Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 40
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
Acta Crystallogr D Biol Crystallogr ; 62(Pt 10): 1162-9, 2006 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-17001093

RESUMO

An automatic data-collection system has been implemented and installed on seven insertion-device beamlines and a bending-magnet beamline at the ESRF (European Synchrotron Radiation Facility) as part of the SPINE (Structural Proteomics In Europe) development of an automated structure-determination pipeline. The system allows remote interaction with beamline-control systems and automatic sample mounting, alignment, characterization, data collection and processing. Reports of all actions taken are available for inspection via database modules and web services.


Assuntos
Genes/genética , Síncrotrons/estatística & dados numéricos , Coleta de Dados/métodos , Gestão da Informação , Estrutura Molecular , Controle de Qualidade , Software
2.
Acta Crystallogr D Biol Crystallogr ; 62(Pt 10): 1251-9, 2006 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-17001102

RESUMO

A standard sample holder and vial for cryocooled macromolecular crystals has been defined for use with robotic sample changers. This SPINE standard sample holder is a modified version, with added features and specifications, of sample holders in common use. In particular, the SPINE standard meets the precision required for automatic sample exchange and includes a cap that is identified by a two-dimensional datamatrix code as well as an optional vial. At the ESRF, the sample holder standard is in use with the EMBL/ESRF/BM14 robotic sample changer (SC3) which is installed on eight beamlines. The SC3 can hold up to 50 crystals stored in five baskets. A datamatrix reader in the SC3 ensures safe management of the sample flow and facilitates fully automatic screening and characterization of samples. Tools for handling and transporting 50 samples in a dry shipping dewar have been developed. In addition to the SC3, the SPINE sample holder is currently compatible with a number of other robotic sample changers.


Assuntos
Cristalografia/instrumentação , Automação , Cristalografia/normas , Eletrônica , Magnetismo , Padrões de Referência , Robótica , Software , Síncrotrons
3.
Acta Crystallogr D Biol Crystallogr ; 62(Pt 1): 65-71, 2006 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-16369095

RESUMO

Undulator radiation is the X-ray source of choice for modern macromolecular crystallography beamlines. Here, the basic properties of undulator sources are described and it is indicated why they make such good X-ray sources for macromolecular crystallography. Collection of excellent data from these beamlines is not always straightforward; therefore, a number of rules are postulated for undulator data collection and guidelines are offered which will help to ensure a satisfactory experiment.


Assuntos
Cristalografia por Raios X , Coleta de Dados/instrumentação , Magnetismo/instrumentação , Proteínas/química , Síncrotrons/instrumentação , Cristalização , Coleta de Dados/métodos , Coleta de Dados/estatística & dados numéricos
4.
Acta Crystallogr D Biol Crystallogr ; 58(Pt 1): 70-80, 2002 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-11752780

RESUMO

The serum transferrins are monomeric proteins with a molecular mass of around 80 kDa and are responsible for the transport of iron in vertebrates. The three-dimensional structures of diferric porcine and rabbit serum transferrin have been refined against X-ray diffraction data extending to 2.15 and 2.60 A, respectively. Data for both proteins were collected using synchrotron radiation at temperatures of 277 K. The porcine protein crystallizes in the space group C2, with unit-cell parameters a = 223.8, b = 44.9, c = 78.9 A, beta = 105.4 degrees with one molecule in the asymmetric unit. The structure was solved by molecular-replacement methods using rabbit serum transferrin as the search model. The structure was refined using REFMAC, with a final residual of 13.8% (R(free) = 18.2% for a 5% data sample) for all data to 2.15 A. The final model comprises 5254 protein atoms, two Fe(3+) cations and two CO(3)(2-) anions, one N-acetyl glucosamine moiety and 494 water molecules. The rabbit protein crystallizes in space group P4(3)2(1)2, with unit-cell parameters a = 127.2, c = 144.9 A and one molecule per asymmetric unit. The structure was solved using the method of multiple isomorphous replacement and refined using REFMAC to give a final residual of 18.6% (R(free) = 22.2% for a 5% data sample) for all data to 2.60 A. The final model comprises 5216 protein atoms, two Fe(3+) cations and two CO(3)(2-) anions, a Cl(-) anion and 206 solvent molecules; there is no clear indication of the carbohydrate moiety attached to Asn490 (rabbit serum numbering). Both molecules adopt a bilobal structure typical for members of the transferrin family. Each of the structurally homologous lobes contains two dissimilar domains with a single iron-binding site buried within the interdomain cleft. The porcine serum protein lacks an interdomain disulfide bridge close to the connecting peptide between the lobes, but this seems to have little effect on the overall orientation of the lobes. The N-lobes of both proteins possess lysine residues, one from each of the two domains, that lie in close proximity to one another to form the so-called dilysine trigger. The more acid-labile release of iron from serum transferrins than from lactoferrins is discussed.


