5-(Hydroxyethyl)-4-methylthiazole kinase from S. aureus, which is essential to vitamin B1 metabolism, has been crystallized in space group P1. The crystals diffracted to 2.1 Å resolution.
ThiM [5-(hydroxyethyl)-4-methylthiazole kinase; EC 126.96.36.199] from Staphylococcus aureus is an essential enzyme of thiamine or vitamin B1 metabolism and has been crystallized by the vapour-diffusion method. The crystals belonged to the primitive space group P1, with unit-cell parameters a = 62.06, b = 62.40, c = 107.82 Å, α = 92.25, β = 91.37, γ = 101.48° and six protomers in the unit cell, corresponding to a packing parameter V
M of 2.3 Å3 Da−1. Diffraction data were collected to 2.1 Å resolution using synchrotron radiation. The phase problem was solved by molecular replacement.
ThiM; Staphylococcus aureus; 5-(hydroxyethyl)-4-methylthiazole kinase; vitamin B1 metabolism
Crystals of a chitinase from C. vernus were monoclinic, belonging to space group C2 with unit-cell parameters a = 172.3, b = 37.1, c = 126.4 Å, β = 127°, and diffracted to 2.1 Å resolution.
A chitinase has been isolated and purified from Crocus vernus corms. N-terminal amino-acid sequence analysis of the approximately 30 kDa protein showed 33% identity to narbonin, a seed protein from Vicia narbonensis L. The C. vernus chitinase was crystallized by the hanging-drop vapour-diffusion method using PEG 8000 as the main precipitant. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 172.3, b = 37.1, c = 126.4 Å, β = 127° and two molecules per asymmetric unit. Diffraction data were collected to a resolution of 2.1 Å.
chitinases; Crocus vernus
Crystals of the thiaminase type II from S. aureus are orthorhombic, belonging to space group P212121 with unit-cell parameters a = 103.5, b = 104.1, c = 109.6 Å, and diffracted to 2.6 Å resolution.
Thiaminase type II (TenA) catalyzes the deamination of aminopyrimidines, including the cleavage of thiamine to 4-amino-5-hydroxymethyl-2-methylpyrimidine and 5-(2-hydroxyethyl)-4-methylthiazole in the metabolism of thiamine (vitamin B1), in Staphylococcus aureus (Sa). SaTenA was crystallized by the vapour-diffusion method and the resulting crystal diffracted to 2.6 Å resolution usng synchrotron radiation. The crystal is orthorhombic, belonging to space group P212121 with unit-cell parameters a = 103.5, b = 104.1, c = 109.6 Å. With four molecules in the asymmetric unit, the Matthews coefficient is 2.85 Å3 Da−1. Initial attempts to solve the structure by molecular-replacement techniques were successful.
thiaminase type II; TenA; Staphylococcus aureus
Excitation of intrinsic fluorescence at wavelengths longer than 300 nm is effective in the detection of protein crystals in crystallization trials set up in the most commonly used hardware.
It is well known that most proteins and many other biomolecules fluoresce when illuminated with UV radiation, but it is also commonly accepted that utilizing this property to detect protein crystals in crystallization setups is limited by the opacity of the materials used to contain and seal them. For proteins, this fluorescence property arises primarily from the presence of tryptophan residues in the sequence. Studies of protein crystallization results in a variety of setup configurations show that the opacity of the containment hardware can be overcome at longer excitation wavelengths, where typical hardware materials are more transparent in the UV, by the use of a powerful UV-light source that is effective in excitation even though not at the maximum of the excitation response. The results show that under these circumstances UV evaluation of crystallization trials and detection of biomolecular crystals in them is not limited by the hardware used. It is similarly true that a deficiency in tryptophan or another fluorescent component that limits the use of UV light for these purposes can be effectively overcome by the addition of fluorescent prostheses that bind to the biomolecule under study. The measurements for these studies were made with a device consisting of a potent UV-light source and a detection system specially adapted (i) to be tunable via a motorized and software-controlled absorption-filter system and (ii) to convey the excitation light to the droplet or capillary hosting the crystallization experiment by quartz-fibre light guides.
UV fluorescence; detection of protein crystals
An all-LNA duplex was designed from the stem region of an RNA aptamer which has been generated against ricin. The LNA duplex was crystallized and preliminary X-ray diffraction analysis revealed diffraction to a resolution of up to 2.8 Å.
