Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Purification, crystallization and preliminary X-ray analysis of the PCNA2-PCNA3 complex from Sulfolobus tokodaii strain 7.

ABSTRACT: Crenarchaeal PCNA is known to consist of three subunits (PCNA1, PCNA2 and PCNA3) that form a heterotrimer (PCNA123). Recently, another heterotrimeric PCNA composed of only PCNA2 and PCNA3 was identified in Sulfolobus tokodaii strain 7 (stoPCNAs). In this study, the purified stoPCNA2-stoPCNA3 complex was crystallized by hanging-drop vapour diffusion. The crystals obtained belonged to the orthorhombic space groups I222 and P2(1)2(1)2, with unit-cell parameters a = 91.1, b = 111.8, c = 170.9 A and a = 91.1, b = 160.6, c = 116.6 A, respectively. X-ray diffraction data sets were collected to 2.90 A resolution for the I222 crystals and to 2.80 A resolution for the P2(1)2(1)2 crystals.

SUBMITTER: Kawai A

PROVIDER: S-EPMC2802881 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Purification, crystallization and preliminary X-ray analysis of the PCNA2-PCNA3 complex from Sulfolobus tokodaii strain 7.

Kawai Akito A Higuchi Shigesada S Tsunoda Masaru M Nakamura Kazuo T KT Miyamoto Shuichi S

Acta crystallographica. Section F, Structural biology and crystallization communications 20091127 Pt 12

Crenarchaeal PCNA is known to consist of three subunits (PCNA1, PCNA2 and PCNA3) that form a heterotrimer (PCNA123). Recently, another heterotrimeric PCNA composed of only PCNA2 and PCNA3 was identified in Sulfolobus tokodaii strain 7 (stoPCNAs). In this study, the purified stoPCNA2-stoPCNA3 complex was crystallized by hanging-drop vapour diffusion. The crystals obtained belonged to the orthorhombic space groups I222 and P2(1)2(1)2, with unit-cell parameters a = 91.1, b = 111.8, c = 170.9 A and ...[more]

PMID: 20054129

Similar Datasets

Purification, crystallization and preliminary X-ray analysis of uracil-DNA glycosylase from Sulfolobus tokodaii strain 7.

Project description:Uracil-DNA glycosylase (UDG) specifically removes uracil from DNA by catalyzing hydrolysis of the N-glycosidic bond, thereby initiating the base-excision repair pathway. Although a number of UDG structures have been determined, the structure of archaeal UDG remains unknown. In this study, a deletion mutant of UDG isolated from Sulfolobus tokodaii strain 7 (stoUDG?) and stoUDG? complexed with uracil were crystallized and analyzed by X-ray crystallography. The crystals were found to belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 52.2, b = 52.3, c = 74.7?Å and a = 52.1, b = 52.2, c = 74.1 Å for apo stoUDG? and stoUDG? complexed with uracil, respectively.

| S-EPMC3433208 | biostudies-literature

Crystallization and preliminary X-ray analysis of the YjgF/YER057c/UK114-family protein ST0811 from Sulfolobus tokodaii strain 7.

Project description:ST0811 from Sulfolobus tokodaii strain 7, a member of the YjgF/YER057c/UK114 protein family, was crystallized by the sitting-drop vapour-diffusion method using PEG 10,000 as precipitant. The crystals diffracted X-rays to beyond 2.0 A resolution using an in-house rotating-anode generator. The crystals belonged to the rhombohedral space group R3, with hexagonal unit-cell parameters a = b = 55.0, c = 223.2 A. The crystals contained two molecules in the asymmetric unit (VM = 2.3 A3 Da(-1)) and had a solvent content of 47%.

| S-EPMC1978107 | biostudies-literature

Purification, crystallization and preliminary X-ray crystallographic analysis of ST1022, a putative member of the Lrp/AsnC family of transcriptional regulators isolated from Sulfolobus tokodaii strain 7.

Project description:The Lrp/AsnC family of transcriptional regulators, also known as feast/famine transcriptional regulators, are widely distributed among bacteria and archaea. This family of proteins are likely to be involved in cellular metabolism, with exogenous amino acids functioning as effectors. Here, the crystallization and preliminary X-ray diffraction analysis of ST1022, a member of the Lrp/AsnC family of proteins, is reported with and without exogenous glutamine as the effector molecule. The crystals of native ST1022 and of the putative complex belong to the tetragonal space group I422, with unit-cell parameters a = b = 103.771, c = 73.297 A and a = b = 103.846, c = 73.992 A, respectively. Preliminary X-ray diffraction data analysis and molecular-replacement solution revealed the presence of one monomer per asymmetric unit.

| S-EPMC2339745 | biostudies-literature

Crystallization and preliminary X-ray crystallographic study of a putative aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7.

Project description:Genome analysis suggests that the aspartyl-tRNA synthetase of the crenarchaeon Sulfolobus tokodaii strain 7 belongs to the nondiscriminating type that is believed to catalyze aspartylation of tRNA(Asp) and tRNA(Asn). This protein has been overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method from 100 mM sodium HEPES buffer pH 7.5 containing 100 mM NaCl and 1.6 M (NH4)2SO4 as the crystallizing reagent. Diffraction data were collected to 2.3 A resolution using synchrotron radiation. The crystal belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 116.0, b = 139.3, c = 75.3 A. The estimated Matthews coefficient (3.10 A3 Da(-1); 60.3% solvent content) suggests the presence of two subunits in the asymmetric unit. The structure has been successfully solved by the molecular-replacement method. Full refinement of the structure may reveal it to be the original ancestor of the nondiscriminating AspRS.

| S-EPMC2335148 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray analysis of the HER3-9E12 Fab complex.