Assuntos
Transferrina/química , Animais , Ânions , Sítios de Ligação , Carboidratos/química , Carbonatos/metabolismo , Cristalografia por Raios X , Dissulfetos/química , Ferro/metabolismo , Conformação Proteica , Coelhos , Suínos , Transferrina/metabolismo
5.
Acta Crystallogr D Biol Crystallogr ; 57(Pt 9): 1230-7, 2001 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-11526314

RESUMO

The previously unknown crystal structure of the C(1) subunit of the carotenoid-binding protein alpha-crustacyanin has been determined using the anomalous scattering available at 1.77 A wavelength to determine the partial structure of the S atoms intrinsic to the native protein. The resulting 'heavy-atom' phases, in conjunction with near-atomic resolution (d(min) = 1.15 A) data, were then used to initiate successful structure determination using a direct-methods approach. This is, to the authors' knowledge, the first time such a small anomalous signal ( approximately 1%) has been used to aid the determination of a macromolecular structure. As well as the structure itself, the methods used during data collection and those used in the elucidation of the sulfur 'heavy-atom' partial structure are described here. As predicted, the C(1) subunit adopts a tertiary structure typical of the lipocalin superfamily: an eight-stranded antiparallel beta-barrel with a repeated +1 topology. The beta-barrel has a calyx shape with the two molecules in the asymmetric unit interacting in such a way that the open ends of each calyx face each other, although they do not form a single elongated pocket. A comparison of this structure with those of other members of the lipocalin superfamily has allowed speculation as to the nature of carotenoid binding by the protein.


Assuntos
Proteínas/química , Sequência de Aminoácidos , Proteínas de Transporte , Cristalização , Cristalografia por Raios X , Dimerização , Modelos Moleculares , Dados de Sequência Molecular , Peso Molecular , Conformação Proteica , Espalhamento de Radiação , Homologia de Sequência de Aminoácidos
6.
Nat Struct Biol ; 8(6): 521-5, 2001 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-11373620

RESUMO

Pteridine reductase (PTR1) is a short-chain reductase (SDR) responsible for the salvage of pterins in parasitic trypanosomatids. PTR1 catalyzes the NADPH-dependent two-step reduction of oxidized pterins to the active tetrahydro-forms and reduces susceptibility to antifolates by alleviating dihydrofolate reductase (DHFR) inhibition. Crystal structures of PTR1 complexed with cofactor and 7,8-dihydrobiopterin (DHB) or methotrexate (MTX) delineate the enzyme mechanism, broad spectrum of activity and inhibition by substrate or an antifolate. PTR1 applies two distinct reductive mechanisms to substrates bound in one orientation. The first reduction uses the generic SDR mechanism, whereas the second shares similarities with the mechanism proposed for DHFR. Both DHB and MTX form extensive hydrogen bonding networks with NADP(H) but differ in the orientation of the pteridine.


Assuntos
Di-Hidropteridina Redutase/química , Di-Hidropteridina Redutase/metabolismo , Resistência a Medicamentos , Leishmania major/metabolismo , Pterinas/metabolismo , Sequência de Aminoácidos , Animais , Sítios de Ligação , Cristalografia por Raios X , Di-Hidropteridina Redutase/antagonistas & inibidores , Antagonistas do Ácido Fólico/metabolismo , Antagonistas do Ácido Fólico/farmacologia , Ligação de Hidrogênio , Leishmania major/enzimologia , Leishmania major/genética , Metotrexato/metabolismo , Metotrexato/farmacologia , Modelos Moleculares , Dados de Sequência Molecular , NADP/metabolismo , Oxirredução , Estrutura Secundária de Proteína , Selenometionina/metabolismo , Especificidade por Substrato , Tetra-Hidrofolato Desidrogenase/metabolismo
7.
Acta Crystallogr D Biol Crystallogr ; 56(Pt 9): 1194-7, 2000 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-10957644