Locked nucleic acids (LNAs) are modified nucleic acids which contain a modified sugar such as β-d-2′-O,4′-C methylene-bridged ribofuranose or other sugar derivatives in LNA analogues. The β-d-2′-O,4′-C methylene ribofuranose LNAs in particular possess high stability and melting temperatures, which makes them of interest for stabilizing the structure of different nucleic acids. Aptamers, which are DNAs or RNAs targeted against specific ligands, are candidates for substitution with LNAs in order to increase their stability. A 7-mer helix derived from the terminal part of an aptamer that was targeted against ricin was chosen. The ricin aptamer originally consisted of natural RNA building blocks and showed high affinity in ricin binding. For future stabilization of the aptamer, the terminal helix has been constructed as an ‘all-locked’ LNA and was successfully crystallized in order to investigate its structural properties. Optimization of crystal growth succeeded by the use of different metal salts as additives, such as CuCl2, MgCl2, MnCl2, CaCl2, CoCl2 and ZnSO4. Preliminary X-ray diffraction data were collected and processed to 2.8 Å resolution. The LNA crystallized in space group P65, with unit-cell parameters a = 50.11, b = 50.11, c = 40.72 Å. The crystals contained one LNA helix per asymmetric unit with a Matthews coefficient of 3.17 Å3 Da−1, which implies a solvent content of 70.15%.
locked nucleic acids; stability of nucleic acids; aptamers; ricin
A completely ‘all-locked’ nucleic acid duplex was designed from an E. coli tRNASer microhelix. The helix consists exclusively of LNA building blocks and was crystallized. The crystals diffracted to 1.9 Å resolution.
Modified nucleic acids are of great interest with respect to their nuclease resistance and enhanced thermostability. In therapeutical and diagnostic applications, such molecules can substitute for labile natural nucleic acids that are targeted against particular diseases or applied in gene therapy. The so-called ‘locked nucleic acids’ contain modified sugar moieties such as 2′-O,4′-C-methylene-bridged β-d-ribofuranose and are known to be very stable nucleic acid derivatives. The structure of locked nucleic acids in single or multiple LNA-substituted natural nucleic acids and in LNA–DNA or LNA–RNA heteroduplexes has been well investigated, but the X-ray structure of an ‘all-locked’ nucleic acid double helix has not been described to date. Here, the crystallization and X-ray diffraction data analysis of an ‘all-locked’ nucleic acid helix, which was designed as an LNA originating from a tRNASer microhelix RNA structure, is presented. The crystals belonged to space group C2, with unit-cell parameters a = 77.91, b = 40.74, c = 30.06 Å, β = 91.02°. A high-resolution and a low-resolution data set were recorded, with the high-resolution data showing diffraction to 1.9 Å resolution. The crystals contained two double helices per asymmetric unit, with a Matthews coefficient of 2.48 Å3 Da−1 and a solvent content of 66.49% for the merged data.
locked nucleic acids; stability of nucleic acids; tRNASer microhelix; RNA
Various E. coli tRNAArg acceptor-stem microhelix isoacceptors have been crystallized and investigated by high-resolution X-ray diffraction analysis.
The aminoacylation of tRNA is a crucial step in cellular protein biosynthesis. Recognition of the cognate tRNA by the correct aminoacyl-tRNA synthetase is ensured by tRNA identity elements. In tRNAArg, the identity elements consist of the anticodon, parts of the D-loop and the discriminator base. The minor groove of the aminoacyl stem interacts with the arginyl-tRNA synthetase. As a consequence of the redundancy of the genetic code, six tRNAArg isoacceptors exist. In the present work, three different Escherichia coli tRNAArg acceptor-stem helices were crystallized. Two of them, the tRNAArg microhelices RR-1660 and RR-1662, were examined by X-ray diffraction analysis and diffracted to 1.7 and 1.8 Å resolution, respectively. The tRNAArg RR-1660 helix crystallized in space group P1, with unit-cell parameters a = 26.28, b = 28.92, c = 29.00 Å, α = 105.74, β = 99.01, γ = 97.44°, whereas the tRNAArg RR-1662 helix crystallized in space group C2, with unit-cell parameters a = 33.18, b = 46.16, c = 26.04 Å, β = 101.50°.
E. coli tRNAArg; acceptor-stem helices; isoacceptors; arginyl-tRNA synthetases
The tRNAGly acceptor-stem microhelix isoacceptor from human cytoplasm was crystallized and X-ray diffraction analysis revealed diffraction to 1.18 Å resolution. The sequence of the microhelix was derived from the gene sequence with tRNA Database ID DG9990.
