Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallization and preliminary X-ray analysis of pyridoxine 4-oxidase, the first enzyme in pyridoxine degradation pathway I.

ABSTRACT: Vitamin B(6)-degradation pathway I has recently been identified in Mesorhizobium loti MAFF303099. Pyridoxine 4-oxidase, an FAD-dependent enzyme, is the first enzyme in this pathway and catalyzes the irreversible oxidation of pyridoxine to pyridoxal. The enzyme was overexpressed in Escherichia coli with a His(6) tag and purified. The recombinant enzyme was crystallized at 277 K by the sitting-drop vapour-diffusion method using PEG 4000 as the precipitant. The crystal, which belonged to space group P2(1)2(1)2(1) with unit-cell parameters a = 62.38, b = 79.44, c = 136.43 Å, diffracted to 2.2 Å resolution. The calculated V(M) value (3.19 Å(3) Da(-1)) suggested that the asymmetric unit contained one molecule.

SUBMITTER: Mugo AN

PROVIDER: S-EPMC3253838 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallization and preliminary X-ray analysis of pyridoxine 4-oxidase, the first enzyme in pyridoxine degradation pathway I.

Mugo Andrew Njagi AN Kobayashi Jun J Mikami Bunzo B Ohnishi Kouhei K Yagi Toshiharu T

Acta crystallographica. Section F, Structural biology and crystallization communications 20111224 Pt 1

Vitamin B(6)-degradation pathway I has recently been identified in Mesorhizobium loti MAFF303099. Pyridoxine 4-oxidase, an FAD-dependent enzyme, is the first enzyme in this pathway and catalyzes the irreversible oxidation of pyridoxine to pyridoxal. The enzyme was overexpressed in Escherichia coli with a His(6) tag and purified. The recombinant enzyme was crystallized at 277 K by the sitting-drop vapour-diffusion method using PEG 4000 as the precipitant. The crystal, which belonged to space grou ...[more]

PMID: 22232175

Similar Datasets

Crystallization and preliminary X-ray analysis of AAMS amidohydrolase, the final enzyme in degradation pathway I of pyridoxine.

Project description:alpha-(N-Acetylaminomethylene)succinic acid (AAMS) amidohydrolase from Mesorhizobium loti MAFF303099, which is involved in a degradation pathway of vitamin B(6) and catalyzes the degradation of AAMS to acetic acid, ammonia, carbon dioxide and succinic semialdehyde, has been overexpressed in Escherichia coli. To elucidate the reaction mechanism based on the tertiary structure, the recombinant enzyme was purified and crystallized by the sitting-drop vapour-diffusion method using PEG 8000 as precipitant. A crystal of the enzyme belonged to the monoclinic space group C2, with unit-cell parameters a = 393.2, b = 58.3, c = 98.9 A, beta = 103.4 degrees , and diffraction data were collected to 2.7 A resolution. The V(M) value and calculation of the self-rotation function suggested that three dimers with a threefold symmetry were possibly present in the asymmetric unit.

| S-EPMC2720345 | biostudies-literature

Cloning, expression, purification, crystallization and preliminary X-ray studies of a pyridoxine 5'-phosphate oxidase from Mycobacterium smegmatis.

Project description:Pyridoxine 5'-phosphate oxidases (PNPOxs) are known to catalyse the terminal step in pyridoxal 5'-phosphate biosynthesis in a flavin mononucleotide-dependent manner in humans and Escherichia coli. Recent reports of a putative PNPOx from Mycobacterium tuberculosis, Rv1155, suggest that the cofactor or catalytic mechanism may differ in Mycobacterium species. To investigate this, a putative PNPOx from M. smegmatis, Msmeg_3380, has been cloned. This enzyme has been recombinantly expressed in E. coli and purified to homogeneity. Good-quality crystals of selenomethionine-substituted Msmeg_3380 were obtained by the hanging-drop vapour-diffusion technique and diffracted to 1.2 A using synchrotron radiation.

| S-EPMC2376410 | biostudies-literature

Crystallization and preliminary X-ray analysis of Aspergillus oryzae catechol oxidase.

Project description:Catechol oxidase is an enzyme that catalyzes the oxidation of o-diphenols to the corresponding o-quinones. It is a copper-containing enzyme with a binuclear copper active site. Here, the crystallization and multiple-wavelength anomalous dispersion data collection of catechol oxidase from the mould fungus Aspergillus oryzae are described. During the purification, three forms of the enzyme (39.3, 40.5 and 44.3?kDa) were obtained. A mixture of these three forms was initially crystallized and gave crystals that diffracted to 2.5?Å resolution and belonged to space group P3(2)21, with unit-cell parameters a = b = 118.9, c = 84.5?Å, ? = ? = 90, ? = 120°. A preparation containing only the shorter form (39.3?kDa) produced crystals that diffracted to 2.9?Å resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 51.8, b = 95.3, c = 139.5?Å, ? = ? = ? = 90°.

| S-EPMC3107139 | biostudies-literature

Crystallization and preliminary X-ray analysis of formate oxidase, an enzyme of the glucose-methanol-choline oxidoreductase family.

Project description:Formate oxidase (FOD), which catalyzes the oxidation of formate to yield carbon dioxide and hydrogen peroxide, belongs to the glucose-methanol-choline oxidoreductase (GMCO) family. FOD from Aspergillus oryzae RIB40, which has a modified FAD as a cofactor, was crystallized at 293 K by the hanging-drop vapour-diffusion method. The crystal was orthorhombic and belonged to space group C222(1). Diffraction data were collected from a single crystal to 2.4 A resolution.

| S-EPMC2935228 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of polyphenol oxidase from Juglans regia (jrPPO1).

