Identification of mouse selenomethionine alpha,gamma-elimination enzyme: cystathionine gamma-lyase catalyzes its reaction to generate methylselenol

The purpose of this study was to identify the seleno-L-methionine (L-SeMet) alpha,gamma-elimination enzyme that catalyzes L-SeMet to generate methylselenol (CH3SeH), a notable intermediate for the metabolism of selenium compounds, in mammalian tissues. The enzyme purified from ICR mouse liver was separated by one-dimensional gel electrophoresis, and the specific band was subjected to in-gel trypsin digestion followed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometric analysis. In the peptide mass fingerprinting search, the mass numbers of 14 peptides produced by tryptic digestion of the enzyme were consistent with the theoretical mass numbers calculated from the amino acid sequence of murine cystathionine gamma-lyase (E.C. 4.4.1.1). The peptide sequence tags search was also performed to obtain the amino acid sequence data of five tryptic peptides. These peptides were significantly identical to the partial amino acid sequences of cystathionine gamma-lyase. This enzyme was clearly shown to catalyze the alpha,gamma-elimination reaction of L-cystathionine by the enzymological research. The Km value for the catalysis of L-cystathionine was 0.81 mM and Vmax was 0.0013 unit/mg protein. These results suggested that cystathionine gamma-lyase catalyzes L-SeMet to generate CH3SeH by its alpha,gamma-elimination reaction.

Chiral Speciation and Determination of DL-Selenomethionine Enantiomers on a Novel Chiral Ligand-Exchange Stationary Phase

A new type of chiral ligand-exchange stationary phase (CLES) was successfully synthesized by treating silica gel with beta-(3,4-epoxycyclohexyl)ethyltrimethoxy silane and opening the epoxy ring by L-isoleucine. The chiral speciation of DL-selenomethionine (DL-SeMet) by high-performance liquid chromatography (HPLC) with UV absorbance on the CLES column was studied. The influences of the contents of copper ion and methanol as well as the pH value in the mobile phase and temperature of the column on the efficiency of resolution of DL-SeMet were investigated in detail. DL-SeMet could be completely resolved within 40 min under the optimal operating conditions of 0.1 mmol/L Cu2+ at 0.05 mol/L KH2PO4 buffer (pH = 5.5) and 35 degrees C temperature of the column. The limits of detection of D- and L-SeMet were 255 ppb and 286 ppb, respectively. This method was applied to determine the D- and L-enantiomers of DL-SeMet in real samples, such as selenized yeast powder and garlic.

Crystallization and preliminary X-ray analysis of the Streptomyces olivaceoviridis NgcE binding protein of the ABC transporter for N-acetylglucosamine

The NgcE protein binds N-acetylglucosamine (GIcNAc) as well asN,N'-diacetylchitobiose and is a component of the ABC transporter Ngc for GIcNAc uptake in Streptomyces olivaceoviridis. After cloning the corresponding gene in an Escherichia coli host, the NgcE protein was overproduced in a soluble form within the cytoplasm and purified to homogeneity by four consecutive chromatographic processes. Crystals of NgcE that grew in the presence of 1 mM GlcNAc,20%(w/v) PEG MME 2000 and 100 mM Tris-HCI pH 8.5 had a plate-like shape and belonged to either space group P21212 (unit-cell parameters a = 59.9, b = 153.0, c = 41.7 A) or P212121 (a = 58.1, b = 96.3, c = 151.7 A). The former crystals diffracted to 1.8 A resolution andthe latter to 2.2 A. Selenomethionine-containing crystals were generated under the same conditions and belonged to space group P212121 with unit-cell parameters a = 58.4, b = 96.6, c = 152.5 A, and diffracted to 2.0 A resolution.

Novel structure and nucleotide binding properties of HI1480 from Haemophilus influenzae: a protein with no known sequence homologues

The crystal structure of the Haemophilus influenzae protein HI1480 was determined at 2.1-A resolution. The amino acid sequence of HI1480 is unique, having no homology with other known protein sequences. The protein adopts a novel alpha+beta fold, and associates into a dimer of tightly associated dimers. The tight dimers are formed by intermolecular interactions that are mediated by an antiparallel beta-barrel involving both monomers. Helical regions of two dimers mediate the tetramer formation. The helical region contains a four-helix bundle that has been seen only in the anticodon binding domains of class I tRNA synthetases. A cluster of four residues, Tyr18, Arg134, Glu26, and Lys12 is located in a depression formed at the four-helix bundle/ beta-barrel interface. The arrangement is suggestive of an active center, possibly a catalytic site. The HI1480 gene is located within the Mu-like prophage region of H. influenzae, has no homology to bacteriophage genes, and is flanked by transposases. Hence, this is an example of horizontal transfer from an unknown organism. Gel mobility shift assays revealed that HI1480 binds DNA and RNA molecules. Double-stranded DNA is favored over single-stranded DNA, and longer DNA molecules are bound better than shorter ones.

Highly UV-absorbing complex in selenomethionine-substituted alcohol dehydrogenase from Sulfolobus solfataricus

The aim of this work was to explain the previously discovered effect of significant decrease in intrinsic fluorescence intensity of SsADH caused by replacement of S atoms of methionine residues to Se (Giordano, A.; Raia, C. A. J. Fluorescence 2003, 13, 17-24) on the basis of the analysis of its 3D structure. It was found that all selenium atoms are located far from both Trp95 and Trp117 and could not cause their fluorescence quenching. At the same time, it was determined that substitution of S by Se causes enhanced protein absorption in the UV-region. This effect was explained by the formation of Se complex with some groups of protein. It was revealed that this complex does not participate in fluorescence and does not transfer excitation energy to tryptophan or tyrosine residues.

Isotope and elemental effects indicate a rate-limiting methyl transfer as the initial step in the reaction catalyzed by Escherichia coli cyclopropane fatty acid synthase

