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1.
Acta Crystallogr D Biol Crystallogr ; 62(Pt 10): 1251-9, 2006 Oct.
Article in English | MEDLINE | ID: mdl-17001102

ABSTRACT

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.


Subject(s)
Crystallography/instrumentation , Automation , Crystallography/standards , Electronics , Magnetics , Reference Standards , Robotics , Software , Synchrotrons
2.
Acta Crystallogr D Biol Crystallogr ; 62(Pt 10): 1162-9, 2006 Oct.
Article in English | MEDLINE | ID: mdl-17001093

ABSTRACT

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.


Subject(s)
Genes/genetics , Synchrotrons/statistics & numerical data , Data Collection/methods , Information Management , Molecular Structure , Quality Control , Software
3.
Acta Crystallogr D Biol Crystallogr ; 62(Pt 1): 65-71, 2006 Jan.
Article in English | MEDLINE | ID: mdl-16369095

ABSTRACT

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.


Subject(s)
Crystallography, X-Ray , Data Collection/instrumentation , Magnetics/instrumentation , Proteins/chemistry , Synchrotrons/instrumentation , Crystallization , Data Collection/methods , Data Collection/statistics & numerical data
4.
Acta Crystallogr D Biol Crystallogr ; 58(Pt 1): 70-80, 2002 Jan.
Article in English | MEDLINE | ID: mdl-11752780

ABSTRACT

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.


Subject(s)
Transferrin/chemistry , Animals , Anions , Binding Sites , Carbohydrates/chemistry , Carbonates/metabolism , Crystallography, X-Ray , Disulfides/chemistry , Iron/metabolism , Protein Conformation , Rabbits , Swine , Transferrin/metabolism
5.
Acta Crystallogr D Biol Crystallogr ; 57(Pt 9): 1230-7, 2001 Sep.
Article in English | MEDLINE | ID: mdl-11526314

ABSTRACT

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.


Subject(s)
Proteins/chemistry , Amino Acid Sequence , Carrier Proteins , Crystallization , Crystallography, X-Ray , Dimerization , Models, Molecular , Molecular Sequence Data , Molecular Weight , Protein Conformation , Scattering, Radiation , Sequence Homology, Amino Acid
6.
Nat Struct Biol ; 8(6): 521-5, 2001 Jun.
Article in English | MEDLINE | ID: mdl-11373620

ABSTRACT

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.


Subject(s)
Dihydropteridine Reductase/chemistry , Dihydropteridine Reductase/metabolism , Drug Resistance , Leishmania major/metabolism , Pterins/metabolism , Amino Acid Sequence , Animals , Binding Sites , Crystallography, X-Ray , Dihydropteridine Reductase/antagonists & inhibitors , Folic Acid Antagonists/metabolism , Folic Acid Antagonists/pharmacology , Hydrogen Bonding , Leishmania major/enzymology , Leishmania major/genetics , Methotrexate/metabolism , Methotrexate/pharmacology , Models, Molecular , Molecular Sequence Data , NADP/metabolism , Oxidation-Reduction , Protein Structure, Secondary , Selenomethionine/metabolism , Substrate Specificity , Tetrahydrofolate Dehydrogenase/metabolism
7.
Acta Crystallogr D Biol Crystallogr ; 56(Pt 9): 1194-7, 2000 Sep.
Article in English | MEDLINE | ID: mdl-10957644

ABSTRACT

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.


Subject(s)
Escherichia coli/enzymology , Oxidoreductases/chemistry , Crystallization , Crystallography, X-Ray , Methionine Sulfoxide Reductases , Selenomethionine/chemistry
8.
Nat Struct Biol ; 7(5): 398-402, 2000 May.
Article in English | MEDLINE | ID: mdl-10802738

ABSTRACT

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.


