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At least 343 records · Page 19Linked to original sources
PubMed2003

Crystallization of [Fe3S4]-ferredoxin from the hyperthermophile archaeon Pyrococcus furiosus.

Recombinant Pyrococcus furiosus ferredoxin with a [Fe3S4]-cluster was crystallized through steps of optimization and X-ray diffraction data were collected from several crystal forms. Flat plate-like crystals were grown by hanging-drop vapour diffusion. The precipitant used was 30% PEG 400; the pH was varied between 7.0 and 8.0 and hexaamminecobalt(III) chloride was essential for crystal formation. The best crystals belong to space group P2(1), with unit-cell parameters a = 31.23, b = 47.51, c = 52.03 A, beta = 103.86 degrees, and diffract to 1.5 A resolution.

Archaeal Proteins↗
PubMed2003

Crystallization and preliminary X-ray analysis of the glycogen synthase from Pyrococcus 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↗
PubMed2003

Purification, crystallization and preliminary X-ray diffraction data of L7Ae sRNP core protein from Pyrococcus abyssii.

The L7Ae sRNP core protein from Pyrococcus abyssii was crystallized using the sitting-drop vapour-diffusion method. Crystals were obtained in the presence of MgCl(2), PEG 2000 MME and acetate buffer at pH 4.0. A native data set has been collected at 2.9 A resolution using a rotating-anode generator at room temperature. Crystals belong to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 70.7, b = 112.9, c = 34.8 A. There are two monomers of MW 14 200 Da per asymmetric unit and the packing density V(M) is 2.45 A(3) Da(-1). A molecular-replacement analysis gave solutions for the rotation and translation functions.

Archaeal Proteins↗
PubMed2003

W3Y single mutant of rubredoxin from Pyrococcus furiosus: a preliminary time-of-flight neutron study.

Rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus maintains its native structure at high temperatures (373 K). In order to investigate the role of hydrogen bonding, hydration and chain dynamics in this thermostability, wavelength-resolved Laue neutron diffraction data have been collected from the W3Y single mutant (Trp3-->Tyr3) on the spallation neutron protein crystallography station (PCS) at Los Alamos Neutron Science Center. Data were measured at room temperature from nine crystal settings, each of approximately 12 h duration. The total data-measurement period was less than 5 d from a single crystal that had undergone H(2)O/D(2)O exchange. The nominal resolution of the data is 2.1 A.

Crystallization↗
PubMed2004

Crystallization and preliminary X-ray analysis of inorganic pyrophosphatase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.

Inorganic pyrophosphatase (PPase; EC 3.6.1.1) from the hyperthermophile Pyrococcus horikoshii was crystallized by the hanging-drop vapour-diffusion method at pH 5.0 using polyethyleneglycol 4000 as the precipitant. The crystal belongs to space group P2(1)2(1)2, with unit-cell parameters a = 71.7, b = 86.5, c = 92.5 A, alpha = beta = gamma = 90 degrees. There are two molecules in the asymmetric unit. The crystals were stable during exposure to X-rays and a full set of X-ray diffraction data was collected to 2.7 A resolution in-house.

Crystallization↗
PubMed2004

Cloning, purification, crystallization and preliminary crystallographic analysis of acylphosphatase from Pyrococcus horikoshii OT3.

Acylphosphatase is one of the smallest enzymes and catalyzes the hydrolysis of the carboxy-phosphate bond. An extremely thermostable acylphosphatase from a hyperthermophilic archaea, Pyrococcus horikoshii OT3, has been cloned, expressed in Escherichia coli, purified and crystallized using the sitting-drop vapour-diffusion method with potassium/sodium tartrate as the precipitant at pH 5.5. X-ray diffraction data have been collected to a highest resolution of 1.72 angstroms on a synchrotron-radiation source. The crystals belong to space group P3(2)21, with approximate unit-cell parameters a = b = 86.6, c = 75.4 angstroms and two monomers in the asymmetric unit.

Acid Anhydride Hydrolases↗
PubMed2004

Structure analysis of PH1161 protein, a transcriptional activator TenA homologue from the hyperthermophilic archaeon Pyrococcus horikoshii.

The crystal structure of the Bacillus subtilis TenA-homologue protein PH1161 from the hyperthermophilic archaebacterium Pyrococcus horikoshii was determined. TenA is known to belong to a new family of activators that stimulate the production of extracellular proteases in B. subtilis. A sequence-similarity search revealed that TenA-homologue proteins are widespread in bacteria and archaea, suggesting that this family of proteins plays an essential role in these organisms. In the present study, the first three-dimensional structure of a member of the TenA family of proteins was determined, unexpectedly revealing that the protein has a fold identical to that of haem oxygenase-1. Analysis has also shown that the protein has a unique ligand-binding pocket. Electron density of a bound ligand molecule was observed in this pocket. These results provide a valuable insight into the functional understanding of the TenA family of proteins.

