Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallization and preliminary X-ray study of the deaminase AmnE from Pseudomonas sp. AP-3.

ABSTRACT: The amnE gene from Pseudomonas sp. AP-3 has been verified as encoding a deaminase with 142 amino-acid residues. In order to change the substrate specificity via structure-based protein engineering, the amnE gene, after gene-code optimization, was chemically synthesized and cloned into the expression vector pET-28a. The protein was expressed in Escherichia coli BL21 (DE3) and purified by Ni(2+)-chelating affinity chromatography. Diffraction-quality crystals were obtained using the hanging-drop vapour-diffusion method and diffracted to a resolution of 2.09 Å. The crystals belonged to the orthorhombic space group C2221, with unit-cell parameters a = 63.23, b = 88.93, c = 137.83 Å.

SUBMITTER: Yu D

PROVIDER: S-EPMC3702332 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallization and preliminary X-ray study of the deaminase AmnE from Pseudomonas sp. AP-3.

Yu Dan D Jiang Yongji Y Hou Jianfeng J Chen Shuai S Zhang Guofang G Liu Xiang X Dong Hui H Yu Bo B

Acta crystallographica. Section F, Structural biology and crystallization communications 20130630 Pt 7

The amnE gene from Pseudomonas sp. AP-3 has been verified as encoding a deaminase with 142 amino-acid residues. In order to change the substrate specificity via structure-based protein engineering, the amnE gene, after gene-code optimization, was chemically synthesized and cloned into the expression vector pET-28a. The protein was expressed in Escherichia coli BL21 (DE3) and purified by Ni(2+)-chelating affinity chromatography. Diffraction-quality crystals were obtained using the hanging-drop va ...[more]

PMID: 23832215

Similar Datasets

Crystallization and preliminary X-ray study of biosynthetic alanine racemase from Pseudomonas aeruginosa PAO1.

Project description:Biosynthetic alanine racemase (AlrPA) from Pseudomonas aeruginosa PAO1 carrying a His6 tag was expressed in Escherichia coli BL21 (DE3) cells and purified by Ni(2+)-chelating affinity and anion-exchange chromatography for X-ray crystallographic analysis. Crystals were grown by the hanging-drop vapour-diffusion method at 289?K in a solution consisting of 4%(v/v) Tacsimate pH 5.0, 14%(w/v) polyethylene glycol 3350 with a protein concentration of 8?mg?ml(-1). The crystal diffracted to 2.76?Å resolution and belonged to the orthorhombic space group P212121, with unit-cell parameters a = 74.12, b = 76.97, c = 154.80?Å, ? = ? = ? = 90°.

| S-EPMC4259224 | biostudies-literature

Crystallization and preliminary X-ray diffraction analysis of the amidase domain of allophanate hydrolase from Pseudomonas sp. strain ADP.

Project description:The allophanate hydrolase from Pseudomonas sp. strain ADP was expressed and purified, and a tryptic digest fragment was subsequently identified, expressed and purified. This 50?kDa construct retained amidase activity and was crystallized. The crystals diffracted to 2.5?Å resolution and adopted space group P21, with unit-cell parameters a = 82.4, b = 179.2, c = 112.6?Å, ? = 106.6°.

| S-EPMC3944691 | biostudies-literature

Crystallization and preliminary X-ray analysis of the hypothetical deaminase RPB_0146 from Rhodopseudomonas palustris HaA2.

Project description:RPB_0146, a putative deaminase from Rhodopseudomonas palustris HaA2, was expressed in Escherichia coli BL21 (DE3) cells and purified using a His6 tag by Ni2+-chelating affinity chromatography for X-ray crystallographic analysis. Diffraction-quality crystals were grown by the hanging-drop vapour-diffusion method at 289?K and diffracted to a resolution of 2.44?Å using a wavelength of 1.000?Å at the Photon Factory (KEK), Japan. The crystals belonged to the orthorhombic space group P2?2?2?, with unit-cell parameters a=66.26, b=123.94, c=155.95?Å.

| S-EPMC4231866 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of biodegradative threonine deaminase (TdcB) from Salmonella typhimurium.