Cyclopropane fatty acid (CFA) synthases catalyze the formation of cyclopropane rings on unsaturated fatty acids (UFAs) that are natural components of membrane phospholipids. The methylene carbon of the cyclopropane ring derives from the activated methyl group of S-adenosyl-L-methionine (AdoMet), affording S-adenosyl-L-homocysteine (AdoHcys) and a proton as the remaining products. This reaction is unique among AdoMet-dependent enzymes, because the olefin of the UFA substrate is isolated and unactivated toward nucleophilic or electrophilic addition, raising the question as to the timing and mechanism of proton loss from the activated methyl group of AdoMet. Two distinct reaction schemes have been proposed for this transformation; however, neither was based on detailed in vitro mechanistic analysis of the enzyme. In the preceding paper [Iwig, D. F. and Booker, S. J. (2004) Biochemistry 43, http://dx.doi.org/10.1021/bi048693+], we described the synthesis of two analogues of AdoMet, Se-adenosyl-L-selenomethionine (SeAdoMet) and Te-adenosyl-L-telluromethionine (TeAdoMet), and their intrinsic reactivity toward polar chemistry in which AdoMet is known to be involved. We found that the electrophilicity of AdoMet and its onium congeners followed the series SeAdoMet > AdoMet > TeAdoMet, while the acidity of the carbons adjacent to the relevant heteroatom followed the series AdoMet > SeAdoMet > TeAdoMet. When each of these compounds was used as the methylene donor in the CFA synthase reaction, the kinetic parameters of the reaction, k(cat) and k(cat) K(M)(-1), followed the series SeAdoMet > AdoMet > TeAdoMet, suggesting that the reaction takes place via methyl transfer followed by proton loss, rather than by processes that are initiated by proton abstraction from AdoMet. Use of S-adenosyl-L-[methyl-d(3)]methionine as the methylene donor resulted in an inverse isotope effect of 0.87 +/- 0.083, supporting this conclusion and also indicating that the methyl transfer takes place via a tight s(N)2 transition state.

Crystallization and preliminary X-ray diffraction analysis of bacteriophage ϕ12 packaging factor P7

Bacteriophage varphi12 protein P7 is a structural component of the polymerase complex and ensures stable packaging of the genomic RNA. varphi12 P7 has been cloned, purified and crystallized. Crystals belong to space group P3(2)21, with unit-cell parameters a = 75.7, b = 75.7, c = 45.2 A, alpha = 90, beta = 90, gamma = 120 degrees , and diffract beyond 2.0 A. Multiple anomalous dispersion data have been collected from crystals of selenomethionylated P7. Mass spectroscopy showed proteolysis of the crystallized protein and a truncated form, P7DeltaC, gave crystals of similar morphology. Cross-linking experiments implicated the N-terminal domain of P7 as being essential for dimerization.

L-Methioninium chloride andL-selenomethioninium chloride at 103 K

The crystal structures of the title compounds, (S)-1-carboxy-3-(methylsulfanyl)propanaminium chloride, C(5)H(12)NO(2)S(+).Cl(-), and (S)-1-carboxy-3-(methylselanyl)propanaminium chloride, C(5)H(12)NO(2)Se(+).Cl(-), are isomorphous. The protonated L-methionine and L-selenomethionine molecules have almost identical conformations and create very similar contacts with the Cl(-) anions in the crystal structures of both compounds. The amino acid cations and the Cl(-) anions are linked viaN-H...Cl(-) and O-H...Cl(-) hydrogen bonds.

Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes

dCTP deaminase (EC 3.5.4.13) catalyzes the deamination of dCTP forming dUTP that via dUTPase is the main pathway providing substrate for thymidylate synthase in Escherichia coli and Salmonella typhimurium. dCTP deaminase is unique among nucleoside and nucleotide deaminases as it functions without aid from a catalytic metal ion that facilitates preparation of a water molecule for nucleophilic attack on the substrate. Two active site amino acid residues, Arg(115) and Glu(138), were identified by mutational analysis as important for activity in E. coli dCTP deaminase. None of the mutant enzymes R115A, E138A, or E138Q had any detectable activity but circular dichroism spectra for all mutant enzymes were similar to wild type suggesting that the overall structure was not changed. The crystal structures of wild-type E. coli dCTP deaminase and the E138A mutant enzyme have been determined in complex with dUTP and Mg(2+), and the mutant enzyme also with the substrate dCTP and Mg(2+). The enzyme is a third member of the family of the structurally related trimeric dUTPases and the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii. However, the C-terminal fold is completely different from dUTPases resulting in an active site built from residues from two of the trimer subunits, and not from three subunits as in dUTPases. The nucleotides are well defined as well as Mg(2+) that is tridentately coordinated to the nucleotide phosphate chains. We suggest a catalytic mechanism for the dCTP deaminase and identify structural differences to dUTPases that prevent hydrolysis of the dCTP triphosphate.

The crystal structure of the herpes simplex virus 1 ssDNA-binding protein suggests the structural basis for flexible, cooperative single-stranded DNA binding

All organisms including animal viruses use specific proteins to bind single-stranded DNA rapidly in a non-sequence-specific, flexible, and cooperative manner during the DNA replication process. The crystal structure of a 60-residue C-terminal deletion construct of ICP8, the major single-stranded DNA-binding protein from herpes simplex virus-1, was determined at 3.0 A resolution. The structure reveals a novel fold, consisting of a large N-terminal domain (residues 9-1038) and a small C-terminal domain (residues 1049-1129). On the basis of the structure and the nearest neighbor interactions in the crystal, we have presented a model describing the site of single-stranded DNA binding and explaining the basis for cooperative binding. This model agrees with the beaded morphology observed in electron micrographs.

Structural analysis of Escherichia coli OpgG, a protein required for the biosynthesis of osmoregulated periplasmic glucans

Osmoregulated periplasmic glucans (OPGs) G protein (OpgG) is required for OPGs biosynthesis. OPGs from Escherichia coli are branched glucans, with a backbone of beta-1,2 glucose units and with branches attached by beta-1,6 linkages. In Proteobacteria, OPGs are involved in osmoprotection, biofilm formation, virulence and resistance to antibiotics. Despite their important biological implications, enzymes synthesizing OPGs are poorly characterized. Here, we report the 2.5 A crystal structure of OpgG from E.coli. The structure was solved using a selenemethionine derivative of OpgG and the multiple anomalous diffraction method (MAD). The protein is composed of two beta-sandwich domains connected by one turn of 3(10) helix. The N-terminal domain (residues 22-388) displays a 25-stranded beta-sandwich fold found in several carbohydrate-related proteins. It exhibits a large cleft comprising many aromatic and acidic residues. This putative binding site shares some similarities with enzymes such as galactose mutarotase and glucodextranase, suggesting a potential catalytic role for this domain in OPG synthesis. On the other hand, the C-terminal domain (residues 401-512) has a seven-stranded immunoglobulin-like beta-sandwich fold, found in many proteins where it is mainly implicated in interactions with other molecules. The structural data suggest that OpgG is an OPG branching enzyme in which the catalytic activity is located in the large N-terminal domain and controlled via the smaller C-terminal domain.