Interest has been focused on comparative X-ray structure analyses of different tRNAGly acceptor-stem helices. tRNAGly/glycyl-tRNA synthetase belongs to the so-called class II system, in which the tRNA identity elements consist of simple and unique determinants that are located in the tRNA acceptor stem and the discriminator base. Comparative structure investigations of tRNAGly microhelices provide insight into the role of tRNA identity elements. Predominant differences in the structures of glycyl-tRNA synthetases and in the tRNA identity elements between prokaryotes and eukaryotes point to divergence during the evolutionary process. Here, the crystallization and high-resolution X-ray diffraction analysis of a human tRNAGly acceptor-stem microhelix with sequence 5′-G1C2A3U4U5G6G7-3′, 5′-C66C67A68A69U70G71C72-3′ is reported. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 37.32, b = 37.61, c = 30.47 Å, β = 112.60° and one molecule per asymmetric unit. A data set was collected using synchrotron radiation and data were processed within the resolution range 50.0–1.18 Å. The structure was solved by molecular replacement.
human tRNAGly; isoacceptors; aminoacyl-tRNA stem; tRNA identity elements; class II aminoacyl-tRNA/synthetase system; glycyl-tRNA synthetases
A novel l-amino-acid oxidase was isolated from V. ammodytes ammodytes venom and crystallized. The solution conditions under which the protein sample was monodisperse were optimized using dynamic light scattering prior to crystallization. Preliminary diffraction data were collected to 2.6 Å resolution.
l-Amino-acid oxidase from the venom of Vipera ammodytes ammodytes, the most venomous snake in Europe, was isolated and crystallized using the sitting-drop vapour-diffusion method. The solution conditions under which the protein sample was monodisperse were optimized using dynamic light scattering prior to crystallization. The crystals belonged to space group C2, with unit-cell parameters a = 198.37, b = 96.38, c = 109.11 Å, β = 92.56°. Initial diffraction data were collected to 2.6 Å resolution. The calculated Matthews coefficient is approximately 2.6 Å3 Da−1 assuming the presence of four molecules in the asymmetric unit.
l-amino-acid oxidase; snake venoms
A 5S rRNA A-helix 7-mer oligonucleotide was chemically synthesized both as d-RNA and as l-RNA, biochemically investigated, crystallized as a stochiometric racemate and examined by X-ray diffraction.
Chemically synthesized RNAs with the unnatural l-configuration possess enhanced in vivo stability and nuclease resistance, which is a highly desirable property for pharmacological applications. For a structural comparison, both l- and d-RNA oligonucleotides of a shortened Thermus flavus 5S rRNA A-helix were chemically synthesized. The enantiomeric RNA duplexes were stochiometrically cocrystallized as a racemate, which enabled analysis of the d- and l-RNA enantiomers in the same crystals. In addition to a biochemical investigation, diffraction data were collected to 3.0 Å resolution using synchrotron radiation. The crystals belonged to space group P3121, with unit-cell parameters a = b = 35.59, c = 135.30 Å, γ = 120° and two molecules per asymmetric unit.
5S rRNA; oligonucleotides; RNA racemates; spiegelmers; d- and l-RNA enantiomers; microhelices
The human tRNAGly acceptor-stem microhelix was crystallized and preliminary X-ray diffraction analysis revealed diffraction to a resolution of up to 1.2 Å.
The major dissimilarities between the eukaryotic/archaebacterial-type and eubacterial-type glycyl-tRNA synthetase systems (GlyRS; class II aminoacyl-tRNA synthetases) represent an intriguing example of evolutionarily divergent solutions to similar biological functions. The differences in the identity elements of the respective tRNAGly systems are located within the acceptor stem and include the discriminator base U73. In the present work, the human tRNAGly acceptor-stem microhelix was crystallized in an attempt to analyze the structural features that govern the correct recognition of tRNAGly by the eukaryotic/archaebacterial-type glycyl-tRNA synthetase. The crystals of the human tRNAGly acceptor-stem helix belong to the monoclinic space group C2, with unit-cell parameters a = 37.12, b = 37.49, c = 30.38 Å, α = γ = 90, β = 113.02°, and contain one molecule per asymmetric unit. A high-resolution data set was acquired using synchrotron radiation and the data were processed to 1.2 Å resolution.