RESUMO

Peptide methionine sulfoxide reductase mediates the reduction of protein sulfoxide methionyl residues back to methionines and could thus be implicated in the antioxidant defence of organisms. Hexagonal crystals of the Escherichia coli enzyme (MsrA) were obtained by the hanging-drop vapour-diffusion technique. They belong to space group P6(5)22, with unit-cell parameters a = b = 102.5, c = 292.3 A, gamma = 120 degrees. A native data set was collected at 1.9 A resolution. Crystals of selenomethionine-substituted MsrA were also grown under the same crystallization conditions. A three-wavelength MAD experiment has led to the elucidation of the positions of the Se atoms and should result in a full structure determination.


Assuntos
Escherichia coli/enzimologia , Oxirredutases/química , Cristalização , Cristalografia por Raios X , Metionina Sulfóxido Redutases , Selenometionina/química
8.
Nat Struct Biol ; 7(5): 398-402, 2000 May.
Artigo em Inglês | MEDLINE | ID: mdl-10802738

RESUMO

Deoxythymidine diphosphate (dTDP)-L-rhamnose is the precursor of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. dTDP-L-rhamnose is synthesized from glucose-1-phosphate and deoxythymidine triphosphate (dTTP) via a pathway involving four distinct enzymes. This pathway does not exist in humans and the enzymes involved in dTDP-L-rhamnose synthesis are potential targets for the design of new therapeutic agents. Here, the crystal structure of dTDP-6-deoxy-D-xylo-4-hexulose 3,5 epimerase (RmlC, EC5.1.3.13) from Salmonella enterica serovar Typhimurium was determined. The third enzyme of the rhamnose biosynthetic pathway, RmlC epimerizes at two carbon centers, the 3 and 5 positions of the sugar ring. The structure was determined by multiwavelength anomalous diffraction to a resolution of 2.17 A. RmlC is a dimer and each monomer is formed mainly from two beta-sheets arranged in a beta-sandwich. The structure of a dTDP-phenol-RmlC complex shows the substrate-binding site to be located between the two beta-sheets; this site is formed from residues of both monomers. Sequence alignments of other RmlC enzymes confirm that this region is very highly conserved. The enzyme is distinct structurally from other epimerases known and thus, is the first example of a new class of carbohydrate epimerase.


Assuntos
Carboidratos Epimerases/química , Carboidratos Epimerases/classificação , Açúcares de Nucleosídeo Difosfato/metabolismo , Salmonella typhimurium/enzimologia , Nucleotídeos de Timina/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Carboidratos Epimerases/metabolismo , Sequência Conservada , Cristalografia por Raios X , Dimerização , Modelos Moleculares , Dados de Sequência Molecular , Açúcares de Nucleosídeo Difosfato/química , Fenol/química , Fenol/metabolismo , Ligação Proteica , Estrutura Secundária de Proteína , Alinhamento de Sequência , Nucleotídeos de Timina/química
9.
J Mol Biol ; 298(1): 123-33, 2000 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-10756109

RESUMO

Cyclosporin A (CsA) is a potent anti-malarial compound in vitro and in vivo in mice though better known for its immunosuppressive properties in humans. Crystal structures of wild-type and a double mutant Plasmodium falciparum cyclophilin (PfCyP19 and mPfCyP19) complexed with CsA have been determined using diffraction terms to a resolution of 2.1 A (1 A=0.1 nm). The wild-type has a single PfCyP19/CsA complex per asymmetric unit in space group P1 and refined to an R-work of 0.15 and R-free of 0.19. An altered cyclophilin, with two accidental mutations, Phe120 to Leu in the CsA binding pocket and Leu171 to Trp at the C terminus, presents two complexes per asymmetric unit in the orthorhombic space group P2(1)2(1)2. This refined to an R-work of 0.18 and R-free 0.21. The mutations were identified from the crystallographic analysis and the C-terminal alteration helps to explain the different crystal forms obtained. PfCyP19 shares approximately 61 % sequence identity with human cyclophilin A (hCyPA) and the structures are similar, consisting of an eight-stranded antiparallel beta-barrel core capped by two alpha-helices. The fold creates a hydrophobic active-site, the floor of which is formed by side-chains of residues from four antiparallel beta-strands and the walls from loops and turns. We identified C-H.O hydrogen bonds between the drug and protein that may be an important feature of cyclophilins and suggest a general mode of interaction between hydrophobic molecules. Comparisons with cyclophilin-dipeptide complexes suggests that a specific C-H.O hydrogen bonding interaction may contribute to ligand binding. Residues Ser106, His99 and Asp130, located close to the active site and conserved in most cyclophilins, are arranged in a manner reminiscent of a serine protease catalytic triad. A Ser106Ala mutant was engineered to test the hypothesis that this triad contributes to CyP function. Mutant and wild-type enzymes were found to have similar catalytic properties.