Structure of the topoisomerase IV C-terminal domain: a broken beta-propeller implies a role as geometry facilitator in catalysis

Bacteria possess two closely related yet functionally distinct essential type IIA topoisomerases (Topos). DNA gyrase supports replication and transcription with its unique supercoiling activity, whereas Topo IV preferentially relaxes (+) supercoils and is a decatenating enzyme required for chromosome segregation. Here we report the crystal structure of the C-terminal domain of Topo IV ParC subunit (ParC-CTD) from Bacillus stearothermophilus and provide a structure-based explanation for how Topo IV and DNA gyrase execute distinct activities. Although the topological connectivity of ParC-CTD is similar to the recently determined CTD structure of DNA gyrase GyrA subunit (GyrA-CTD), ParC-CTD surprisingly folds as a previously unseen broken form of a six-bladed beta-propeller. Propeller breakage is due to the absence of a DNA gyrase-specific GyrA box motif, resulting in the reduction of curvature of the proposed DNA binding region, which explains why ParC-CTD is less efficient than GyrA-CTD in mediating DNA bending, a difference that leads to divergent activities of the two homologous enzymes. Moreover, we found that the topology of the propeller blades observed in ParC-CTD and GyrA-CTD can be achieved from a concerted beta-hairpin invasion-induced fold change event of a canonical six-bladed beta-propeller; hence, we proposed to name this new fold as "hairpin-invaded beta-propeller" to highlight the high degree of similarity and a potential evolutionary linkage between them. The possible role of ParC-CTD as a geometry facilitator during various catalytic events and the evolutionary relationships between prokaryotic type IIA Topos have also been discussed according to these new structural insights.

Structure of theThermus thermophilusputative periplasmic glutamate/glutamine-binding protein

As part of a structural genomics project, the crystal structure of a 314-amino-acid protein encoded by Thermus thermophilus HB8 gene TT1099 was solved to 1.75 A using the multiple-wavelength anomalous dispersion (MAD) method and a selenomethionine-incorporated protein. The native protein structure was solved to 1.5 A using the molecular-replacement method. Both structures revealed a bound ligand, L-glutamate or L-glutamine, and a fold related to the periplasmic substrate-binding proteins (PSBP). Further comparative structural analysis with other PSBP-fold proteins revealed the conservation of the predicted membrane permease binding surface area and indicated that the T. thermophilus HB8 molecule is most likely to be an L-glutamate and/or an L-glutamine-binding protein related to the cluster 3 periplasmic receptors. However, the geometry of ligand binding is unique to the T. thermophilus HB8 molecule.

Expression, purification and preliminary crystallographic analysis of dipeptidyl peptidase IV fromPorphyromonas gingivalis

The asaccharolytic periodontopathogen Porphyromonas gingivalis produces membrane-anchored proteases such as dipeptidyl peptidase IV that are involved in the destruction of host periodontal tissue. The extracellular domain of this enzyme was overexpressed in Escherichia coli as an N-terminal His-tag fusion protein, purified using standard metal-affinity chromatography and crystallized using the hanging-drop vapour-diffusion technique in 40% 2-methyl-2,4-pentanediol and 100 mM Tris-HCl pH 8.0. Diffraction data to 2.7 A resolution were collected using synchrotron radiation. The crystals belong to space group P2(1), with unit-cell parameters a = 117.0, b = 112.9, c = 310.0 A, beta = 95.0 degrees. There are ten molecules per asymmetric unit, indicating a solvent content of 50%. Data were also collected from selenomethionine-derived crystals and structure solution by SAD or MAD is in progress.

Crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaeonPyrococcus horikoshii

The leucyl-tRNA synthetase (LeuRS) from the archaeon Pyrococcus horikoshii was overexpressed in a C-terminally truncated form in Escherichia coli, purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as a precipitant. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = b = 186.20, c = 91.43 A, alpha = beta = 90, gamma = 120 degrees. The asymmetric unit contains one molecule of LeuRS, with a corresponding crystal volume per protein weight of 3.2 A3 Da(-1) and a solvent content of 60.7%. A data set diffracting to 2.2 A resolution was collected from a single crystal at 100 K. Selenomethionine-substituted protein crystals were prepared in order to solve the structure by the SAD phasing method.

A dimerized coiled-coil domain and an adjoining part of geminin interact with two sites on Cdt1 for replication inhibition

Geminin is a cellular protein that associates with Cdt1 and inhibits Mcm2-7 loading during S phase. It prevents multiple cycles of replication per cell cycle and prevents episome replication. It also directly inhibits the HoxA11 transcription factor. Here we report that geminin forms a parallel coiled-coil homodimer with atypical residues in the dimer interface. Point mutations that disrupt the dimerization abolish interaction with Cdt1 and inhibition of replication. An array of glutamic acid residues on the coiled-coil domain surface interacts with positive charges in the middle of Cdt1. An adjoining region interacts independently with the N-terminal 100 residues of Cdt1. Both interactions are essential for replication inhibition. The negative residues on the coiled-coil domain and a different part of geminin are also required for interaction with HoxA11. Therefore a rigid cylinder with negative surface charges is a critical component of a bipartite interaction interface between geminin and its cellular targets.

Selenomethionine and selenocysteine double labeling strategy for crystallographic phasing

A protocol for the quantitative incorporation of both selenomethionine and selenocysteine into recombinant proteins overexpressed in Escherichia coli is described. This methodology is based on the use of a suitable cysteine auxotrophic strain and a minimal medium supplemented with selenium-labeled methionine and cysteine. The proteins chosen for these studies are the cathelin-like motif of protegrin-3 and a nucleoside-diphosphate kinase. Analysis of the purified proteins by electrospray mass spectrometry and X-ray crystallography revealed that both cysteine and methionine residues were isomorphously replaced by selenocysteine and selenomethionine. Moreover, selenocysteines allowed the formation of unstrained and stable diselenide bridges in place of the canonical disulfide bonds. In addition, we showed that NDP kinase contains a selenocysteine adduct on Cys122. This novel selenium double-labeling method is proposed as a general approach to increase the efficiency of the MAD technique used for phase determination in protein crystallography.

X-ray structure analysis of a designed oligomeric miniprotein reveals a discrete quaternary architecture

The x-ray crystal structure of an oligomeric miniprotein has been determined to a 1.2-A resolution by means of multiwavelength anomalous diffraction phasing with selenomethionine analogs that retain the biophysical characteristics of the native peptide. Peptide 1, comprising alpha and beta secondary structure elements with only 21 aa per monomer, associates as a discrete tetramer. The peptide adopts a previously uncharacterized quaternary structure in which alpha and beta components interact to form a tightly packed and well defined hydrophobic core. The structure provides insight into the origins of the unusual thermal stability of the oligomer. The miniprotein shares many characteristics of larger proteins, including cooperative folding, lack of 1-anilino-8-naphthalene sulfonate binding, and limited deuterium exchange, and possesses a buried surface area typical of native proteins.