human tRNAGly; acceptor-stem helix; tRNA identity elements; glycyl-tRNA synthetase (GlyRS); divergent evolution
S. typhimurium uridine phosphorylase has been isolated and crystallized in the presence of ligand.
Uridine phosphorylase (UPh; EC 188.8.131.52) is a member of the pyrimidine nucleoside phosphorylase family of enzymes which catalyzes the phosphorolytic cleavage of the C—N glycoside bond of uridine, with the formation of ribose 1-phosphate and uracil. This enzyme has been shown to be important in the activation and catabolism of fluoropyrimidines. Modulation of its enzymatic activity may affect the therapeutic efficacy of chemotherapeutic agents. The structural investigation of the bacterial uridine phosphorylases, both unliganded and complexed with substrate/product analogues and inhibitors, may help in understanding the catalytic mechanism of the phosphorolytic cleavage of uridine. Salmonella typhimurium uridine phosphorylase has been crystallized with 2,2′-anhydrouridine. X-ray diffraction data were collected to 2.15 Å. Preliminary analysis of the diffraction data indicates that the crystal belongs to space group P212121, with unit-cell parameters a = 88.52, b = 123.98, c = 133.52 Å. The solvent content is 45.51%, assuming the presence of one hexamer molecule per asymmetric unit.
nucleoside phosphorylases; uridine phosphorylase–inhibitor complex; 2,2′-anhydrouridine
Two trypsins from the gastric fluid of the marine crab C. pagurus were purified and crystallized and X-ray data were collected to 0.97 and 3.2 Å resolution.
The digestive fluid of the marine crab Cancer pagurus (Decapoda, Brachyura) contains highly stable proteases which display enhanced activity in aqueous mixtures of organic solvents. Three trypsins were isolated from the gastric fluid and two of them, C.p.TryII and C.p.TryIII, were purified to homogeneity by anion-exchange chromatography and crystallized by hanging-drop vapour diffusion. Diffraction data were collected at a synchrotron to 0.97 and 3.2 Å resolution, respectively. The crystal of C.p.TryII belongs to the orthorhombic space group P212121, with unit-cell parameters a = 52.06, b = 62.00, c = 71.66 Å. Based on the Matthews coefficient, one protein molecule per asymmetric unit is suggested. In contrast, crystals of C.p.TryIII, which belong to the cubic space group P213 with unit-cell parameters a = b = c = 215.4 Å, are assumed to contain 12 molecules per asymmetric unit.
Crustacea; crabs; Cancer pagurus; gastric fluid; digestive enzymes; trypsin
In order to investigate the identity elements of the E. coli tRNAGly/GlyRS class II system, a tRNAGly acceptor-stem microhelix was crystallized and a data set was collected to 2.0 Å resolution using synchrotron radiation.
The tRNAGly and glycyl-tRNA synthetase (GlyRS) system is an evolutionary special case within the class II aminoacyl-tRNA synthetases because two divergent types of GlyRS exist: an archaebacterial/human type and an eubacterial type. The tRNA identity elements which determine the correct aminoacylation process are located in the aminoacyl domain of tRNAGly. To obtain further insight concerning structural investigation of the identity elements, the Escherichia coli seven-base-pair tRNAGly acceptor-stem helix was crystallized. Data were collected to 2.0 Å resolution using synchrotron radiation. Crystals belong to space group P3121 or P3221, with unit-cell parameters a = b = 35.35, c = 130.82 Å, α = β = 90, γ = 120° and two molecules in the asymmetric unit.
tRNA acceptor-stem microhelix; tRNA identity elements; tRNAGly; glycyl-tRNA synthetase; class II aminoacyl-tRNA synthetases
Locked nucleic acid (LNA) nucleotides are RNA analogues with a useful additional conformational constraint; the current investigation will provide the first crystallographic view of an all-LNA duplex.
The pharmacokinetic properties of an aptamer against the tumour-marker protein tenascin-C have recently been successfully improved by the introduction of locked nucleic acids (LNAs) into the terminal stem of the aptamer. Since it is believed that this post-SELEX optimization is likely to provide a more general route to enhance the in vitro and in vivo stability of aptamers, elucidation of the structural basis of this improvement was embarked upon. Here, the crystallographic and X-ray diffraction data of the isolated aptamer stem encompassed in a six-base-pair duplex both with and without the LNA modification are presented. The obtained all-LNA crystals belong to space group P41212 or P43212, with unit-cell parameters a = b = 52.80, c = 62.83 Å; the all-RNA crystals belong to space group R32, with unit-cell parameters a = b = 45.21, c = 186.97 Å, γ = 120.00°.
locked nucleic acids; LNA; tenascin-C; aptamer; TTA1
In order to investigate tRNA identity elements, an elongator tRNASer acceptor-stem helix was crystallized and a data set was collected to 1.8 Å resolution aiming at a comparison with the corresponding region in suppressor tRNASec.