Project description:Biodegradative threonine deaminase (TdcB) catalyzes the deamination of L-threonine to alpha-ketobutyrate, the first reaction in the anaerobic breakdown of L-threonine to propionate. Unlike the biosynthetic threonine deaminase, TdcB is insensitive to L-isoleucine and is activated by AMP. Here, the cloning of TdcB (molecular weight 36 kDa) from Salmonella typhimurium with an N-terminal hexahistidine affinity tag and its overexpression in Escherichia coli is reported. TdcB was purified to homogeneity using Ni-NTA affinity column chromatography and crystallized using the hanging-drop vapour-diffusion technique in three different crystal forms. Crystal forms I (unit-cell parameters a = 46.32, b = 55.30, c = 67.24 A, alpha = 103.09, beta = 94.70, gamma = 112.94 degrees) and II (a = 56.68, b = 76.83, c = 78.50 A, alpha = 66.12, beta = 89.16, gamma = 77.08 degrees) belong to space group P1 and contain two and four molecules of TdcB, respectively, in the asymmetric unit. Poorly diffracting form III crystals were obtained in space group C2 and based on the unit-cell volume are most likely to contain one molecule per asymmetric unit. Two complete data sets of resolutions 2.2 A (crystal form I) and 1.7 A (crystal form II) were collected at 100 K using an in-house X-ray source.

| S-EPMC2197173 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray analysis of Pseudomonas aeruginosa AlgX.

Project description:AlgX is a periplasmic protein required for the production of the exopolysaccharide alginate in Pseudomonas sp. and Azotobacter vinelandii. AlgX has been overexpressed and purified and diffraction-quality crystals have been grown using iterative seeding and the hanging-drop vapor-diffusion method. The crystals grew as flat plates with unit-cell parameters a = 46.4, b = 120.6, c = 86.9 A, beta = 95.7 degrees . The crystals exhibited the symmetry of space group P2(1) and diffracted to a minimum d-spacing of 2.1 A. On the basis of the Matthews coefficient (V(M) = 2.25 A(3) Da(-1)), two molecules were estimated to be present in the asymmetric unit.

| S-EPMC2864699 | biostudies-literature

Crystallization and preliminary X-ray analysis of the complex of NADH and 3alpha-hydroxysteroid dehydrogenase from Pseudomonas sp. B-0831.

Project description:The NAD(P)(+)-dependent enzyme 3alpha-hydroxysteroid dehydrogenase (3alpha-HSD) catalyzes the reversible interconversion of hydroxyl and oxo groups at position 3 of the steroid nucleus. The complex of NADH and 3alpha-HSD from Pseudomonas sp. B-0831 was crystallized by the hanging-drop vapour-diffusion method. Refinement of crystallization conditions with microseeding improved the quality of the X-ray diffraction data to a resolution of 1.8 A. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 62.46, b = 82.25, c = 86.57 A, and contained two molecules, reflecting dimer formation of 3alpha-HSD, in the asymmetric unit.

| S-EPMC2243091 | biostudies-literature

Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Bacillus megaterium.

Project description:The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor which is covalently linked by a thioether bridge to an invariant cysteine residue. Expression in Escherichia coli of a His-tagged form of Bacillus megaterium PBGD permitted the crystallization and preliminary X-ray analysis of the enzyme from this species at high resolution.

| S-EPMC3729171 | biostudies-literature

Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Arabidopsis thaliana.

Project description:The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step of the haem-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor which is covalently linked by a thioether bridge to an invariant cysteine residue. Since PBGD catalyses a reaction which is common to the biosynthesis of both haem and chlorophyll, structural studies of a plant PBGD enzyme offer great potential for the discovery of novel herbicides. Until recently, structural data have only been available for the Escherichia coli and human forms of the enzyme. Expression in E. coli of a codon-optimized gene for Arabidopsis thaliana PBGD has permitted for the first time the crystallization and preliminary X-ray analysis of the enzyme from a plant species at high resolution.

| S-EPMC3509971 | biostudies-literature

Crystallization and preliminary X-ray analysis of alginate importer from Sphingomonas sp. A1.

Project description:Sphingomonas sp. A1 directly incorporates alginate polysaccharides through a 'superchannel' comprising a pit on the cell surface, alginate-binding proteins in the periplasm and an ABC transporter (alginate importer) in the inner membrane. Alginate importer, consisting of four subunits, AlgM1, AlgM2 and two molecules of AlgS, was crystallized in the presence of the binding protein AlgQ2. Preliminary X-ray analysis showed that the crystal diffracted to 3.3 Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 72.5, b = 136.8, c = 273.3 Å, suggesting the presence of one complex in the asymmetric unit.

| S-EPMC3310540 | biostudies-literature

Crystallization and preliminary X-ray study of alkaline beta-mannanase from the alkaliphilic Bacillus sp. N16-5.

Project description:The catalytic domain of an alkaline beta-mannanase from the alkaliphilic Bacillus sp. N16-5 has been expressed and purified. The recombinant enzyme was crystallized using the hanging-drop vapour-diffusion method at 298 K. X-ray diffraction data were collected to 1.6 A resolution. The crystal belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 59.03, b = 63.31, c = 83.34 A. Initial phasing was carried out by molecular replacement using the three-dimensional structure of a mannanase from the alkaliphilic Bacillus sp. JAMB602 as a search model.

| S-EPMC2564887 | 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