Temperature and cryoprotectant influence secondary quinone binding position in bacterial reaction centers

We have determined the first de novo position of the secondary quinone QB in the Rhodobacter sphaeroides reaction center (RC) using phases derived by the single wavelength anomalous dispersion method from crystals with selenomethionine substitution. We found that in frozen RC crystals, QB occupies primarily the proximal binding site. In contrast, our room temperature structure showed that QB is largely in the distal position. Both data sets were collected in dark-adapted conditions. We estimate that the occupancy of the QB site is 80% with a proximal: distal ratio of 4:1 in frozen RC crystals. We could not separate the effect of freezing from the effect of the cryoprotectants ethylene glycol or glycerol. These results could have far-reaching implications in structure/function studies of electron transfer in the acceptor quinone complex because the above are the most commonly used cryoprotectants in spectroscopic experiments.

The family 11 carbohydrate-binding module of Clostridium thermocellum Lic26A-Cel5E accommodates beta-1,4- and beta-1,3-1,4-mixed linked glucans at a single binding site

Modular glycoside hydrolases that attack recalcitrant polymers generally contain noncatalytic carbohydrate-binding modules (CBMs), which play a critical role in the action of these enzymes by localizing the appended catalytic domains onto the surface of insoluble polysaccharide substrates. Type B CBMs, which recognize single polysaccharide chains, display ligand specificities that are consistent with the substrates hydrolyzed by the associated catalytic domains. In enzymes that contain multiple catalytic domains with distinct substrate specificities, it is unclear how these different activities influence the evolution of the ligand recognition profile of the appended CBM. To address this issue, we have characterized the properties of a family 11 CBM (CtCBM11) in Clostridium thermocellum Lic26A-Cel5E, an enzyme that contains GH5 and GH26 catalytic domains that display beta-1,4- and beta-1,3-1,4-mixed linked endoglucanase activity, respectively. Here we show that CtCBM11 binds to both beta-1,4- and beta-1,3-1,4-mixed linked glucans, displaying K(a) values of 1.9 x 10(5), 4.4 x 10(4), and 2 x 10(3) m(-1) for Glc-beta1,4-Glc-beta1,4-Glc-beta1,3-Glc, Glc-beta1,4-Glc-beta1,4-Glc-beta1,4-Glc, and Glc-beta1,3-Glc-beta1,4-Glc-beta1,3-Glc, respectively, demonstrating that CBMs can display a preference for mixed linked glucans. To determine whether these ligands are accommodated in the same or diverse sites in CtCBM11, the crystal structure of the protein was solved to a resolution of 1.98 A. The protein displays a beta-sandwich with a concave side that forms a potential binding cleft. Site-directed mutagenesis revealed that Tyr(22), Tyr(53), and Tyr(129), located in the putative binding cleft, play a central role in the recognition of all the ligands recognized by the protein. We propose, therefore, that CtCBM11 contains a single ligand-binding site that displays affinity for both beta-1,4- and beta-1,3-1,4-mixed linked glucans.

Structure of the molybdenum-cofactor biosynthesis protein MoaB of Escherichia coli

The moaABC operon of Escherichia coli is involved in early steps of the biosynthesis of the molybdenum-binding cofactor molybdopterin, but the precise functions of the cognate proteins are not known. The crystal structure of the MoaB protein from E. coli was determined by multiple anomalous dispersion at 2.1 angstroms A resolution and refined to an R factor of 20.4% (Rfree = 25.0%). The protein is a 32-symmetric hexamer, with the monomers consisting of a central beta-sheet flanked by helices on both sides. The overall fold of the monomer is similar to those of the MogA protein of E. coli, the G-domains of rat and human gephyrin and the G-domains of Cnx1 protein from A. thaliana, all of which are involved in the insertion of an unknown molybdenum species into molybdopterin to form the molybdenum cofactor. Furthermore, the MoaB protein shows significant sequence similarity to the cinnamon protein from Drosophila melanogaster. In addition to other functions, all these proteins are involved in the biosynthesis of the molybdenum cofactor and have been shown to bind molybdopterin. The close structural homology to MogA and the gephyrin and Cnx1 domains suggests that MoaB may bind a hitherto unidentified pterin compound, possibly an intermediate in molybdopterin biosynthesis.

Crystallization and preliminary X-ray analysis of α-isopropylmalate synthase fromMycobacterium tuberculosis

alpha-Isopropylmalate synthase catalyses the aldol condensation of alpha-ketoisovalerate and acetyl coenzyme A to produce alpha-isopropylmalate. This reaction is the first committed step of leucine biosynthesis, which is interrelated with the pathways for production of the other branched-chain amino acids, valine and isoleucine. The absence of these pathways in mammals suggests that these enzymes could be useful targets for drug design against microbial pathogens. The gene for alpha-IPMS in Mycobacterium tuberculosis (Rv3710) has been cloned, expressed in Escherichia coli, both in native and selenomethionine-substituted forms, and crystallized. The SeMet crystals are suitable for high-resolution X-ray structural analysis. These crystals are monoclinic, with unit-cell parameters a = 54.25, b = 154.73, c = 68.82 angstoms, space group P2(1) and two molecules in the asymmetric unit. X-ray diffraction data to 2.0 angstroms resolution have been collected.

Structure determination of the extracellular xylanase from Geobacillus stearothermophilus by selenomethionyl MAD phasing

Xylanases are hemicellulases that hydrolyze the internal beta-1,4-glycoside bonds of xylan. The extracellular thermostable endo-1,4-beta-xylanase (EC 3.2.1.8; XT6) produced by the thermophilic bacterium Geobacillus stearothermophilus T-6 was shown to bleach pulp optimally at pH 9 and 338 K and was successfully used in a large-scale biobleaching mill trial. The xylanase gene was cloned and sequenced. The mature enzyme consists of 379 amino acids, with a calculated molecular weight of 43 808 Da and a pI of 9.0. Crystallographic studies of XT6 were performed in order to study the mechanism of catalysis and to provide a structural basis for the rational introduction of enhanced thermostability by site-specific mutagenesis. XT6 was crystallized in the primitive trigonal space group P3(2)21, with unit-cell parameters a = b = 112.9, c = 122.7 A. A full diffraction data set for wild-type XT6 has been measured to 2.4 A resolution on flash-frozen crystals using synchrotron radiation. A fully exchanged selenomethionyl XT6 derivative (containing eight Se atoms per XT6 molecule) was also prepared and crystallized in an isomorphous crystal form, providing full selenium MAD data at three wavelengths and enabling phase solution and structure determination. The structure of wild-type XT6 was refined at 2.4 A resolution to a final R factor of 15.6% and an R(free) of 18.6%. The structure demonstrates that XT6 is made up of an eightfold TIM-barrel containing a deep active-site groove, consistent with its 'endo' mode of action. The two essential catalytic carboxylic residues (Glu159 and Glu265) are located at the active site within 5.5 A of each other, as expected for 'retaining' glycoside hydrolases. A unique subdomain was identified in the carboxy-terminal part of the enzyme and was suggested to have a role in xylan binding. The three-dimensional structure of XT6 is of great interest since it provides a favourable starting point for the rational improvement of its already high thermal and pH stabilities, which are required for a number of biotechnological and industrial applications.