Assuntos
Antimaláricos/metabolismo , Ciclosporina/metabolismo , Peptidilprolil Isomerase/química , Peptidilprolil Isomerase/metabolismo , Plasmodium falciparum/química , Sequência de Aminoácidos , Substituição de Aminoácidos , Animais , Antimaláricos/química , Sítios de Ligação , Catálise , Sequência Conservada , Cristalografia por Raios X , Ciclosporina/química , Humanos , Ligação de Hidrogênio , Modelos Moleculares , Dados de Sequência Molecular , Mutação/genética , Peptidilprolil Isomerase/genética , Plasmodium falciparum/genética , Estrutura Secundária de Proteína , Alinhamento de Sequência , Relação Estrutura-Atividade
10.
Structure ; 7(11): 1345-52, 1999 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-10574798

RESUMO

BACKGROUND: The mammalian signal recognition particle (SRP) is an essential cytoplasmic ribonucleoprotein complex involved in targeting signal-peptide-containing proteins to the endoplasmic reticulum. Assembly of the SRP requires protein SRP19 to bind first to helix 6 of the SRP RNA before the signal-peptide-recognizing protein, SRP54, can bind to helix 8 of the RNA. Helix 6 is closed by a GGAG tetraloop, which has been shown to form part of the SRP19-binding site. RESULTS: The high-resolution (2.0 A) structure of a fragment of human SRP RNA comprising 29 nucleotides of helix 6 has been determined using the multiple anomalous dispersion (MAD) method and bromine-labelled RNA. In the crystal the molecule forms 28-mer duplexes rather than the native monomeric hairpin structure, although two chemically equivalent 11 base pair stretches of the duplex represent the presumed native structure. The duplex has highly distorted A-RNA geometry caused by the occurrence of several non-Watson-Crick base pairs. These include a 5'-GGAG-3'/3'-GAGG-5' purine bulge (which replaces the tetraloop) and a 5'-AC-3'/3'-CA-5' tandem mismatch that, depending on the protonation state of the adenine bases, adopts a different conformation in the two native-like parts of the structure. The structure also shows the 2'3'-cyclic phosphate reaction product of the hammerhead ribozyme cleavage reaction. CONCLUSIONS: The 29-mer RNA is the first RNA structure of the human SRP and provides some insight into the binding mode of SRP19. The observed strong irregularities of the RNA helix make the major groove wide enough and flat enough to possibly accommodate an alpha helix of SRP19. The variety of non-canonical base pairs observed enlarges the limited repertoire of irregular RNA folds known to date and the observed conformation of the 2'3'-cyclic phosphate containing Ade29 is consistent with the current understanding of the hammerhead ribozyme reaction mechanism.


Assuntos
Conformação de Ácido Nucleico , RNA/química , Partícula de Reconhecimento de Sinal/genética , Sequência de Bases , Humanos , Magnésio/química , Ligação Proteica , Partícula de Reconhecimento de Sinal/metabolismo
11.
J Biol Chem ; 274(36): 25613-22, 1999 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-10464297