In order to understand elongator tRNASer and suppressor tRNASec identity elements, the respective acceptor-stem helices have been synthesized and crystallized in order to analyse and compare their structures in detail at high resolution. The synthesis, crystallization and preliminary X-ray diffraction results for a seven-base-pair tRNASer acceptor-stem helix are presented here. Diffraction data were collected to 1.8 Å, applying synchrotron radiation and cryogenic cooling. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 36.14, b = 38.96, c = 30.81 Å, β = 110.69°.
tRNA acceptor-stem microhelix; tRNA identity elements; tRNASer; tRNASec; EF-Tu; SELB
S. typhimurium uridine phosphorylase is a homohexamer and is structurally homologous to the hexameric purine nucleoside phosphorylases.
Uridine phosphorylase (UPh) catalyzes the phosphorolytic cleavage of the C—N glycosidic bond of uridine to ribose 1-phosphate and uracil in the pyrimidine-salvage pathway. The crystal structure of the Salmonella typhimurium uridine phosphorylase (StUPh) has been determined at 2.5 Å resolution and refined to an R factor of 22.1% and an R
free of 27.9%. The hexameric StUPh displays 32 point-group symmetry and utilizes both twofold and threefold non-crystallographic axes. A phosphate is bound at the active site and forms hydrogen bonds to Arg91, Arg30, Thr94 and Gly26 of one monomer and Arg48 of an adjacent monomer. The hexameric StUPh model reveals a close structural relationship to Escherichia coli uridine phosphorylase (EcUPh).
uridine phosphorylase; pyrimidine salvage; purine nucleoside phosphorylases
The structures of mistletoe lectin I in complex with lactose and galactose reveal differences in binding by the two known sites in subdomains α1 and γ2 and suggest the presence of a third low-affinity site in subdomain β1.
The structures of mistletoe lectin I (ML-I) from Viscum album complexed with lactose and galactose have been determined at 2.3 Å resolution and refined to R factors of 20.9% (R
free = 23.6%) and 20.9 (R
free = 24.6%), respectively. ML-I is a heterodimer and belongs to the class of ribosome-inactivating proteins of type II, which consist of two chains. The A-chain has rRNA N-glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B-chain is a lectin and preferentially binds to galactose-terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains α1 and γ2 of the ML-I B-chain separated by ∼62 Å from each other. The favoured binding of galactose in subdomain α1 is achieved via hydrogen bonds connecting the 4-hydroxyl and 3-hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar–lectin complex. In the galactose-binding site II of subdomain γ2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen-bonding partners for galactose. In the case of the galactose-binding site I, the 2-hydroxyl group also stabilizes the sugar–protein complex, an interaction thus far rarely detected in galactose-specific lectins. Finally, a potential third low-affinity galactose-binding site in subunit β1 was identified in the present ML-I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound.
ribosome-inactivation proteins; mistletoe lectin I; sugar-binding sites
The crystallization and preliminary X-ray structure at 1.9 Å resolution of the fungal laccase from C. maxima are presented.
Laccases are members of the blue multi-copper oxidase family that oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. Crystals of the laccase from Cerrena maxima have been obtained and X-ray data were collected to 1.9 Å resolution using synchrotron radiation. A preliminary analysis shows that the enzyme has the typical laccase structure and several carbohydrate sites have been identified. The carbohydrate chains appear to be involved in stabilization of the intermolecular contacts in the crystal structure, thus promoting the formation of well ordered crystals of the enzyme. Here, the results of an X-ray crystallographic study on the laccase from the fungus Cerrena maxima are reported. Crystals that diffract well to a resolution of at least 1.9 Å (R factor = 18.953%; R
free = 23.835; r.m.s.d. bond lengths, 0.06 Å; r.m.s.d. bond angles, 1.07°) have been obtained despite the presence of glycan moieties. The overall spatial organization of C. maxima laccase and the structure of its copper-containing active centre have been determined by the molecular-replacement method using the laccase from Trametes versicolor (Piontek et al., 2002 ▶) as a structural template. In addition, four glycan-binding sites were identified and the 1.9 Å X-ray data were used to determine the previously unknown primary structure of this protein. The identity (calculated from sequence alignment) between the C. maxima laccase and the T. versicolor laccase is about 87%. Tyr196 and Tyr372 show significant extra density at the ortho positions and this has been interpreted in terms of NO2 substituents.
blue multi-copper enzymes; laccases; Cerrena maxima