Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Structure of Debaryomyces castellii CBS 2923 phytase.

ABSTRACT: Phytate (myo-inositol hexakisphosphate) is the primary storage form of phosphate in seeds and legumes (Reddy et al., 1982). Phytases are phosphatases that hydrolyze phytate to less phosphorylated myo-inositol derivatives and inorganic phosphate. The crystal structure of phytase from Debaryomyces castellii has been determined at 2.3 A resolution. The crystals belonged to space group P6(5)22, with unit-cell parameters a = 121.65, c = 332.24 A. The structure was solved by molecular replacement and refined to a final R factor of 15.7% (R(free) = 20.9%). The final model consists of a dimer (with two monomers of 458 residues), five NAG molecules and 628 water molecules.

SUBMITTER: Ragon M

PROVIDER: S-EPMC2664750 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Structure of Debaryomyces castellii CBS 2923 phytase.

Ragon M M Hoh F F Aumelas A A Chiche L L Moulin G G Boze H H

Acta crystallographica. Section F, Structural biology and crystallization communications 20090325 Pt 4

Phytate (myo-inositol hexakisphosphate) is the primary storage form of phosphate in seeds and legumes (Reddy et al., 1982). Phytases are phosphatases that hydrolyze phytate to less phosphorylated myo-inositol derivatives and inorganic phosphate. The crystal structure of phytase from Debaryomyces castellii has been determined at 2.3 A resolution. The crystals belonged to space group P6(5)22, with unit-cell parameters a = 121.65, c = 332.24 A. The structure was solved by molecular replacement and ...[more]

PMID: 19342770

Similar Datasets

Phytase

Project description:Experimental trial using phytase in the diet for broiler

| PRJEB12987 | ENA

Debaryomyces fabryi strain:CBS 789

Project description:Debaryomyces fabryi strain:CBS 789 Genome sequencing and assembly

| PRJNA288902 | ENA

Chicen microbiota phytase

Project description:Comparison of two phytase products assessed by different regression approaches and the ileal microbiota

| PRJEB38381 | ENA

Transgenic soybean expressing a thermostable phytase as substitution for feed additive phytase.

Project description:Phytase is one of the most effective feed additives to increase the availability of phosphorus and minerals by catalyzing the hydrolysis of phytic acid. A modified appA gene (mappA) was transformed into soybean (Glycine max) under the control of a seed-specific promoter from common bean (Phaselous vulgaris). The soybean recombinant phytase showed optimal activity at pH 4.5 and 70?°C. A slight increase in enzyme activity occurred when the recombinant enzyme was pre-incubated with n-hexane. In addition, the phytase activity from our transgenic soybean does not reduce even after 2?hours of extraction with n-hexane at 55~65?°C. In conclusion, the oil extraction process using n-hexane does not inactivate the phytase expressed in the mAppA transgenic soybean, and the meal derived from the transgenic soybean processing can be used as feed supplement to livestock.

| S-EPMC6779883 | biostudies-literature

Structure of a cereal purple acid phytase provides new insights to phytate degradation in plants.

Project description:Grain phytate, a mixed metal ion salt of inositol hexakisphosphate, accounts for 60%-80% of stored phosphorus in plants and is a potent antinutrient of non-ruminant animals including humans. Through neofunctionalization of purple acid phytases (PAPhy), some cereals such as wheat and rye have acquired particularly high mature grain phytase activity. As PAPhy activity supplies phosphate, liberates metal ions necessary for seedling emergence, and obviates antinutrient effects of phytate, its manipulation and control are targeted crop traits. Here we show the X-ray crystal structure of the b2 isoform of wheat PAPhy induced during germination. This high-resolution crystal structure suggests a model for phytate recognition that, validated by molecular dynamics simulations, implicates elements of two sequence inserts (termed PAPhy motifs) relative to a canonical metallophosphoesterase (MPE) domain in forming phytate-specific substrate specificity pockets. These motifs are well conserved in PAPhys from monocot cereals, enzymes which are characterized by high specificity for phytate. Tested by mutagenesis, residues His229 in PAPhy motif 4 and Lys410 in the MPE domain, both conserved in PAPhys, are found to strongly influence phytase activity. These results explain the observed phytase activity of cereal PAPhys and open the way to the rational engineering of phytase activity in planta.

| S-EPMC9073318 | biostudies-literature

Phytase activity in lichens.