RESUMO

Tryparedoxin-I is a recently discovered thiol-disulfide oxidoreductase involved in the regulation of oxidative stress in parasitic trypanosomatids. The crystal structure of recombinant Crithidia fasciculata tryparedoxin-I in the oxidized state has been determined using multi-wavelength anomalous dispersion methods applied to a selenomethionyl derivative. The model comprises residues 3 to 145 with 236 water molecules and has been refined using all data between a 19- and 1.4-A resolution to an R-factor and R-free of 19.1 and 22.3%, respectively. Despite sharing only about 20% sequence identity, tryparedoxin-I presents a five-stranded twisted beta-sheet and two elements of helical structure in the same type of fold as displayed by thioredoxin, the archetypal thiol-disulfide oxidoreductase. However, the relationship of secondary structure with the linear amino acid sequences is different for each protein, producing a distinctive topology. The beta-sheet core is extended in the trypanosomatid protein with an N-terminal beta-hairpin. There are also differences in the content and orientation of helical elements of secondary structure positioned at the surface of the proteins, which leads to different shapes and charge distributions between human thioredoxin and tryparedoxin-I. A right-handed redox-active disulfide is formed between Cys-40 and Cys-43 at the N-terminal region of a distorted alpha-helix (alpha1). Cys-40 is solvent-accessible, and Cys-43 is positioned in a hydrophilic cavity. Three C-H...O hydrogen bonds donated from two proline residues serve to stabilize the disulfide-carrying helix and support the correct alignment of active site residues. The accurate model for tryparedoxin-I allows for comparisons with the family of thiol-disulfide oxidoreductases and provides a template for the discovery or design of selective inhibitors of hydroperoxide metabolism in trypanosomes. Such inhibitors are sought as potential therapies against a range of human pathogens.


Assuntos
Crithidia fasciculata/química , Dobramento de Proteína , Tiorredoxinas/química , Sequência de Aminoácidos , Animais , Crithidia fasciculata/genética , Crithidia fasciculata/metabolismo , Humanos , Dados de Sequência Molecular , Oxirredução , Estrutura Secundária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Tiorredoxinas/genética , Tiorredoxinas/metabolismo
12.
J Mol Biol ; 287(2): 383-94, 1999 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-10080900

RESUMO

The structure of a class II fructose-1,6-bisphosphate aldolase in complex with the substrate analogue and inhibitor phosphoglycolohydroxamate (PGH) has been determined using X-ray diffraction terms to a resolution of 2.0 A (1 A=0.1 nm). The crystals are trigonal, space group P3121 with a=b=78.24 A, c=289.69 A. The asymmetric unit is a homodimer of (alpha/beta)8 barrels and the model has refined to give R-work 19.2 %, R-free (based on 5 % of the data) 23.0 %. PGH resembles the ene-diolate transition state of the physiological substrate dihydroxyacetone phosphate. It is well ordered and bound in a deep polar cavity at the C-terminal end of the (alpha/beta)8 barrel, where it chelates the catalytic zinc ion using hydroxyl and enolate oxygen atoms. Trigonal bipyramidal coordination of the zinc ion is completed by three histidine residues. The complex network of hydrogen bonds at the catalytic centre is required to organise the position of key functional groups and metal ion ligands. A well-defined monovalent cation-binding site is observed following significant re-organisation of loop structures. This assists the formation of a phosphate-binding site on one side of the barrel that tethers PGH in the catalytic site. The positions of functional groups of substrate and putative interactions with key amino acid residues are identified. Knowledge of the complex structure complements the results of spectroscopic and site-directed mutagenesis studies, and contributes to our understanding of the mechanism and substrate specificity of this family of enzymes. A reaction mechanism distinct from that proposed for other class II aldolases is discussed. The results suggest that the class II aldolases should be sub-divided into two groups on the basis of both distinct folds and mechanism.


Assuntos
Inibidores Enzimáticos/química , Escherichia coli/enzimologia , Frutose-Bifosfato Aldolase/química , Ácidos Hidroxâmicos/química , Sítios de Ligação , Catálise , Fosfato de Di-Hidroxiacetona/química , Dimerização , Ligação de Hidrogênio , Modelos Moleculares , Difração de Raios X , Zinco/química
13.
Acta Crystallogr D Biol Crystallogr ; 55(Pt 2): 399-402, 1999 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-10089346