Amino Acid Sequence↗
PubMed2004

Crystallization and preliminary crystallographic analysis of an acylphosphatase from the hyperthermophilic archaeon Pyrococcus horikoshii.

Acylphosphatases catalyse the hydrolysis of the carboxyl phosphate bond in metabolites such as acetyl phosphate, 1,3-bisphosphoglycerate, succinoyl phosphate and carbamoyl phosphate. In this study, acylphosphatase (91 residues) from the hyperthermophilic archaeon Pyrococcus horikoshii has been cloned, overexpressed, purified and crystallized using the sitting-drop vapour-diffusion method using sodium formate as a precipitant at 289 K. The crystals belong to space group P3(2)21, with unit-cell parameters a = b = 85.65, c = 75.51 A. The asymmetric unit contains two molecules of acylphosphatase, with a corresponding crystal volume per protein weight of 3.9 A Da(-1) and a solvent content of 68.6%. A data set diffracting to 1.6 A resolution was collected from a single crystal at 100 K.

Acid Anhydride Hydrolases↗
PubMed2004

Purification, crystallization and preliminary crystallographic analysis of the glycine-cleavage system component T-protein from Pyrococcus horikoshii OT3.

The glycine-cleavage system component T-protein is a folate-dependent enzyme that catalyzes the formation of ammonia and 5,10-CH2-tetrahydrofolate from the aminomethyl intermediate bound to the lipoate cofactor of H-protein. T-protein from Pyrococcus horikoshii OT3 has been cloned, overexpressed in Escherichia coli, purified and crystallized by the microbatch method using PEG 4000 as a precipitant at 296 K. X-ray diffraction data have been collected to 1.50 A resolution at 100 K using synchrotron radiation. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 78.980, b = 95.708, c = 118.331 A. Assuming one homodimer per asymmetric unit gives a VM value of 2.4 A3 Da(-1) and a solvent content of 49.0%.

Aminomethyltransferase↗
PubMed2004

Crystallization and preliminary X-ray diffraction study of the catalytic subunit of archaeal H+ -transporting ATP synthase from Pyrococcus horikoshii OT3.

H+ -transporting ATP synthase (H+ -ATPase) is a multi-subunit complex which acts to produce ATP molecules. The catalytic subunit A of the archaeal-type H+ -ATPase from Pyrococcus horikoshii OT3 was cloned, expressed in Escherichia coli, purified and crystallized by the hanging-drop vapour-diffusion method with MPD as a precipitant. X-ray intensity data were collected to 2.55 A resolution at beamline BL41XU of SPring-8. The crystals belong to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = b = 128.0, c = 104.7 A, and contain one molecule per asymmetric unit.

Catalytic Domain↗
PubMed2004

Expression, crystallization and preliminary X-ray analysis of the Pyrococcus abyssi protein homologue of Saccharomyces cerevisiae Nip7p.

Saccharomyces cerevisiae Nip7p is a nucleolar protein required for accurate processing of the 27S precursor of the 25S and 5.8S ribosomal RNAs. Nip7p homologues are found in eukaryotes and archaea. The Pyrococcus abyssi homologue of Nip7p (PaNip7) was cloned, expressed in Escherichia coli and purified for crystallization. X-ray diffraction data were collected from native crystals and an iodide derivative using synchrotron radiation. PaNip7 native crystals diffract to 1.8 A and belong to space group C2, with unit-cell parameters a = 88.49, b = 90.28, c = 63.35 A, beta = 134.29 degrees. The PaNip7 structure was solved using the SIRAS method.

Cloning, Molecular↗
PubMed2004

Crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaeon Pyrococcus 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.

Crystallography, X-Ray↗
PubMed2004

Crystalization and preliminary X-ray crystallographic analysis of the laminarinase endo-beta-1,3-glucanase from Pyrococcus furiosus.

Laminarinase endo-beta-1,3 glucanase (LamA) from Pyrococcus furiosus is an enzyme which displays its main hydrolytic activity on the 3-1,3-glucose polymer laminarin. This laminarinase is remarkably resistant to denaturation: its secondary structure is unchanged in 8 M guanidinium chloride. This protein belongs to the family 16 glycosyl hydrolases, which are enzymes that are widely distributed among bacteria, fungi and higher plants. Single crystals of P. furiosus LamAhave been obtained by the hanging-drop vapour-diffusion method using 2-methyl-2,4-pentanediol as a precipitant agent. A complete data set has been collected under cryocooling at a synchrotron source. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 44.36, b = 84.76, c = 69.23 A, a = 90, fl = 104.97, y = 90 degrees, and diffract to 2.15 A resolution.

Archaeal Proteins↗
PubMed2005

Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 angstroms resolution.

