Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallization and preliminary X-ray diffraction analysis of the diterpene cyclooctatin synthase (CYC) from Streptomyces sp. LZ35.

ABSTRACT: Terpenoids are a large and highly diverse group of natural products, with the most chemically diverse pool of structures. Terpene synthase is the key enzyme in the process of terpenoid synthesis. In this paper, the first diterpene synthase (CYC) of bacterial origin was successfully crystallized. Native and SeMet-derivative crystals diffracted to 1.75 and 2.6?Å resolution, respectively. The native crystal belonged to space group P212121, with unit-cell parameters a = 59.10, b = 101.73, c = 108.93?Å, and contained two molecules per asymmetric unit. The SeMet-derivative crystal belonged to space group P21, with unit-cell parameters a = 58.64, b = 109.47, c = 58.73?Å, ? = 119.35°, and had two molecules per asymmetric unit.

SUBMITTER: Zhang X

PROVIDER: S-EPMC3944704 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallization and preliminary X-ray diffraction analysis of the diterpene cyclooctatin synthase (CYC) from Streptomyces sp. LZ35.

Zhang Xiulei X Shang Guijun G Gu Lichuan L Shen Yuemao Y

Acta crystallographica. Section F, Structural biology communications 20140220 Pt 3

Terpenoids are a large and highly diverse group of natural products, with the most chemically diverse pool of structures. Terpene synthase is the key enzyme in the process of terpenoid synthesis. In this paper, the first diterpene synthase (CYC) of bacterial origin was successfully crystallized. Native and SeMet-derivative crystals diffracted to 1.75 and 2.6 Å resolution, respectively. The native crystal belonged to space group P212121, with unit-cell parameters a = 59.10, b = 101.73, c = 108.93 ...[more]

PMID: 24598929

Similar Datasets

Crystallization and preliminary X-ray diffraction analysis of AntE, a crotonyl-CoA carboxylase/reductase from Streptomyces sp. NRRL 2288.

Project description:AntE from Streptomyces sp. NRRL 2288 is a crotonyl-CoA carboxylase/reductase that catalyzes the reductive carboxylation of various ?,?-unsaturated acyl-CoAs to provide the building block at the C7 position for antimycin A biosynthesis. Recombinant AntE expressed in Escherichia coli was crystallized by the sitting-drop vapour-diffusion method. The crystals belonged to space group I222 or I2?2?2?, with unit-cell parameters a=76.4, b=96.7, c=129.6?Å, ?=?=?=90.0°. A diffraction data set was collected at the KEK Photon Factory to 2.29?Å resolution.

| S-EPMC4051525 | biostudies-literature

Crystallization and X-ray diffraction analysis of a putative bacterial class I labdane-related diterpene synthase.

Project description:Labdane-related diterpenoids are natural products with potential pharmaceutical applications that are rarely found in bacteria. Here, a putative class I labdane-related diterpene synthase (LrdC) identified by genome mining in a streptomycete was successfully crystallized using the microbatch method. Crystals of the LrdC enzyme were obtained in a holo form with its natural cofactor Mg(2+) (LrdC-Mg(2+)) and in complex with inorganic pyrophosphate (PPi) (LrdC-Mg(2+)-PPi). Crystals of native LrdC-Mg(2+) diffracted to 2.50?Å resolution and belonged to the trigonal space group P3221, with unit-cell parameters a = b = 107.1, c = 89.2?Å. Crystals of the LrdC-Mg(2+)-PPi complex grown in the same conditions as the native enzyme with PEG 8000 diffracted to 2.36?Å resolution and also belonged to the trigonal space group P3221. Crystals of the LrdC-Mg(2+)-PPi complex grown in a second crystallization condition with PEG 3350 diffracted to 2.57?Å resolution and belonged to the monoclinic space group P21, with unit-cell parameters a = 49.9, b = 104.1, c = 66.5?Å, ? = 111.4°. The structure was determined by the single-wavelength anomalous dispersion (SAD) technique using the osmium signal from a potassium hexachloroosmate (IV) derivative.

| S-EPMC4555928 | biostudies-literature

Crystallization and preliminary X-ray diffraction analysis of mouse prostaglandin F2? synthase, AKR1B3.

Project description:Aldo-keto reductase 1B3 (AKR1B3) catalyzes the NADPH-dependent reduction of prostaglandin H(2) (PGH(2)), which is a common intermediate of various prostanoids, to form PGF(2?). AKR1B3 also reduces PGH(2) to PGD(2) in the absence of NADPH. AKR1B3 produced in Escherichia coli was crystallized in complex with NADPH by the sitting-drop vapour-diffusion method. The crystal was tetragonal, belonging to space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = b = 107.62, c = 120.76 Å. X-ray diffraction data were collected to 2.4 Å resolution at 100 K using a synchrotron-radiation source.

| S-EPMC3232157 | biostudies-literature

Crystallization and preliminary X-ray diffraction analysis of the small laccase from Streptomyces coelicolor.