RESUMO

UDP-galactopyranose mutase, the enzyme responsible for the conversion of UDP-galactopyranose to UDP-galactofuranose, has been crystallized in a form suitable for X-ray diffraction studies. UDP-galactofuranose is a key component of mycobacterial cell walls. Crystals of both the native protein and a selenomethionine variant have been grown by the vapour-diffusion method in hanging drops, and diffract to beyond 3.0 A using synchrotron radiation. Equilibration was against a solution of 20%(w/v) polyethylene glycol (4K), 12%(v/v) 2--propanol, 0.1 M HEPES pH 7.6 at 293.5 K. Crystals grow as thin plates of dimensions 0.4 x 0.2 x approximately 0.02 mm. They are monoclinic [corrected], space group P21, with unit-cell dimensions a = 71. 12, b = 58.42, c = 96.38 A, beta = 96.38 degrees. 92% (native) and 94% (selenomethionine) complete data sets have been recorded to 2.9 A (Rmerge = 5.0%) and 3.0 A (Rmerge = 6.9%), respectively. The Matthews coefficient is 2.35 A3 Da-1 for a dimer in the asymmetric unit, the solvent content being 47%. Diffraction data have also been recorded on a putative platinum derivative to 3.5 A.


Assuntos
Proteínas de Escherichia coli , Escherichia coli/enzimologia , Transferases Intramoleculares/química , Sequência de Aminoácidos , Cristalografia por Raios X , Transferases Intramoleculares/isolamento & purificação , Dados de Sequência Molecular , Conformação Proteica , Homologia de Sequência de Aminoácidos
14.
Acta Crystallogr D Biol Crystallogr ; 55(Pt 2): 542-3, 1999 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-10089372

RESUMO

The molybdenum-responsive ModE regulatory protein from Escherichia coli has been purified and used in crystallization trials. Two crystal forms have been observed. Form I is tetragonal, P41212 (or enantiomorph), with a = b = 72.3, c = 246.2 A and diffracts to medium resolution. Form II is orthorhombic, P21212, with a = 82.8, b = 127.9, c = 64.0 A and diffraction has been observed beyond 2.8 A resolution. Structural analysis, in combination with ongoing biochemical characterization, will assist the elucidation of the structure-activity relationship in regulating the uptake of molybdate in bacteria.


Assuntos
Proteínas de Bactérias , Proteínas de Escherichia coli , Fatores de Transcrição/química , Cristalografia por Raios X , Escherichia coli/genética , Proteínas Recombinantes/química
15.
EMBO J ; 18(6): 1435-46, 1999 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-10075916

RESUMO

The molybdate-dependent transcriptional regulator (ModE) from Escherichia coli functions as a sensor of molybdate concentration and a regulator for transcription of operons involved in the uptake and utilization of the essential element, molybdenum. We have determined the structure of ModE using multi-wavelength anomalous dispersion. Selenomethionyl and native ModE models are refined to 1. 75 and 2.1 A, respectively and describe the architecture and structural detail of a complete transcriptional regulator. ModE is a homodimer and each subunit comprises N- and C-terminal domains. The N-terminal domain carries a winged helix-turn-helix motif for binding to DNA and is primarily responsible for ModE dimerization. The C-terminal domain contains the molybdate-binding site and residues implicated in binding the oxyanion are identified. This domain is divided into sub-domains a and b which have similar folds, although the organization of secondary structure elements varies. The sub-domain fold is related to the oligomer binding-fold and similar to that of the subunits of several toxins which are involved in extensive protein-protein interactions. This suggests a role for the C-terminal domain in the formation of the ModE-protein-DNA complexes necessary to regulate transcription. Modelling of ModE interacting with DNA suggests that a large distortion of DNA is not necessary for complex formation.


Assuntos
Proteínas de Bactérias , Proteínas de Escherichia coli , Escherichia coli/metabolismo , Dobramento de Proteína , Fatores de Transcrição/química , Sequência de Aminoácidos , Sítios de Ligação , Clonagem Molecular , Gráficos por Computador , Cristalografia por Raios X/métodos , DNA/química , DNA/metabolismo , Dimerização , Escherichia coli/genética , Substâncias Macromoleculares , Modelos Moleculares , Dados de Sequência Molecular , Molibdênio/metabolismo , Conformação de Ácido Nucleico , Estrutura Secundária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Selenometionina , Software , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
16.
Nucleic Acids Res ; 27(2): 555-61, 1999 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-9862980