The crystal structure of the L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii (PhA) was determined by the multiwavelength anomalous diffraction (MAD) method and was refined to a resolution of 2.16 angstroms with a crystallographic R factor and free R factor of 21.1 and 25.3%, respectively. This is the first report of the three-dimensional structure of a type I L-asparaginase. These enyzmes are known as cytosolic L-asparaginases with lower affinities for substrate than the type II L-asparaginases. Although the overall fold of PhA was closely related to the structure of the well characterized type II L-asparaginase, structural differences were also detected. PhA forms a homodimer that corresponds to half the homotetramer of type II L-asparaginases. Structure comparison at the active site reveals that most catalytic residues are conserved except for two residues that recognize the amino group of the substrate. Additionally, a remarkable structural difference is found in the so-called 'active-site flexible loop'. In PhA this loop is stabilized by beta-hairpin formation and by elaborate interactions with the type-I-specific alpha-helical region derived from the other subunit forming the PhA dimer. The flexible loop of the type II enzyme is considered to serve as a mobile gate to the active site. Therefore, the loop stabilization observed in the PhA structure may cause limitation of the access of the substrate to the active site.

Amino Acid Sequence↗
PubMed2005

Unusual twinning in an acetyl coenzyme A synthetase (ADP-forming) from Pyrococcus furiosus.

A recombinant form of an acetyl coenzyme A synthetase (ADP-forming) from Pyrococcus furiosus has been crystallized. Crystallization was accomplished by the sitting-drop vapour-diffusion technique. Crystals belong to the monoclinic space group C2, with unit-cell parameters a = 131.3, b = 186.1, c = 121.5 angstroms, beta = 122.6 degrees, and diffract to 2.0 angstroms resolution on a synchrotron-radiation source. The unit-cell parameters allow twinning to the higher apparent space-group symmetry F222 by twin-lattice quasi-symmetry. The twinning fraction for the data is close to 40%. Two other data sets in the PDB show similar twinning.

Acetate-CoA Ligase↗
PubMed2005

The 2.35 A structure of the TenA homolog from Pyrococcus furiosus supports an enzymatic function in thiamine metabolism.

TenA (transcriptional enhancer A) has been proposed to function as a transcriptional regulator based on observed changes in gene-expression patterns when overexpressed in Bacillus subtilis. However, studies of the distribution of proteins involved in thiamine biosynthesis in different fully sequenced genomes have suggested that TenA may be an enzyme involved in thiamine biosynthesis, with a function related to that of the ThiC protein. The crystal structure of PF1337, the TenA homolog from Pyrococcus furiosus, is presented here. The protomer comprises a bundle of alpha-helices with a similar tertiary structure and topology to that of human heme oxygenase-1, even though there is no significant sequence homology. A solvent-sequestered cavity lined by phylogenetically conserved residues is found at the core of this bundle in PF1337 and this cavity is observed to contain electron density for 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate, the product of the ThiC enzyme. In contrast, the modestly acidic surface of PF1337 shows minimal levels of sequence conservation and a dearth of the basic residues that are typically involved in DNA binding in transcription factors. Without significant conservation of its surface properties, TenA is unlikely to mediate functionally important protein-protein or protein-DNA interactions. Therefore, the crystal structure of PF1337 supports the hypothesis that TenA homologs have an indirect effect in altering gene-expression patterns and function instead as enzymes involved in thiamine metabolism.

Amino Acid Sequence↗
PubMed2005

Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.

The crystal structure of Pyrococcus abyssi rubredoxin mutant W4L/R5S was solved by direct methods. The model of the air-oxidized protein was refined by partially restrained full-matrix least-squares refinement against intensity data to 0.69 A resolution. This first ultrahigh-resolution structure of a rubredoxin provides very detailed and precise information about the Fe(SCys)(4) centre and its environment, the peptide-backbone stereochemistry, H atoms and hydrogen bonds, static and dynamic disorder, the solvent structure and the electron-density distribution. P. abyssi rubredoxin W4L/R5S is the first of a series of mutants studied by atomic and ultrahigh-resolution X-ray crystallography which are expected to contribute to the understanding of structure-function relationships in iron-sulfur proteins.

Amino Acid Sequence↗
PubMed2005

Structure of a putative 2'-5' RNA ligase from Pyrococcus horikoshii.

Cyclic phosphodiesterase and 2'-5' RNA ligase are members of a superfamily of proteins which share structural similarities even though their homology may be very low. A putative 2'-5' RNA ligase from Pyrococcus horikoshii has been crystallized and its X-ray crystallographic structure determined to 2.4 A. The protein crystallized in the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 44.07, b = 45.47, c = 93.17 A and one protein monomer in the asymmetric unit. The molecular-replacement probe was a 2'-5' RNA ligase from Thermus thermophilus which shares 30% sequence identity. The P. horikoshii RNA ligase has some structural features that have more in common with a cyclic phosphodiesterase from Arabidopsis thaliana with which it has no significant homology, yet an examination of the electrostatic surface potential clearly defines its relationship to the T. thermophilus RNA ligase. However, the size of the active-site cleft is smaller and less positively charged than that of the T. thermophilus homologue, suggesting that the actual substrate may be smaller than that previously postulated for the latter.

Binding Sites↗