Project description:9E12 is a fully human immunoglobulin G1/? monoclonal antibody that is specific for the epidermal growth factor receptor 3 (HER3), the overexpression of which has been detected in many tumour types and is associated with poor survival outcomes. To date, knowledge of the molecular mechanism for targeted antibodies that directly inhibit HER3 signalling is limited. Because knowledge of such therapeutic antibodies would help basic immunological therapeutics, structural insights into the HER3-9E12 Fab complex are important. Recombinant human HER3 and Fab fragments of the 9E12 antibody were cloned, expressed and crystallized, and crystallographic data sets were collected. The crystals belonged to space group P1, with unit-cell parameters a=74.4, b=98.6, c=99.6 Å, ?=106.0, ?=95.0, ?=102.5° and diffracted to a resolution of 2.1?Å.

| S-EPMC4051538 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of Sulfolobus solfataricus thioredoxin reductase.

Project description:A thermostable thioredoxin reductase isolated from Sulfolobus solfataricus (SsTrxR) has been successfully crystallized in the absence and in the presence of NADP. Two different crystal forms have been obtained. Crystals of the form that yields higher resolution data (1.8 A) belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 76.77, b = 120.68, c = 126.85 A. The structure of the enzyme has been solved by MAD methods using the anomalous signal from the Se atoms of selenomethionine-labelled SsTrxR.

| S-EPMC1991316 | biostudies-literature

The hyperthermophilic cystathionine ?-synthase from the aerobic crenarchaeon Sulfolobus tokodaii: expression, purification, crystallization and structural insights.

Project description:Cystathionine ?-synthase (CGS; EC 2.5.1.48), a pyridoxal 5'-phosphate (PLP)-dependent enzyme, catalyzes the formation of cystathionine from an L-homoserine derivative and L-cysteine in the first step of the transsulfuration pathway. Recombinant CGS from the thermoacidophilic archaeon Sulfolobus tokodaii (StCGS) was overexpressed in Escherichia coli and purified to homogeneity by heat treatment followed by hydroxyapatite and gel-filtration column chromatography. The purified enzyme shows higher enzymatic activity at 353?K under basic pH conditions compared with that at 293?K. Crystallization trials yielded three crystal forms from different temperature and pH conditions. Form I crystals (space group P21; unit-cell parameters a = 58.4, b = 149.3, c = 90.2?Å, ? = 108.9°) were obtained at 293?K under acidic pH conditions using 2-methyl-2,4-pentanediol as a precipitant, whereas under basic pH conditions the enzyme crystallized in form II at 293?K (space group C2221; unit-cell parameters a = 117.7, b = 117.8, c = 251.3?Å) and in form II' at 313?K (space group C2221; unit-cell parameters a = 107.5, b = 127.7, c = 251.1?Å) using polyethylene glycol 3350 as a precipitant. X-ray diffraction data were collected to 2.2, 2.9 and 2.7?Å resolution for forms I, II and II', respectively. Structural analysis of these crystal forms shows that the orientation of the bound PLP in form II is significantly different from that in form II', suggesting that the change in orientation of PLP with temperature plays a role in the thermophilic enzymatic activity of StCGS.

| S-EPMC5349309 | biostudies-literature

Purification, crystallization and preliminary X-ray crystallographic analysis of mammalian MSS4-Rab8 GTPase protein complex.

Project description:Rab GTPases function as ubiquitous key regulators of membrane-vesicle transport in eukaryotic cells. MSS4 is an evolutionarily conserved protein that binds to exocytotic Rabs and facilitates nucleotide release. The MSS4 protein in complex with nucleotide-free Rab8 GTPase has been purified and crystallized in a form suitable for structure analysis. The crystals belonged to space group P1, with unit-cell parameters a = 40.92, b = 49.85, c = 83.48 A, alpha = 102.88, beta = 97.46, gamma = 90.12 degrees. A complete data set has been collected to 2 A resolution.

| S-EPMC2150963 | biostudies-literature

Purification, crystallization and preliminary X-ray diffraction analysis of ArsH from Synechocystis sp. strain PCC 6803.

Project description:ArsH is an NADPH-dependent flavin mononucleotide reductase and is frequently encoded as part of an ars operon. The function of the arsH gene remains to be characterized. Crystallization and structural studies may contribute to elucidating the specific biological function of ArsH associated with arsenic resistance. ArsH from Synechocystis sp. strain PCC 6803 was overproduced, purified and crystallized. Crystals were obtained by the sitting-drop vapour-diffusion method. Diffraction data were collected and processed to a resolution of 1.6?Å. The crystals belonged to the tetragonal space group I4122, with unit-cell parameters a = b = 127.94, c = 65.86?Å and one molecule in the asymmetric unit. Size-exclusion chromatography and molecular-replacement results showed that the ArsH formed a tetramer. Further structural analysis and comparison with ArsH from Sinorhizobium meliloti will provide information about the oligomerization of ArsH.

| S-EPMC3976072 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray analysis of maleylacetate reductase from Burkholderia sp. strain SJ98.

Project description:Maleylacetate reductase (EC 1.3.1.32) is an important enzyme that is involved in the degradation pathway of aromatic compounds and catalyzes the reduction of maleylacetate to 3-oxoadipate. The gene pnpD encoding maleylacetate reductase in Burkholderia sp. strain SJ98 was cloned, expressed in Escherichia coli and purified by affinity chromatography. The enzyme was crystallized in both native and SeMet-derivative forms by the sitting-drop vapour-diffusion method using PEG 3350 as a precipitant at 293 K. The crystals belonged to space group P2(1)2(1)2, with unit-cell parameters a = 72.91, b = 85.94, c = 53.07 A. X-ray diffraction data for the native and SeMet-derivative crystal were collected to 2.7 and 2.9 A resolution, respectively.

| S-EPMC2802890 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data