Project description:Phytase activity was investigated in 13 lichen species using a novel assay method. The work tested the hypothesis that phytase is a component of the suite of surface-bound lichen enzymes that hydrolyse simple organic forms of phosphorus (P) and nitrogen (N) deposited onto the thallus surface. Hydrolysis of inositol hexaphosphate (InsP6 , the substrate for phytase) and appearance of lower-order inositol phosphates (InsP5 -InsP1 ), the hydrolysis products, were measured by ion chromatography. Phytase activity in Evernia prunastri was compared among locations with contrasting rates of N deposition. Phytase activity was readily measurable in epiphytic lichens (e.g. 11.3 ?mol InsP6 hydrolysed g(-1) h(-1) in Bryoria fuscescens) but low in two terricolous species tested (Cladonia portentosa and Peltigera membranacea). Phytase and phosphomonoesterase activities were positively correlated amongst species. In E. prunastri both enzyme activities were promoted by N enrichment and phytase activity was readily released into thallus washings. InsP6 was not detected in tree canopy throughfall but was present in pollen leachate. Capacity to hydrolyse InsP6 appears widespread amongst lichens potentially promoting P capture from atmospheric deposits and plant leachates, and P cycling in forest canopies. The enzyme assay used here might find wider application in studies on plant root-fungal-soil systems.

| S-EPMC5029771 | biostudies-literature

Debaryomyces

Project description:Debaryomyces sp. overview

| PRJNA649637 | ENA

Debaryomyces hansenii strain:CBS 767 (ATCC 36239)

Project description:Debaryomyces hansenii strain:CBS 767 (ATCC 36239) Genome sequencing and assembly

| PRJNA970382 | ENA

"In Silico" Characterization of 3-Phytase A and 3-Phytase B from Aspergillus niger.

Project description:Phytases are used for feeding monogastric animals, because they hydrolyze phytic acid generating inorganic phosphate. Aspergillus niger 3-phytase A (PDB: 3K4Q) and 3-phytase B (PDB: 1QFX) were characterized using bioinformatic tools. Results showed that both enzymes have highly conserved catalytic pockets, supporting their classification as histidine acid phosphatases. 2D structures consist of 43% alpha-helix, 12% beta-sheet, and 45% others and 38% alpha-helix, 12% beta-sheet, and 50% others, respectively, and pI 4.94 and 4.60, aliphatic index 72.25 and 70.26 and average hydrophobicity of -0,304 and -0.330, respectively, suggesting aqueous media interaction. Glycosylation and glycation sites allowed detecting zones that can affect folding and biological activity, suggesting fragmentation. Docking showed that H59 and H63 act as nucleophiles and that D339 and D319 are proton donor residues. MW of 3K4Q (48.84 kDa) and 1QFX (50.78 kDa) is similar; 1QFX forms homodimers which will originate homotetramers with several catalytic center accessible to the ligand. 3K4Q is less stable (instability index 45.41) than 1QFX (instability index 33.66), but the estimated lifespan for 3K4Q is superior. Van der Waals interactions generate hydrogen bonds between the active center and O2 or H of the phytic acid phosphate groups, providing greater stability to these temporal molecular interactions.

| S-EPMC5733987 | biostudies-other

Draft Genome Sequence of Lactarius deliciosus Strain CBS 582.63 from the CBS-KNAW Culture Collection.

Project description:A type strain of Lactarius deliciosus was obtained from the CBS-KNAW culture collection. The mycelium was cultured using potato dextrose agar, and the extracted genomic DNA was subjected to PacBio genome sequencing. Upon assembly and annotation, the genome size was estimated to be 54 Mbp, with 12,753 genes.

| S-EPMC7242683 | 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