Project description:The small bacterial laccase from the actinobacterium Streptomyces coelicolor which lacks the second of the three domains of the laccases structurally characterized to date was crystallized. This multi-copper phenol oxidase crystallizes in a primitive tetragonal lattice, with unit-cell parameters a = b = 179.8, c = 175.3 A. The crystals belong to either space group P4(1)2(1)2 or P4(3)2(1)2. The self-rotation function shows the presence of a noncrystallographic threefold axis in the structure. Phases will be determined from the anomalous signal of the natively present copper ions.

| S-EPMC2344102 | biostudies-literature

Preliminary X-ray diffraction analysis of thermostable ?-1,4-xylanase from Streptomyces sp. S9.

Project description:Xylanase, which catalyzes the random hydrolysis of internal xylosidic linkages, is a critical enzyme participating in xylan decomposition and has been widely applied in industrial utilizations. Xylanase isolated from the extremophilic Streptomyces sp. S9 (XynAS9) possesses broad adaptability to temperature and pH and thus is an attractive candidate in industrial applications. In particular, the major products of XynAS9 are xylose and xylobiose, which enable the subsequent bioconversion to be carried out with higher efficiency. Therefore, the three-dimensional structure of XynAS9 and its catalytic machinery are of great interest. Here, recombinant XynAS9 protein was expressed in Pichia pastoris, purified and crystallized. Crystals belonging to the hexagonal space group P6(5)22, with unit-cell parameters a = b = 80.9, c = 289.3?Å, were obtained by the sitting-drop vapour-diffusion method and diffracted to 2.08?Å resolution. Initial phase determination using molecular replacement indicated that the crystal contains one molecule in an asymmetric unit. Further model building and structural refinement are in progress.

| S-EPMC3943089 | biostudies-literature

The purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Clostridium botulinum.

Project description:In recent years, dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) has received considerable attention from both mechanistic and structural viewpoints. This enzyme, which is part of the diaminopimelate pathway leading to lysine, couples (S)-aspartate-beta-semialdehyde with pyruvate via a Schiff base to a conserved active-site lysine. In this paper, the expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPS from Clostridium botulinum, an important bacterial pathogen, are presented. The enzyme was crystallized in a number of forms, predominantly using PEG precipitants, with the best crystal diffracting to beyond 1.9 A resolution and displaying P4(2)2(1)2 symmetry. The unit-cell parameters were a = b = 92.9, c = 60.4 A. The crystal volume per protein weight (V(M)) was 2.07 A(3) Da(-1), with an estimated solvent content of 41%. The structure of the enzyme will help guide the design of novel therapeutics against the C. botulinum pathogen.

| S-EPMC2374160 | biostudies-literature

Expression, purification, crystallization and preliminary X-ray diffraction analysis of EtFPOX from Eupenicillium terrenum sp.

Project description:The flavoenzyme fructosyl peptide oxidase (FPOX) catalyses the oxidative deglycation of fructosyl amino acids or fructosyl dipeptides to produce amino acids, glucosone and hydrogen peroxide. In this study, FPOX protein from Eupenicillium terrenum sp. (EtFPOX) was expressed in Escherichia coli and purified by Ni-affinity and gel-filtration chromatography. EtFPOX crystals were obtained using the sitting-drop vapour-diffusion method with polyethylene glycol 3350 as precipitant. X-ray diffraction data were collected to 1.90 Å resolution using a synchrotron-radiation source. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 65.6, b = 80.0, c = 83.4 Å, and contained one molecule in the asymmetric unit. The calculated Matthews coefficient and solvent content were 2.22 Å(3) Da(-1) and 44.62%, respectively.

| S-EPMC3668590 | biostudies-literature

Purification, crystallization and preliminary X-ray diffraction analysis of Omp6, a protoilludene synthase from Omphalotus olearius.

Project description:Basidiomycetes produce a wide range of industrially relevant natural products. One of the main classes of natural products isolated from fungi are terpenoids, a highly diverse group of secondary metabolites, many of which are bioactive and have been adapted for pharmaceutical purposes. The discovery of a suite of novel sesquiterpene synthases from Omphalotus olearius via genome sequencing and bioinformatic analyses has recently been described. Here, the expression, purification and crystallization of one of these enzymes (Omp6), a protoilludene synthase, is reported. A native crystal diffracted to a resolution of 2.9?Å and belonged to space group P21, with unit-cell parameters a = 43.67, b = 76.76, c = 107.22?Å, ? = ? = 90, ? = 95°. A diffraction data set was collected on a home-source Rigaku/MSC MicroMax-007 X-ray generator.

| S-EPMC3660905 | 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

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

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