Browse
Submit Data
Databases
API
Help

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallization and preliminary X-ray crystallographic analysis of human autotaxin.

ABSTRACT: Autotaxin (ATX), which is also known as ectonucleotide pyrophosphatase/phosphodiesterase 2 (NPP2 or ENPP2) or phosphodiesterase I? (PD-I?), is an extracellular lysophospholipase D which generates lysophosphatidic acid (LPA) from lysophosphatidylcholine (LPC). ATX stimulates tumour-cell migration, angiogenesis and metastasis and is an attractive target for cancer therapy. For crystallographic studies, the ? isoform of human ATX was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 3.0?Å resolution from a monoclinic crystal form belonging to space group C2, with unit-cell parameters a = 311.4, b = 147.9, c = 176.9?Å, ? = 122.6°.

SUBMITTER: Inoue K

PROVIDER: S-EPMC3080147 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallization and preliminary X-ray crystallographic analysis of human autotaxin.

Inoue Keigo K Tanaka Nobutada N Haga Arayo A Yamasaki Kyohei K Umeda Tomonobu T Kusakabe Yoshio Y Sakamoto Yasumitsu Y Nonaka Takamasa T Deyashiki Yoshihiro Y Nakamura Kazuo T KT

Acta crystallographica. Section F, Structural biology and crystallization communications 20110324 Pt 4

Autotaxin (ATX), which is also known as ectonucleotide pyrophosphatase/phosphodiesterase 2 (NPP2 or ENPP2) or phosphodiesterase Iα (PD-Iα), is an extracellular lysophospholipase D which generates lysophosphatidic acid (LPA) from lysophosphatidylcholine (LPC). ATX stimulates tumour-cell migration, angiogenesis and metastasis and is an attractive target for cancer therapy. For crystallographic studies, the α isoform of human ATX was overproduced in Escherichia coli, purified and crystallized using ...[more]

PMID: 21505238

Similar Datasets

Crystallization and preliminary X-ray diffraction analysis of rat autotaxin.

Project description:Rat autotaxin has been cloned, expressed, purified to homogeneity and crystallized via hanging-drop vapour diffusion using PEG 3350 as precipitant and ammonium iodide and sodium thiocyanate as salts. The crystals diffracted to a maximum resolution of 2.05 A and belonged to space group P1, with unit-cell parameters a=53.8, b=63.3, c=70.5 A, alpha=98.8, beta=106.2, gamma=99.8 degrees. Preliminary X-ray diffraction analysis indicated the presence of one molecule per asymmetric unit, with a solvent content of 47%.

| S-EPMC2935245 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of human quinolinate phosphoribosyltransferase.

Project description:Quinolinate phosphoribosyltransferase (QPRTase) is a key NAD-biosynthetic enzyme which catalyzes the transfer of quinolinic acid to 5-phosphoribosyl-1-pyrophosphate, yielding nicotinic acid mononucleotide. Homo sapiens QPRTase (Hs-QPRTase) appeared as a hexamer during purification and the protein was crystallized. Diffraction data were collected and processed at 2.8 Å resolution. Native Hs-QPRTase crystals belonged to space group P2(1), with unit-cell parameters a=76.2, b=137.1, c=92.7 Å, β=103.8°. Assuming the presence of six molecules in the asymmetric unit, the calculated Matthews coefficient is 2.46 Å3 Da(-1), which corresponds to a solvent content of 49.9%.

| S-EPMC3079967 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of human ?-galactosidase.

Project description:?-D-Galactosidase (?-Gal) is an exoglycosidase that cleaves ?-galactosides from glycoproteins, sphingolipids and keratan sulfate. This study reports the expression, purification, crystallization and preliminary X-ray crystallographic analysis of human lysosomal ?-Gal. The sitting-drop vapour-diffusion method was used to crystallize ?-Gal in complexes with its product galactose and with the inhibitor 1-deoxygalactonojirimycin. The resulting crystals were isomorphous and belonged to space group P2(1). The crystals of the ?-Gal-galactose and the ?-Gal-inhibitor complexes had unit-cell parameters a = 94.8, b = 116.1, c = 140.3 Å, ? = 92.2° and a = 94.8, b = 116.0, c = 140.3 Å, ? = 92.2°, respectively. Diffraction data were collected to 1.8 Å resolution for both crystals.

| S-EPMC3253840 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of human myotubularin-related protein 1.

Project description:Myotubularin-related protein 1 is a phosphatase that dephosphorylates phospholipids such as phosphatidylinositol 3-phosphate or phosphatidylinositol 3,5-bisphosphate. In this study, human MTMR1 was overexpressed in Escherichia coli, purified and crystallized at 277?K using polyethylene glycol 20,000 as a precipitant. Diffraction data were collected to 2.0?Å resolution using synchrotron radiation. The crystals belonged to space group P1, with unit-cell parameters a = 67.219, b = 96.587, c = 97.581?Å, ? = 87.597, ? = 86.072, ? = 77.327°. Assuming the presence of four molecules in the asymmetric unit, the calculated Matthews coefficient value was 2.61?Å(3)?Da(-1) and the corresponding solvent content was 52.9%.

| S-EPMC4356299 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of human peptidylarginine deiminase type I.