Project description:Tyrosinase is a type 3 copper enzyme that catalyzes the ortho-hydroxylation of monophenols to diphenols as well as their subsequent oxidation to quinones, which are precursors for the biosynthesis of melanins. The first plant tyrosinase from walnut leaves (Juglans regia) was purified to homogeneity and crystallized. During the purification, two forms of the enzyme differing only in their C-termini [jrPPO1(Asp101-Pro444) and jrPPO1(Asp101-Arg445)] were obtained. The most abundant form jrPPO1(Asp101-Arg445), as described in Zekiri et al. [Phytochemistry (2014), 101, 5-15], was crystallized, resulting in crystals that belonged to space group C121, with unit-cell parameters a=115.56, b=91.90, c=86.87?Å, ?=90, ?=130.186, ?=90°, and diffracted to 2.39?Å resolution. Crystals were only obtained from solutions containing at least 30% polyethylene glycol 5000 monomethyl ether in a close-to-neutral pH range.

| S-EPMC4051548 | biostudies-literature

Crystallization and preliminary X-ray diffraction analysis of an L-amino-acid oxidase from Bothrops jararacussu venom.

Project description:Snake-venom L-amino-acid oxidases (SV-LAAOs) trigger a wide range of local and systematic effects, including inhibition of platelet aggregation, cytotoxicity, haemolysis, apoptosis and haemorrhage. These effects mainly arise from the uncontrolled release of the hydrogen peroxide that is produced by the redox reaction involving L-amino acids catalyzed by these flavoenzymes. Taking their clinical relevance into account, few SV-LAAOs have been structurally characterized and the structural determinants responsible for their broad direct and indirect pharmacological activities remain unclear. In this work, an LAAO from Bothrops jararacussu venom (BJu-LAAO) was purified and crystallized. The BJu-LAAO crystals belonged to space group P2(1), with unit-cell parameters a = 66.38, b = 72.19, c = 101.53 Å, ? = 90.9°. The asymmetric unit contained two molecules and the structure was determined and partially refined at 3.0 Å resolution.

| S-EPMC3274406 | biostudies-literature

Crystallization and preliminary X-ray characterization of the Bacillus amyloliquefaciens YwrO enzyme.

Project description:CB1954 is an anticancer prodrug that is currently in clinical trials coupled with the Escherichia coli flavoenzyme nitroreductase (NTR) for use in directed-enzyme prodrug therapy (DEPT). The NTR enzyme is responsible for the conversion of the prodrug into a cytotoxic agent. The bifunctional alkylating agent produced by this bioactivation process leads to DNA damage and death of cancer cells. Recently, a novel flavoenzyme from Bacillus amyloliquefaciens, YwrO (Bam YwrO), was reported to be able to reduce CB1954 from its noncytotoxic form into its active form. The crystallization and preliminary X-ray diffraction analysis of two crystal forms of Bam YwrO are reported. The first crystal form is orthorhombic, with space group P22(1)2(1), and diffracts X-rays to 2.18 A resolution. The second crystal form is tetragonal, with space group P4(1), and diffracts X-rays to 3.4 A. Determination of the Bam YwrO crystal structure will provide an understanding of the molecular recognition between this enzyme and the anticancer prodrug CB1954.

| S-EPMC2376317 | biostudies-literature

Crystallization and preliminary X-ray analysis of ZHE1, a hatching enzyme from the zebrafish Danio rerio.

Project description:The hatching enzyme of the zebrafish, ZHE1 (29.3 kDa), is a zinc metalloprotease that catalyzes digestion of the egg envelope (chorion). ZHE1 was heterologously expressed in Escherichia coli, purified and crystallized by the hanging-drop vapour-diffusion method using PEG 3350 as the precipitant. Two diffraction data sets with resolution ranges 50.0-1.80 and 50.0-1.14 A were independently collected from two crystals and were merged to give a highly complete data set over the full resolution range 50.0-1.14 A. The space group was assigned as primitive orthorhombic P2(1)2(1)2(1), with unit-cell parameters a = 32.9, b = 62.5, c = 87.4 A. The crystal contained one ZHE1 molecule in the asymmetric unit.

| S-EPMC2765890 | biostudies-literature

Isolation, crystallization and preliminary X-ray diffraction analysis of L-amino-acid oxidase from Vipera ammodytes ammodytes venom.

Project description:L-Amino-acid oxidase from the venom of Vipera ammodytes ammodytes, the most venomous snake in Europe, was isolated and crystallized using the sitting-drop vapour-diffusion method. The solution conditions under which the protein sample was monodisperse were optimized using dynamic light scattering prior to crystallization. The crystals belonged to space group C2, with unit-cell parameters a = 198.37, b = 96.38, c = 109.11 A, beta = 92.56 degrees . Initial diffraction data were collected to 2.6 A resolution. The calculated Matthews coefficient is approximately 2.6 A(3) Da(-1) assuming the presence of four molecules in the asymmetric unit.

| S-EPMC2564880 | biostudies-literature

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of variants of monoamine oxidase from Aspergillus niger.

Project description:Monoamine oxidase from Aspergillus niger (MAO-N) is an FAD-dependent enzyme that catalyses the conversion of terminal amines to their corresponding aldehydes. Variants of MAO-N produced by directed evolution have been shown to possess altered substrate specificity. Crystals of two of these variants (MAO-N-3 and MAO-N-5) have been obtained; the former displays P2(1) symmetry with eight molecules per asymmetric unit and the latter has P4(1)2(1)2 or P4(3)2(1)2 symmetry and two molecules per asymmetric unit. Solution of these structures will help shed light on the molecular determinants of improved activity and high enantioselectivity towards a broad range of substrates.

| S-EPMC2374162 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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