Crystallization and preliminary crystallographic analysis of BbCRASP-1, a complement regulator-acquiring surface protein ofBorrelia burgdorferi

Borrelia burgdorferi is the causative agent of Lyme disease. Serum-resistant strains of the pathogen are able to reduce the host's immune response to infection by recruiting fluid-phase complement regulators from the serum. B. burgdorferi complement regulator-acquiring surface protein-1 (BbCRASP-1) binds factor H and factor-H-like protein-1 to the bacterial surface, where they actively down-regulate complement response. Crystals of native and selenomethionine-substituted BbCRASP-1 have been obtained and a native data set to 2.7 A as well as selenomethionine MAD data to 3.2 A resolution have been collected. The selenium substructure has been solved and initial phases have been refined to 3.0 A by density-modification methods. Model building and refinement are under way.

Crystallization and preliminary analysis of xenobiotic reductase A and ligand complexes fromPseudomonas putidaII-B

Diffraction-quality crystals have been obtained of the xenobiotic reductase A (XenA) from Pseudomonas II-B, which was originally cultured from the contaminated soil of a World War II era munitions-manufacturing plant. Several complete X-ray diffraction data sets have been collected and analyzed. The native XenA data set includes reflections between 35 and 1.65 A. Four-wavelength MAD data sets from selenomethionine-enriched XenA and from three different ligand complexes are also reported. The XenA crystals belong to space group P2(1)2(1)2, with unit-cell parameters a = 84, b = 158, c = 57 A. Experimental phasing from analysis of the MAD data from selenomethionine-enriched XenA reveals the presence of two molecules in the asymmetric unit. They are related by a non-crystallographic 2(1) screw axis nearly parallel to the c axis, but offset by a quarter unit-cell translation. Thus, the local symmetry produces approximate systematic absences along the (00l) principal axis and complicates the space-group determination.

Sulfur and selenium: the role of oxidation state in protein structure and function

Sulfur and selenium occur in proteins as constituents of the amino acids cysteine, methionine, selenocysteine, and selenomethionine. Recent research underscores that these amino acids are truly exceptional. Their redox activity under physiological conditions allows an amazing variety of posttranslational protein modifications, metal free redox pathways, and unusual chalcogen redox states that increasingly attract the attention of biological chemists. Unlike any other amino acid, the "redox chameleon" cysteine can participate in several distinct redox pathways, including exchange and radical reactions, as well as atom-, electron-, and hydride-transfer reactions. It occurs in various oxidation states in the human body, each of which exhibits distinctive chemical properties (e.g. redox activity, metal binding) and biological activity. The position of selenium in the periodic table between the metals and the nonmetals makes selenoproteins ideal catalysts for many biological redox transformations. It is therefore apparent that the chalcogen amino acids cysteine, methionine, selenocysteine, and selenomethionine exhibit a unique biological chemistry that is the source of exciting research opportunities.

Determination of the absolute configuration of selenomethionine from antarctic krill by RP-HPLC/ICP-MS using chiral derivatization agents

A fast and sensitive method was developed for the determination of the absolute configuration of selenomethionine. The enantiomers of selenomethionine were converted into diastereomeric isoindole derivatives by reaction with o-phthaldialdehyde and N-isobutyryl-L-cysteine. This easy-to-handle reaction proceeds quantitatively in a few minutes at room temperature. Separation and detection of the diastereomers was achieved by reversed-phase high-performance liquid chromatography-inductively coupled plasma-mass spectrometry (RP-HPLC/ICP-MS) using a conventional C18 reversed-phase column. Detection limits of about 4 microg L(-1) were obtained. The method was applied to the determination of the configuration of selenomethionine extracted from antarctic krill, which turned out to possess the L-configuration.

Selenomethionine contents of NIST wheat reference materials

Values of the total selenium and selenomethionine (Semet) content of four wheat-based reference materials have been obtained by gas chromatography-stable isotope dilution mass spectrometry methods. The total Se method is an established one, and the results obtained with it are consistent with previously-assigned values. The Semet method (previously reported by our laboratory) is based on reaction with CNBr. Our data indicate that the four wheat samples (wheat gluten, durum wheat, hard red spring wheat, and soft winter wheat), though having a 30-fold range in total Se content, all have about 45% of their total Se values in the form of selenomethionine. Investigation of the CNBr-based method suggests that additional experiments are needed to verify that all selenomethionine in the wheat samples is accounted for, but also indicates that the values obtained are within 15% of the true values. As the form in which Se occurs in foods and dietary supplements is important from a nutritional perspective, adding information about Se speciation to total Se values in appropriate reference materials makes these materials more valuable in relevant analytical work.

Crystallization and preliminary X-ray analysis of family 39 β-D-xylosidase fromGeobacillus stearothermophilusT-6

beta-D-Xylosidases (EC 3.2.1.37) are hemicellulases that hydrolyze short xylooligosaccharides into single xylose units. In this study, the crystallization and preliminary X-ray analysis of the beta-D-xylosidase (XynB1) from Geobacillus stearothermophilus T-6, a family 39 glycoside hydrolase, are described. XynB1 is a tetrameric protein consisting of four identical subunits of 503 amino acids and with a calculated molecular weight of 58 001 Da. Both the native and the selenomethionine-containing XynB1 were crystallized by the hanging-drop vapour-diffusion method and the crystals were found to belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 92.7, b = 165.7, c = 311.0 A. The native crystals diffracted X-rays to a resolution of 2.1 A.

Expression and crystallization of several forms of the Propionibacterium shermanii transcarboxylase 5S subunit

The dimeric outer 5S subunit of transcarboxylase has been expressed in three different forms and crystallized: native 5S, 5S-His(6) and selenomethione-5S-His(6). All the crystals have an orthorhombic space group, but while native 5S forms primitive orthorhombic crystals, 5S-His(6) crystals are either C-centered or primitive and SeMet-5S-His(6) crystals are C-centered. Crystallization of native 5S requires the addition of lithium sulfate, whereas this salt prevented crystallization of 5S-His(6). All 5S crystals diffract to approximately 2.0 A resolution with synchrotron radiation. Efforts are under way to solve the structure of SeMet-5S-His(6) using MAD.