Project description:Peptidylarginine deiminase (PAD) catalyzes the post-translational conversion of peptidylarginine to peptidylcitrulline in the presence of calcium ions. Among the five known human PAD isozymes (PAD1-4 and PAD6), PAD1 exhibits the broadest substrate specificity. Crystals of PAD1 obtained using polyethylene glycol 3350 as a precipitant diffracted to 3.70 Å resolution using synchrotron radiation. Two PAD1 molecules were contained in the asymmetric unit and the crystals belonged to space group P6(1), with unit-cell parameters a = b = 90.3, c = 372.3 Å. The solvent content was 58.2%.

| S-EPMC3855719 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of human Apaf-1-interacting protein.

Project description:Apaf-1-interacting protein (APIP) is known to inhibit two different types of cell death: caspase-1-dependent pyroptosis and caspase-9-dependent apoptosis. APIP is also involved in the methionine-salvage pathway, where it is called 5-methylthioribulose-1-phosphate dehydratase (MtnB). The enzyme activity seems to be essential for inhibition of pyroptosis by APIP, but not for inhibition of apoptosis. In this study, human APIP was overproduced in Escherichia coli, purified and crystallized. An X-ray diffraction data set was collected to 2.40 Å resolution and the crystals belonged to space group C222(1), with unit-cell parameters a=106.61, b=107.50, c=189.76 Å. Given that four APIP molecules exist in the asymmetric unit, the Matthews coefficient is 2.70 Å3 Da(-1) and the corresponding solvent content is 54.4%.

| S-EPMC3509978 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of the human kindlin-2 PH domain.

Project description:Kindlins contribute to the correct assembly of integrin-containing focal adhesion sites through their direct interaction with the cytoplasmic tail of ?-integrin. The FERM domain of kindlins has a unique subdomain organization: the F2 subdomain harbours a centrally located pleckstrin homology (PH) domain that is thought to be involved in the membrane targeting of kindlins. FERM domains are found in a number of cytoskeletal proteins that mediate the interaction between integrins and cytosolic proteins. In the present study, the PH domain of human kindlin-2 was subcloned, solubly expressed in Escherichia coli and crystallized using the hanging-drop vapour-diffusion method. A diffraction data set was collected at 2.8?Å resolution using synchrotron radiation on BL-4A at the Pohang Accelerator Laboratory (Pohang, Republic of Korea).

| S-EPMC3107146 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of human plasma platelet activating factor acetylhydrolase.

Project description:The plasma form of the human enzyme platelet activating factor acetylhydrolase (PAF-AH) has been crystallized, and X-ray diffraction data were collected at a synchrotron source to a resolution of 1.47 A. The crystals belong to space group C2, with unit cell parameters of a = 116.18, b = 83.06, c = 96.71 A, and beta= 115.09 degrees and two molecules in the asymmetric unit. PAF-AH functions as a general anti-inflammatory scavenger by reducing the levels of the signaling molecule PAF. Additionally, the LDL bound enzyme has been linked to atherosclerosis due to its hydrolytic activities of pro-inflammatory agents, such as sn-2 oxidatively fragmented phospholipids.

| S-EPMC3220998 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp6.

Project description:Enpp (ectonucleotide phosphodiesterase/pyrophosphatase) 6 is a membrane-bound glycoprotein that hydrolyzes choline-containing compounds such as lysophosphatidylcholine and glycerophosphorylcholine, and presumably participates in choline metabolism. The catalytic domain of mouse Enpp6 was expressed in HEK293T cells, purified using the TARGET tag/P20.1-Sepharose system and crystallized. An X-ray diffraction data set was collected to 1.8?Å resolution. The crystal belonged to space group P1, with unit-cell parameters a=63.7, b=68.8, c=69.7?Å, ?=60.6, ?=87.0, ?=68.1°. Assuming the presence of two protein molecules per asymmetric unit, the solvent content was estimated to be 49.5%.

| S-EPMC4051540 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp1.

Project description:Enpp1 is an extracellular membrane-bound glycoprotein that regulates bone mineralization by hydrolyzing ATP to generate pyrophosphate. The extracellular region of mouse Enpp1 was expressed in HEK293S GnT1(-) cells, purified using the TARGET tag/P20.1-Sepharose system and crystallized. An X-ray diffraction data set was collected to 3.0?Å resolution. The crystal belonged to space group P3(1), with unit-cell parameters a = b = 105.3, c = 173.7?Å. A single-wavelength anomalous dispersion (SAD) data set was also collected to 2.7?Å resolution using a selenomethionine-labelled crystal. The experimental phases determined by the SAD method produced an interpretable electron-density map.

| S-EPMC3388920 | 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