Subject(s)
Carbohydrate Epimerases/chemistry , Carbohydrate Epimerases/classification , Nucleoside Diphosphate Sugars/metabolism , Salmonella typhimurium/enzymology , Thymine Nucleotides/metabolism , Amino Acid Sequence , Binding Sites , Carbohydrate Epimerases/metabolism , Conserved Sequence , Crystallography, X-Ray , Dimerization , Models, Molecular , Molecular Sequence Data , Nucleoside Diphosphate Sugars/chemistry , Phenol/chemistry , Phenol/metabolism , Protein Binding , Protein Structure, Secondary , Sequence Alignment , Thymine Nucleotides/chemistry
9.
J Mol Biol ; 298(1): 123-33, 2000 Apr 21.
Article in English | MEDLINE | ID: mdl-10756109

ABSTRACT

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.


Subject(s)
Antimalarials/metabolism , Cyclosporine/metabolism , Peptidylprolyl Isomerase/chemistry , Peptidylprolyl Isomerase/metabolism , Plasmodium falciparum/chemistry , Amino Acid Sequence , Amino Acid Substitution , Animals , Antimalarials/chemistry , Binding Sites , Catalysis , Conserved Sequence , Crystallography, X-Ray , Cyclosporine/chemistry , Humans , Hydrogen Bonding , Models, Molecular , Molecular Sequence Data , Mutation/genetics , Peptidylprolyl Isomerase/genetics , Plasmodium falciparum/genetics , Protein Structure, Secondary , Sequence Alignment , Structure-Activity Relationship
10.
Structure ; 7(11): 1345-52, 1999 Nov 15.
Article in English | MEDLINE | ID: mdl-10574798

ABSTRACT

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.


Subject(s)
Nucleic Acid Conformation , RNA/chemistry , Signal Recognition Particle/genetics , Base Sequence , Humans , Magnesium/chemistry , Protein Binding , Signal Recognition Particle/metabolism
11.
J Biol Chem ; 274(36): 25613-22, 1999 Sep 03.
Article in English | MEDLINE | ID: mdl-10464297

ABSTRACT

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.


Subject(s)
Crithidia fasciculata/chemistry , Protein Folding , Thioredoxins/chemistry , Amino Acid Sequence , Animals , Crithidia fasciculata/genetics , Crithidia fasciculata/metabolism , Humans , Molecular Sequence Data , Oxidation-Reduction , Protein Structure, Secondary , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Thioredoxins/genetics , Thioredoxins/metabolism
12.
Acta Crystallogr D Biol Crystallogr ; 55(Pt 2): 399-402, 1999 Feb.
Article in English | MEDLINE | ID: mdl-10089346

ABSTRACT

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.


Subject(s)
Escherichia coli Proteins , Escherichia coli/enzymology , Intramolecular Transferases/chemistry , Amino Acid Sequence , Crystallography, X-Ray , Intramolecular Transferases/isolation & purification , Molecular Sequence Data , Protein Conformation , Sequence Homology, Amino Acid
13.
Acta Crystallogr D Biol Crystallogr ; 55(Pt 2): 542-3, 1999 Feb.
Article in English | MEDLINE | ID: mdl-10089372

ABSTRACT

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.


Subject(s)
Bacterial Proteins , Escherichia coli Proteins , Transcription Factors/chemistry , Crystallography, X-Ray , Escherichia coli/genetics , Recombinant Proteins/chemistry
14.
EMBO J ; 18(6): 1435-46, 1999 Mar 15.
Article in English | MEDLINE | ID: mdl-10075916

ABSTRACT

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.


Subject(s)
Bacterial Proteins , Escherichia coli Proteins , Escherichia coli/metabolism , Protein Folding , Transcription Factors/chemistry , Amino Acid Sequence , Binding Sites , Cloning, Molecular , Computer Graphics , Crystallography, X-Ray/methods , DNA/chemistry , DNA/metabolism , Dimerization , Escherichia coli/genetics , Macromolecular Substances , Models, Molecular , Molecular Sequence Data , Molybdenum/metabolism , Nucleic Acid Conformation , Protein Structure, Secondary , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Selenomethionine , Software , Transcription Factors/genetics , Transcription Factors/metabolism
15.
J Mol Biol ; 287(2): 383-94, 1999 Mar 26.
Article in English | MEDLINE | ID: mdl-10080900

ABSTRACT

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.