Purification, crystallization and preliminary X-ray analysis of native and selenomethionine class I tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes

Tagatose-1,6-bisphosphate aldolase (EC 4.1.2.40) is situated at the branching of the tagatose-6-phosphate and Embden-Meyerhof-Parnas (glycolysis) metabolic pathways, where it catalyzes the reversible cleavage of tagatose-1,6-bisphosphate to dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. The recombinant protein from Streptococcus pyogenes was overexpressed in Escherichia coli in its native and selenomethionine-derivative forms and purified using ion-exchange and hydrophobic interaction chromatography. Orthorhombic crystals suitable for structural analysis were obtained by the hanging-drop vapour-diffusion method for both isoforms. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 63.7, b = 108.1, c = 238.7 A for the native form and a = 64.1, b = 108.3, c = 239.8 A for the selenomethionine derivative. The asymmetric unit contains four protomers, corresponding to a crystal volume per protein weight (V(M)) of 2.8 A(3) Da(-1) and a solvent content of 56% by volume.

Production, crystallization and preliminary X-ray crystallographic studies of the bacteriophage phi 12 packaging motor

The hexameric ATPase P4 from bacteriophage phi 12 is responsible for packaging single-stranded genomic precursors into the viral procapsid. P4 was overexpressed in Escherichia coli and purified. Crystals of native and selenomethionine-derivatized P4 have been obtained that belong to space group I222, with half a hexamer in the asymmetric unit and unit-cell parameters a = 105.0, b = 130.5, c = 158.9 A. A second crystal form of different morphology can occur in the same crystallization drop. The second form belongs to space group P1, with four hexamers in the asymmetric unit and unit-cell parameters a = 114.9, b = 125.6, c = 153.9 A, alpha = 90.1, beta = 91.6, gamma = 90.4 degrees. Synchrotron X-ray diffraction data have been collected for the I222 and P1 crystal forms to 2.0 and 2.5 A resolution, respectively.

Crystallization and preliminary crystallographic analysis of Mycoplasma arthritidis-derived mitogen complexed with peptide/MHC class II antigen

Mycoplasma arthritidis-derived mitogen (MAM), a bacterial superantigen, has been crystallized in complex with its human receptor, major histocompatibility complex (MHC) class II antigen, by the hanging-drop vapor-diffusion method. Crystals were obtained under three conditions, with ammonium sulfate, phosphate salt and PEG 8000 as the precipitant. The crystals grown under these conditions all belong to space group I222, with the same unit-cell parameters: a = 137.4, b = 178.2, c = 179.6 A. Diffraction data were collected to 3.3 and 3.4 A resolution from crystals of native and selenomethionylated MAM-MHC complexes, respectively. Self- and cross-rotation function calculations suggest the presence of two complex molecules in the asymmetric unit, resulting in a V(M) of 4.0 and a solvent content of 69%. An interpretable electron-density map was produced using a combination of molecular replacement and SAD phasing.

Identification and characterization of Se-methyl selenomethionine in Brassica juncea roots

The present work shows the identification and characterization of Se-methyl selenomethionine (SeMMet) as an important Se species in Brassica juncea roots when grown in the presence of Se-methionine (SeMet) as the Se source. SeMMet was isolated by liquid chromatography employing two different liquid chromatographic mechanisms: reversed-phase ion-pairing using heptafluorobutyric acid as counter ion and cation exchange using a pyridinium formate gradient (pH 3). Inductively coupled plasma mass spectrometry was used for the detection of Se. SeMMet was characterized by electrospray quadrupole time-of-flight MS in both a synthesized standard and in the roots extract using collision-induced dissociation of the selected ion. Preliminary evidence suggests that Brassica juncea may also produce dimethylselenonium propionate, although to a much lesser extent.

Crystallization and preliminary X-ray analysis of the controller protein C.AhdI from Aeromonas hydrophilia

Single crystals of purified homodimeric controller protein from Aeromonas hydrophilia (C.AhdI) have been grown under several different conditions using vapour diffusion. X-ray diffraction data have been collected using synchrotron radiation from crystals of both the native and a selenomethionine (SeMet) derivative of the protein. The native crystal form belongs to space group P2(1) and data were collected to a resolution of 2.2 A. Two crystal forms of the SeMet protein have been obtained and were found to belong to space groups P1 and P2(1); data have been recorded to 2.0 and 1.7 A resolution, respectively, for the two crystal forms. Three-wavelength MAD data were collected to 1.7 A for the SeMet derivative crystal, which is isomorphous with the native P2(1) crystal.

Crystallization and preliminary X-ray diffraction studies of the quorum-sensing regulator TraM fromAgrobacterium tumefaciens

TraM is a 11.4 kDa protein involved in the control of the conjugal transfer of Agrobacterium tumefaciens Ti plasmids by quorum-sensing. TraM was overexpressed and purified from Escherichia coli. This protein binds to the transcriptional regulator TraR, abolishing its function. Size-exclusion chromatography and dynamic light scattering show that the recombinant protein has an apparent molecular weight of 30 kDa in solution. Crystals have been obtained of both native and selenomethionine-substituted TraM by the vapour-diffusion method. Crystals diffract to 1.67 A and belong to the space group P2(1)2(1)2, with unit-cell parameters a = 76.43, b = 47.09, c = 47.46 A and two molecules in the asymmetric unit. A two-wavelength MAD data set for the selenomethionine-substituted form has been collected to a resolution of 2.0 A. The selenium substructure (five out of six possible sites) has been solved using direct methods.

Multiple methionine substitutions are tolerated in T4 lysozyme and have coupled effects on folding and stability

In order to further explore the tolerance of proteins to amino acid substitutions within the interior, a series of core residues was replaced by methionine within the C-terminal domain of T4 lysozyme. By replacing leucine, isoleucine, valine and phenylalanine residues a total of 10 methionines could be introduced, which corresponds to a third of the residues that are buried in this domain. As more methionines are incorporated the protein gradually loses stability. This is attributed in part to a reduction in hydrophobic stabilization, in part to the increased entropic cost of localizing the long, flexible methionine sidechains, and in part to steric clashes. The changes in structure of the mutants relative to the wildtype protein are modest but tend to increase in an additive fashion as more methionines are included. In the most extreme case, namely the 10-methionine mutant, much of the C-terminal domain remains quite similar to wildtype (root-mean-square backbone shifts of 0.56 A), while the F and G helices undergo rotations of approximately 20 degrees and center-of-mass shifts of approximately 1.4 A. For up to six methionine substitutions the changes in stability are additive. Beyond this point, however, the multiple mutants are somewhat more stable than suggested from the sum of their constituents, especially for those including the replacement Val111-->Met. This is interpreted in terms of the larger structural changes associated with this substitution. The substituted sidechains in the mutant structures have somewhat higher crystallographic thermal factors than their counterparts in WT*. Nevertheless, the interiors of the mutant proteins retain a well-defined structure with little suggestion of molten-globule characteristics. Lysozymes in which selenomethionine has been incorporated rather than methionine tend to have increased stability. At the same time they also fold faster. This provides further evidence that, at the rate-limiting step in folding, the structure of the C-terminal domain of T4 lysozyme is similar to that of the fully folded protein.

