; and Arc uses a different part of its protein surface for dimer-dimer interactions.

Base Sequence↗
PubMed2000

Interaction between the lipoamide-containing H-protein and the lipoamide dehydrogenase (L-protein) of the glycine decarboxylase multienzyme system 2. Crystal structures of H- and L-proteins.

The glycine decarboxylase complex consists of four different component enzymes (P-, H-, T- and L-proteins). The 14-kDa lipoamide-containing H-protein plays a pivotal role in the complete sequence of reactions as its prosthetic group (lipoic acid) interacts successively with the three other components of the complex and undergoes a cycle of reductive methylamination, methylamine transfer and electron transfer. With the aim to understand the interaction between the H-protein and its different partners, we have previously determined the crystal structure of the oxidized and methylaminated forms of the H-protein. In the present study, we have crystallized the H-protein in its reduced state and the L-protein (lipoamide dehydrogenase or dihydrolipoamide dehydrogenase). The L-protein has been overexpressed in Escherichia coli and refolded from inclusion bodies in an active form. Crystals were obtained from the refolded L-protein and the structure has been determined by X-ray crystallography. This first crystal structure of a plant dihydrolipoamide dehydrogenase is similar to other known dihydrolipoamide dehydrogenase structures. The crystal structure of the H-protein in its reduced form has been determined and compared to the structure of the other forms of the protein. It is isomorphous to the structure of the oxidized form. In contrast with methylaminated H-protein where the loaded lipoamide arm was locked into a cavity of the protein, the reduced lipoamide arm appeared freely exposed to the solvent. Such a freedom is required to allow its targeting inside the hollow active site of L-protein. Our results strongly suggest that a direct interaction between the H- and L-proteins is not necessary for the reoxidation of the reduced lipoamide arm bound to the H-protein. This hypothesis is supported by biochemical data [Neuburger, M., Polidori, A.M., Piètre, E., Faure, M., Jourdain, A., Bourguignon, J., Pucci, B. & Douce, R. (2000) Eur. J. Biochem. 267, 2882-2889] and by small angle X-ray scattering experiments reported herein.

Amino Acid Oxidoreductases↗
PubMed1997

Crystal structure of the adenylyl cyclase activator Gsalpha.

The crystal structure of Gsalpha, the heterotrimeric G protein alpha subunit that stimulates adenylyl cyclase, was determined at 2.5 A in a complex with guanosine 5'-O-(3-thiotriphosphate) (GTPgammaS). Gsalpha is the prototypic member of a family of GTP-binding proteins that regulate the activities of effectors in a hormone-dependent manner. Comparison of the structure of Gsalpha.GTPgammaS with that of Gialpha.GTPgammaS suggests that their effector specificity is primarily dictated by the shape of the binding surface formed by the switch II helix and the alpha3-beta5 loop, despite the high sequence homology of these elements. In contrast, sequence divergence explains the inability of regulators of G protein signaling to stimulate the GTPase activity of Gsalpha. The betagamma binding surface of Gsalpha is largely conserved in sequence and structure to that of Gialpha, whereas differences in the surface formed by the carboxyl-terminal helix and the alpha4-beta6 loop may mediate receptor specificity.

Adenylyl Cyclases↗
PubMed2002

Crystal structure of a DNA decamer containing a cis-syn thymine dimer.

It is well known that exposure to UV induces DNA damage, which is the first step in mutagenesis and a major cause of skin cancer. Among a variety of photoproducts, cyclobutane-type pyrimidine photodimers (CPD) are the most abundant primary lesion. Despite its biological importance, the precise relationship between the structure and properties of DNA containing CPD has remained to be elucidated. Here, we report the free (unbound) crystal structure of duplex DNA containing a CPD lesion at a resolution of 2.0 A. Our crystal structure shows that the overall helical axis bends approximately 30 degrees toward the major groove and unwinds approximately 9 degrees, in remarkable agreement with some previous theoretical and experimental studies. There are also significant differences in local structure compared with standard B-DNA, including pinching of the minor groove at the 3' side of the CPD lesion, a severe change of the base pair parameter in the 5' side, and serious widening of both minor and major groves both 3' and 5' of the CPD. Overall, the structure of the damaged DNA differs from undamaged DNA to an extent that DNA repair proteins may recognize this conformation, and the various components of the replicational and transcriptional machinery may be interfered with due to the perturbed local and global structure.

Bromodeoxyuridine↗
PubMed2001

Novel boxlike dinuclear or chain polymeric silver(I) complexes with polypyridyl bridging ligands: syntheses, crystal structures, and spectroscopic and electrochemical properties.