Subject(s)
Enzyme Inhibitors/chemistry , Escherichia coli/enzymology , Fructose-Bisphosphate Aldolase/chemistry , Hydroxamic Acids/chemistry , Binding Sites , Catalysis , Dihydroxyacetone Phosphate/chemistry , Dimerization , Hydrogen Bonding , Models, Molecular , X-Ray Diffraction , Zinc/chemistry
16.
Nucleic Acids Res ; 27(2): 555-61, 1999 Jan 15.
Article in English | MEDLINE | ID: mdl-9862980

ABSTRACT

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.


Subject(s)
Nucleic Acid Heteroduplexes/chemistry , Oligodeoxyribonucleotides/chemistry , Oligoribonucleotides/chemistry , Circular Dichroism , Crystallography, X-Ray , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular , Nucleic Acid Conformation , Ribonuclease H/metabolism , Solutions , Substrate Specificity
17.
Acta Crystallogr D Biol Crystallogr ; 55(Pt 12): 2043-6, 1999 Dec.
Article in English | MEDLINE | ID: mdl-10666586

ABSTRACT

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.


Subject(s)
Carbohydrate Dehydrogenases/chemistry , Carbohydrate Dehydrogenases/isolation & purification , Salmonella typhimurium/enzymology , Carbohydrate Dehydrogenases/genetics , Crystallization , Crystallography, X-Ray , Escherichia coli/genetics , Gene Expression , Genes, Bacterial , Nucleoside Diphosphate Sugars/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Salmonella typhimurium/genetics , Thymine Nucleotides/biosynthesis
18.
Acta Crystallogr D Biol Crystallogr ; 54(Pt 6 Pt 2): 1422-4, 1998 Nov 01.
Article in English | MEDLINE | ID: mdl-10089526

ABSTRACT

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.


Subject(s)
Bacterial Proteins/chemistry , Lactococcus lactis/enzymology , Phosphogluconate Dehydrogenase/chemistry , Bacterial Proteins/isolation & purification , Crystallization , Crystallography, X-Ray , Dimerization , Pentose Phosphate Pathway , Phosphogluconate Dehydrogenase/isolation & purification , Protein Conformation , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/isolation & purification
19.
Structure ; 4(11): 1303-15, 1996 Nov 15.
Article in English | MEDLINE | ID: mdl-8939754

ABSTRACT

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.


Subject(s)
Bacterial Proteins , Escherichia coli Proteins , Escherichia coli/enzymology , Fructose-Bisphosphate Aldolase/chemistry , Metalloproteins/chemistry , Zinc/chemistry , Amino Acid Sequence , Binding Sites , Cations/chemistry , Computer Simulation , Crystallography, X-Ray , Dimerization , Fructose-Bisphosphate Aldolase/classification , Metalloproteins/classification , Models, Molecular , Molecular Sequence Data , Potassium/chemistry , Protein Conformation , Protein Structure, Secondary
20.
Br J Cancer ; 74(7): 1109-13, 1996 Oct.
Article in English | MEDLINE | ID: mdl-8855983

ABSTRACT

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.


Subject(s)
Adjuvants, Immunologic/administration & dosage , Carcinoma, Renal Cell/therapy , Interleukin-2/administration & dosage , Kidney Neoplasms/therapy , Levamisole/administration & dosage , Melanoma/therapy , Adjuvants, Immunologic/adverse effects , Adult , Carcinoma, Renal Cell/immunology , Humans , Interleukin-2/adverse effects , Kidney Neoplasms/immunology , Leukocyte Count/drug effects , Levamisole/adverse effects , Lymphocytes/drug effects , Melanoma/immunology
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