RESUMO

The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC) has been solved and refined at 2.5 A resolution. The refinement procedure converged at R = 0.181 for all reflections in the range 20.0-2.5 A. In the crystal, the RNA/DNA hybrid duplex has an A' conformation with all but one of the nucleotide sugar moieties adopting a C3'- endo (N) conformation. Both strands in the double helix adopt a global conformation close to the A-form and the width of the minor groove is typical of that found in the crystal structures of other A-form duplexes. However, differences are observed between the RNA and DNA strands that make up the hybrid at the local level. In the central portion of the duplex, the RNA strand has backbone alpha, beta and gamma torsion angles that alternate between the normal gauche -/ trans / gauche + conformation and an unusual trans / trans / trans conformation. Coupled with this so-called 'alpha/gamma flipping' of the backbone torsion angles, the distance between adjacent phosphorous atoms on the RNA strand systematically varies. Neither of these phenomena are observed on the DNA strand. The structure of the RNA/DNA hybrid presented here differs significantly from that found in solution for this and other sequences. Possible reasons for these differences and their implications for the current model of RNase H activity are discussed.


Assuntos
Ácidos Nucleicos Heteroduplexes/química , Oligodesoxirribonucleotídeos/química , Oligorribonucleotídeos/química , Dicroísmo Circular , Cristalografia por Raios X , Modelos Moleculares , Ressonância Magnética Nuclear Biomolecular , Conformação de Ácido Nucleico , Ribonuclease H/metabolismo , Soluções , Especificidade por Substrato
17.
Acta Crystallogr D Biol Crystallogr ; 55(Pt 12): 2043-6, 1999 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-10666586

RESUMO

L-Rhamnose is an essential component of the cell wall of many pathogenic bacteria. Its precursor, dTDP-L-rhamnose, is synthesized from alpha-D-glucose-1-phosphate and dTTP via a pathway requiring four distinct enzymes: RmlA, RmlB, RmlC and RmlD. RmlD catalyses the terminal step of this pathway by converting dTDP-6-deoxy-L-lyxo-4-hexulose to dTDP-L-rhamnose. RmlD from -Salmonella enterica serovar Typhimurium has been overexpressed in Escherichia coli. The recombinant protein was purified by a two--step protocol involving anion-exchange and hydrophobic chromatography. Dynamic light-scattering experiments indicated that the recombinant protein is monodisperse. Crystals of native and selenomethionine-enriched RmlD have been obtained using the sitting-drop vapour-diffusion method with polyethylene glycol as precipitant. Diffraction data have been collected from orthorhombic crystals of both native and selenomethionyl-derivatized protein, allowing tracing of the protein structure.


Assuntos
Desidrogenases de Carboidrato/química , Desidrogenases de Carboidrato/isolamento & purificação , Salmonella typhimurium/enzimologia , Desidrogenases de Carboidrato/genética , Cristalização , Cristalografia por Raios X , Escherichia coli/genética , Expressão Gênica , Genes Bacterianos , Açúcares de Nucleosídeo Difosfato/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Salmonella typhimurium/genética , Nucleotídeos de Timina/biossíntese
18.
Acta Crystallogr D Biol Crystallogr ; 54(Pt 6 Pt 2): 1422-4, 1998 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-10089526

RESUMO

6-Phosphogluconate dehydrogenase is one of the seven enzymes involved in the pentose phosphate pathway. Crystals of a mammalian and a protozoan enzyme have been obtained previously and structures determined. It is reported here that a bacterial 6-phosphogluconate dehydrogenase, from Lactococcus lactis, has been purified and used in crystallization trials. Large prisms suitable for a detailed structural analysis have been obtained and characterized as orthorhombic, space group F222, with a = 70.4, b = 105.7, c = 474.6 A. Diffraction has been observed to 2.2 A resolution using synchrotron radiation. Structural analysis, in combination with ongoing biochemical characterization, will assist the elucidation of the structure-activity relationships of this enzyme.


Assuntos
Proteínas de Bactérias/química , Lactococcus lactis/enzimologia , Fosfogluconato Desidrogenase/química , Proteínas de Bactérias/isolamento & purificação , Cristalização , Cristalografia por Raios X , Dimerização , Via de Pentose Fosfato , Fosfogluconato Desidrogenase/isolamento & purificação , Conformação Proteica , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/isolamento & purificação
19.
Structure ; 4(11): 1303-15, 1996 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-8939754