The syntheses, characterization, crystal structures, and photophysical and electrochemical properties of two dinuclear and two polymeric Ag(I) complexes with three polypyridyl ligands, 2,3-di-2-pyridylquinoxaline (L(1)), 2,3-di-2-pyridyl-5,8-dimethoxyquinoxaline (L(2)), and 2,3,7,8-tetrakis(2-pyridyl)pyrazino[2,3-g] quinoxaline (L(3)), are described. The structures of the two boxlike dinuclear complexes with L(1) and L(2) and two chemically the same but differently crystallized one-dimensional zigzag chain coordination polymers also consisting of boxlike dinuclear subunits have been elucidated by X-ray analysis. [AgL(1)(CH(3)CN)](2)-(BF(4))(2).2CHCl(3) (1): monoclinic, C2/c; a = 28.631(2), b = 12.2259(11), c = 14.3058(12) A; beta = 99.180(2) degrees; Z = 4. [AgL(2)(CH(3)CN)(2)](2)(ClO(4))(2) (2): triclinic, P1; a = 12.3398(2), b = 13.750(2), c = 14.326(7) A; alpha = 83.494(3), beta = 74.631(3), gamma = 76.422(3) degrees; Z = 4. [[Ag(2)L(3)(NO(3))(2)].CH(3)CN](infinity) (3a): monoclinic, P2(1)/c; a = 9.5836(8), b = 13.4691(12), c = 14.0423(12) A; beta = 107.753(2) degrees; Z = 4. [Ag(2)L(3)()(NO(3))(2)](infinity) (3b): monoclinic, P2(1)/c; a = 8.4689(6), b = 16.0447(12), c = 11.7307(8) A; beta = 102.051(1) degrees; Z = 2. The structures of the dinuclear complexes 1 and 2 are similar to each other, with the two intramolecular Ag(I) centers of each complex being spanned by two ligands thus forming a unique boxlike cyclic dimer. In 1, each Ag(I) center is four-coordinated by three nitrogen atoms of two L(1) ligands and a CH(3)CN nitrogen donor, taking a distorted tetrahedral coordination geometry. The coordination environment of Ag(I) in 2 is similar to that in 1, except the formation of an additional weak coordination bond with the oxygen atom of the methoxy group of L(2). The structures of 3a,b are very similar to each other, except for the stacking patterns in the crystal lattices, and the cyclic boxlike dinuclear unit, which is similar to the structure of 1, constitutes the fundamental building block to form the one-dimensional zigzag chain structures due to the "end-on" nature of L(3). 1-3 exhibit metal-perturbed intraligand transitions in solution in 360-390 nm regions. Cyclic voltammetric studies of these complexes show the presence of reduction peak at approximately -0.5 V vs Fc(+/0). In the solid state at 77 K, they exhibit broad emission that may be assignable to originate from the metal-perturbed intraligand transitions.

Journal Article↗
PubMed1998

Molecular modelling of steroidogenic cytochromes P450 from families CYP11, CYP17, CYP19 and CYP21 based on the CYP102 crystal structure.

The results of homology modelling of mammalian steroidogenic cytochromes P450 (CYP) from families CYP11, CYP17, CYP19 and CYP21 are reported, based on a novel protein sequence alignment with CYP102, a bacterial P450 of known crystal structure. The molecular models generated from the CYP102 crystal structure template are consistent with experimental information from site-directed mutagenesis studies, steroidal substrate specificity and active site inhibitor studies. Interactive docking studies with both substrates and inhibitors of these enzymes indicate key residue interactions with the putative active site regions of each isoform investigated, which point to potential determinants of substrate specificity within these related enzymes.

Amino Acid Sequence↗
PubMed1989

Crystal structure of L-2-oxothiazolidine-4-carboxylic acid.

Crystals of the title compound, L-2-oxothiazolidine-4-carboxylic acid, OTC (C4H5NO3S), grown from an aqueous solution are orthorhombic, space group P2(1)2(1)2(1) with the following cell parameters at 22 +/- 3 degrees: a = 5.381(1), b = 5.961(1), c = 17.929(3)A, V = 575.1A(3), Mr = 146.2, Dc = 1.688 g.cm-3, mu = 43.9 cm-1 and Z = 4. The crystal structure was solved by the application of direct methods and refined to an R value of 0.032 for 596 reflections with I greater than 3 sigma(I). The thiazolidine ring adopts a "twist" conformation. This structure contains a short (2.619(3)A) intermolecular hydrogen bond between the carboxyl OH and the oxygen of the 2-oxo moiety, a feature common to most acyl amino acids and acyl peptides.

Crystallization↗