Molecules of Escherichia coli MobB assemble into densely packed hollow cylinders in a crystal lattice with 75% solvent content

The crystal structure of Escherichia coli MobB, an enzyme involved in the final step of molybdenum-cofactor biosynthesis, forms intertwined dimers. Each molecule consists of two segments and requires the second monomer for stable folding. Dimerization buries a quarter of the solvent-accessible area of the monomer. These dimers assemble into a hexagonal lattice with P6(4)22 symmetry and occupy only approximately 25% of the unit-cell volume. The symmetry-related dimers associate tightly into a helical structure with a diameter of 250 A and a pitch of 98 A. Two such helices are intertwined, shifted by 49 A along the sixfold axis. Within the crystal, these helices form thin-walled cylinders with an external diameter of 250 A and an internal diameter of 190 A. Their center is filled with solvent. These cylinders pack closely together, forming a hexagonal lattice with the highest possible packing density. This arrangement of dimers allows extensive intermolecular contacts with 75% solvent content in the crystal.

Crystallization and preliminary X-ray analysis of the glycogen synthase fromPyrococcus abyssi

Glycogen synthase catalyzes the transfer of glucosyl residues from ADP- or UDP-glucose to the non-reducing end of a growing alpha-1,4-glucan chain. To date, no crystallographic structure of an animal/fungal glycogen synthase (family 3 of the glycosyl transferases) or a bacterial/plant glycogen/starch synthase (family 5) has been reported. This paper describes the recombinant expression, crystallization and preliminary X-ray analysis of the glycogen synthase from the hyperthermophilic archaeon Pyrococcus abyssi, the smallest enzyme of the members of families 3 and 5 of the glycosyl transferases. Crystals from this protein and from its selenomethionyl variant were grown in 100 mM sodium citrate pH 5.6 containing 20% PEG and 20% dioxane by the hanging-drop vapour-diffusion method at 293 K. The crystals, which grew as thin needles, diffracted to 3.5 A resolution and belong to space group C2, with unit-cell parameters a = 202, b = 73, c = 149 A, beta = 131 degrees. The crystallographic and biochemical data are consistent with either a dimer or a tetramer in the crystal asymmetric unit and a volume solvent content of 70 or 39%, respectively.

Crystallization of RusA Holliday junction resolvase from Escherichia coli

Crystals of the Escherichia coli Holliday junction resolvase RusA have been obtained using the hanging-drop method and characterized. The crystals have a primitive monoclinic form and belong to space group P2(1). The V(M) value suggests the presence of two copies of the monomer in the asymmetric unit. A full three-wavelength MAD data collection on a selenomethionine-incorporated form has been undertaken and structure determination is under way using data collected to 2.1 A resolution.

Crystallization and preliminary crystallographic characterization of an SH3 domain from the IB1 scaffold protein

IB1 is a mammalian scaffold protein that interacts with components of the c-Jun N-terminal kinase (JNK) signal-transduction pathway mainly via its protein-protein interaction domains. Crystallization of the key Src homology 3 (SH3) domain of IB1 has been achieved. Crystallization experiments with unmodified protein and deliberately oxidized protein have led to different crystal forms. X-ray data have been collected to 3.0 A resolution from a crystal form with rectangular prism morphology. These crystals are orthorhombic (P2(1)2(1)2(1)), with unit-cell parameters a = 45.9, b = 57.0, c = 145.5 A. These are the first crystallographic data on a scaffold molecule such as IB1 to be reported.

Crystallization and preliminary crystallographic studies of the C-terminal domain of human FKBP52

FKBP52 is a high-molecular-weight immunophilin belonging to the FKBP (FK506-binding protein) family. FKBP52 is one of several chaperone proteins associated with untransformed steroid receptors in steroid receptor-hsp90 heterocomplexes. Here, the C-terminal domain (amino acids 145-459) has been cloned, overexpressed and purified. Crystals were obtained using the hanging-drop vapour-diffusion technique with ammonium sulfate as precipitant in 0.1 M Tris pH 8.0 solution. Diffraction data to 2.7 A were collected from a selenomethionine-containing crystal belonging to space group C222(1), with unit-cell parameters a = 114.4, b = 143.1, c = 171.2 A, alpha = beta = gamma = 90 degrees. There are three molecules per asymmetric unit.

Expression, crystallization and preliminary X-ray crystallographic studies ofArthrobacter globiformisinulin fructotransferase

A recombinant form of Arthrobacter globiformis inulin fructotransferase (DFAIII-producing) has been overexpressed in Escherichia coli and purified to homogeneity. Crystals were obtained at 293 K by the hanging-drop vapour-diffusion technique using 0.1 M Na HEPES pH 7.5 buffer containing 1.5 M lithium sulfate as a precipitant. Crystals of the recombinant wild-type enzyme diffracted to better than 1.5 A at 100 K using a synchrotron-radiation source at the Photon Factory. The crystal belonged to space group R32, with unit-cell parameters a = b = 92.02, c = 229.82 A in the hexagonal axes. Assuming the presence of one molecule in the asymmetric unit, the V(M) value for the crystal was 2.15 A(3) Da(-1), indicating a solvent content of 42.8%. Selenomethionine-derivative crystals belonged to a different space group, C2, with unit-cell parameters a = 159.32, b = 91.92, c = 92.58 A, beta = 125.06. Matthews coefficient calculations suggested that the C2 selenomethionine-derivative crystal contained three molecules per asymmetric unit.

Crystallization and preliminary X-ray analysis ofN-acetyl-1-D-myo-inosityl-2-deoxy-α-D-glucopyranoside deacetylase (MshB) fromMycobacterium tuberculosis

Mycobacteria synthesize mycothiol (MSH) as a low-molecular-weight thiol that protects against oxidative stress in a similar role to that of glutathione in many other species. The absence of MSH in mammals suggests that enzymes from its biosynthetic pathway in Mycobacterium tuberculosis could be useful targets for drug design. The gene for MshB (Rv1170), the enzyme that catalyses the second step in MSH biosynthesis in M. tuberculosis, has been cloned and the protein has been expressed in Escherichia coli both in native and SeMet-substituted forms and crystallized in two crystal forms. One of these, prepared in the presence of beta-octylglucoside as a key additive, is suitable for high-resolution X-ray structural analysis. The crystals are orthorhombic, with unit-cell parameters a = 71.69, b = 83.74, c = 95.65 A, space group P2(1)2(1)2(1) and two molecules in the asymmetric unit. X-ray diffraction data to 1.9 A resolution have been collected.