RESUMO

BACKGROUND: [corrected] Aldolases catalyze a variety of condensation and cleavage reactions, with exquisite control on the stereochemistry. These enzymes, therefore, are attractive catalysts for synthetic chemistry. There are two classes of aldolase: class I aldolases utilize Schiff base formation with an active-site lysine whilst class II enzymes require a divalent metal ion, in particular zinc. Fructose-1,6-bisphosphate aldolase (FBP-aldolase) is used in gluconeogenesis and glycolysis; the enzyme controls the condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to yield fructose-1,6-bisphosphate. Structures are available for class I FBP-aldolases but there is a paucity of detail on the class II enzymes. Characterization is sought to enable a dissection of structure/activity relationships which may assist the construction of designed aldolases for use as biocatalysts in synthetic chemistry. RESULTS: The structure of the dimeric class II FBP-aldolase from Escherichia coli has been determined using data to 2.5 A resolution. The asymmetric unit is one subunit which presents a familiar fold, the (alpha/beta)8 barrel. The active centre, at the C-terminal end of the barrel, contains a novel bimetallic-binding site with two metal ions 6.2 A apart. One ion, the identity of which is not certain, is buried and may play a structural or activating role. The other metal ion is zinc and is positioned at the surface of the barrel to participate in catalysis. CONCLUSIONS: Comparison of the structure with a class II fuculose aldolase suggests that these enzymes may share a common mechanism. Nevertheless, the class II enzymes should be subdivided into two categories on consideration of subunit size and fold, quaternary structure and metal-ion binding sites.


Assuntos
Proteínas de Bactérias , Proteínas de Escherichia coli , Escherichia coli/enzimologia , Frutose-Bifosfato Aldolase/química , Metaloproteínas/química , Zinco/química , Sequência de Aminoácidos , Sítios de Ligação , Cátions/química , Simulação por Computador , Cristalografia por Raios X , Dimerização , Frutose-Bifosfato Aldolase/classificação , Metaloproteínas/classificação , Modelos Moleculares , Dados de Sequência Molecular , Potássio/química , Conformação Proteica , Estrutura Secundária de Proteína
20.
Br J Cancer ; 74(7): 1109-13, 1996 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-8855983

RESUMO

We have examined the efficacy, toxicity and host immunological response of two different dose schedules of interleukin 2 (IL-2) given subcutaneously, daily for 3 months in patients with renal cell carcinoma (RCC) or metastatic melanoma (MM). We also examined the effect of adding the immune modulator levamisole to the two different schedules of IL-2. Thirty-nine patients were entered into two sequential phase I/II studies. Eighteen patients entered study 1 and were randomised to receive IL-2, 3 x 10(6) IU m-2 day-1, subcutaneously for 3 months with or without levamisole 50 mg t.d.s. p.o. on days 1-3 on alternate weeks. Twenty-one patients entered study 2 and were randomised to receive 5.4 x 10(6) IU m-2 day-1 subcutaneously for 3 months with or without levamisole 50 mg t.d.s. p.o. on days 1-3 on alternate weeks. Blood was taken for peripheral blood lymphocyte (PBL) phenotype analysis, and measurement of IL-2, soluble IL-2 receptor (sIL-2R) and neopterin concentration. Two patients with metastatic melanoma, one in each study, responded (11.8%); both received IL-2 alone. Observations of immunological parameters showed that treatment with subcutaneous IL-2 resulted in a significant rise in the percentage of PBLs bearing CD25, CD3/HLA-DR, CD56 and levels of IL-2 receptor and neopterin. The total white blood cell count (WBC) and total lymphocyte count rose significantly on day 18 compared with pretreatment levels. The addition of levamisole to either IL-2 schedule resulted in no significant changes in any immunological parameters. This study illustrates that prolonged subcutaneous IL-2 can be given safely in the outpatient setting. There was no evidence that levamisole acts as an immunomodulator in this study.


Assuntos
Adjuvantes Imunológicos/administração & dosagem , Carcinoma de Células Renais/terapia , Interleucina-2/administração & dosagem , Neoplasias Renais/terapia , Levamisol/administração & dosagem , Melanoma/terapia , Adjuvantes Imunológicos/efeitos adversos , Adulto , Carcinoma de Células Renais/imunologia , Humanos , Interleucina-2/efeitos adversos , Neoplasias Renais/imunologia , Contagem de Leucócitos/efeitos dos fármacos , Levamisol/efeitos adversos , Linfócitos/efeitos dos fármacos , Melanoma/imunologia
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...