Purification, crystallization and preliminary X-ray diffraction analysis ofS-formylglutathione hydrolase fromArabidopsis thaliana: effects of pressure and selenomethionine substitution on space-group changes

S-Formylglutathione hydrolase (SFGH) has activity toward several xenobiotic carboxyesters and catalyses the final step of formaldehyde detoxification: the hydrolysis of S-formylglutathione to formate and glutathione. The Arabidopsis thaliana enzyme (AtSFGH) was crystallized in space group C2, with unit-cell parameters a = 128.5, b = 81.1, c = 94.3 A, beta = 93.3 degrees and three molecules in the asymmetric unit. A second crystal form of AtSFGH could be obtained by pressurizing the monoclinic crystals at 2 MPa for 30 min. The resulting space group is either P3(1)21 or P3(2)21, with unit-cell parameters a = 75.1, c = 92.8 A and one molecule in the asymmetric unit. Crystallographic data have been collected for both crystal forms to resolutions of 1.7 A for the monoclinic crystal and 1.6 A for the trigonal crystal. The structure has been solved by MAD phasing using a three-wavelength data set collected from a monoclinic crystal of selenomethionine-labelled AtSFGH.

Crystallization and preliminary X-ray analysis of the small component of 4-hydroxyphenylacetate 3-monooxygenase (HpaC) and its cofactor complex fromThermus thermophilusHB8

The small component of 4-hydroxyphenylacetate 3-monooxygenase (HpaC) is an NADH oxidoreductase containing a flavin molecule as a cofactor. HpaC reduces a flavin molecule and reduced flavin is subsequently supplied to the large component of 4-hydroxyphenylacetate 3-monooxygenase (HpaB). The HpaC protein from Thermus thermophilus HB8 has been overexpressed in Escherichia coli and crystallized. During purification, the eluted HpaC protein solutions were separated into colourless and yellow-coloured fractions (i.e. apo-HpaC and HpaC-flavin complex, respectively). Crystals of apo-HpaC grown in 5%(v/v) isopropyl alcohol, 0.1 M HEPES-NaOH pH 7.0, 40%(w/v) polyethylene glycol (PEG) 4000 and 10%(v/v) glycerol diffracted X-rays to a resolution of 1.85 A, whereas crystals of the HpaC-flavin complex grown in 20%(w/v) PEG 1000, 10%(w/v) PEG 8000 and 10%(v/v) glycerol diffracted X-rays to a resolution of 1.3 A. Both crystals belong to the monoclinic system, space group P2(1), with similar unit-cell parameters. Selenomethionyl protein crystals of the HpaC-flavin complex grown under similar conditions to the native crystals diffracted X-rays to a resolution of 1.8 A. They also belong to the monoclinic space group P2(1), but are not isomorphous to crystals of the HpaC-flavin complex of the native protein. MAD data for structure determination were successfully collected using these crystals.

Selling candles in a post-Edison world: phasing with noble gases bound within engineered sites

The utility of noble gases for phase determination has been limited by the lack of naturally occurring binding sites in proteins. Wild-type T4 lysozyme contains one such binding site. By mutating large hydrophobic residues to alanine, additional noble-gas binding sites have been successfully introduced into this protein. Using data from xenon derivatives of the wild type, two single mutants and the corresponding double mutant, experimental phases for T4 lysozyme have been determined using standard multiple isomorphous replacement (MIR) techniques. These phases, which were obtained from room-temperature data collected on a rotating-anode source, are comparable in quality with phases calculated using selenomethionine-based multiwavelength anomalous dispersion (MAD) methods on frozen crystals at a synchrotron. In addition, this method of introducing noble-gas binding sites near specific residues should provide useful information for determining the register of amino acids within electron-density maps and the positions of molecules within the unit cell.

Purification and crystallization of Escherichia coli pseudouridine synthase RluD

RluD is the pseudouridine (Psi) synthase responsible for forming Psi1911, Psi1915 and Psi1917 in Escherichia coli 23S RNA. Out of the 11 Psi synthases in E. coli, only cells lacking RluD show a severe growth defect. In addition, RluD belongs to the RluA family of Psi synthases, one of the two remaining families without a representative crystal structure. In this paper, the crystallization of selenomethionine-substituted RluD by the hanging-drop method is reported. The crystals diffract to 1.9 A and belong to space group P4(3)2(1)2, with unit-cell parameters a = b = 75.14, c = 181.81 A. Synchrotron radiation was used on a single crystal to collect a complete multiwavelength anomalous dispersion (MAD) data set to 2.0 A resolution.

Purification, crystallization and preliminary crystallographic analysis of phosphoglucose isomerase from the hyperthermophilic archaeonPyrococcus furiosus

The glycolytic enzyme phosphoglucose isomerase catalyses the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus, which shows no sequence similarity to any known bacterial or eukaryotic phosphoglucose isomerase, has been cloned and overexpressed in Escherichia coli, purified and subsequently crystallized by the hanging-drop method of vapour diffusion using 1.6 M sodium citrate as the precipitant at pH 6.5. Multiple-wavelength anomalous dispersive X-ray data have been collected to a maximum resolution of 1.92 A on a single selenomethionine-incorporated crystal. This crystal belongs to space group C2, with approximate unit-cell parameters a = 84.7, b = 42.4, c = 57.3 A, beta = 120.6 degrees and a monomer in the asymmetric unit.

Crystal structure of Pyrococcus furiosus phosphoglucose isomerase. Implications for substrate binding and catalysis

Phosphoglucose isomerase (PGI) catalyzes the reversible isomerization between d-fructose 6-phosphate and d-glucose 6-phosphate as part of the glycolytic pathway. PGI from the Archaea Pyrococcus furiosus (Pfu) was crystallized, and its structure was determined by x-ray diffraction to a 2-A resolution. Structural comparison of this archaeal PGI with the previously solved structures of bacterial and eukaryotic PGIs reveals a completely different structure. Each subunit of the homodimeric Pfu PGI consists of a cupin domain, for which the overall structure is similar to other cupin domain-containing proteins, and includes a conserved transition metal-binding site. Biochemical data on the recombinant enzyme suggests that Fe2+ is bound to Pfu PGI. However, as catalytic activity is not strongly influenced either by the replacement of Fe2+ by a range of transition metals or by the presence or absence of the bound metal ion, we suggest that the metal may not be directly involved in catalysis but rather may be implicated in substrate recognition.