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 a family 10 alkali-thermostable xylanase from alkalophilic Bacillus sp. strain NG-27.

ABSTRACT: Xylanases (EC 3.2.1.8) catalyze the hydrolysis of beta-1,4-glycosidic linkages within xylan, a major hemicellulose component in the biosphere. The extracellular endoxylanase (XylnA) from the alkalophilic Bacillus sp. strain NG-27 belongs to family 10 of the glycoside hydrolases. It is active at 343 K and pH 8.4. Moreover, it has attractive features from the point of view of utilization in the paper pulp, animal feed and baking industries since it is an alkali-thermostable protein. In this study, XylnA was purified from the native host source and crystallized by the hanging-drop vapour-diffusion method. The crystals belong to the monoclinic space group C2, with unit-cell parameters a = 174.5, b = 54.7, c = 131.5 A, beta = 131.2 degrees, and diffract to better than 2.2 A resolution.

SUBMITTER: Manikandan K

PROVIDER: S-EPMC1952343 | biostudies-literature | 2005 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallization and preliminary X-ray study of a family 10 alkali-thermostable xylanase from alkalophilic Bacillus sp. strain NG-27.

Manikandan K K Bhardwaj Amit A Ghosh Amit A Reddy V S VS Ramakumar S S

Acta crystallographica. Section F, Structural biology and crystallization communications 20050708 Pt 8

Xylanases (EC 3.2.1.8) catalyze the hydrolysis of beta-1,4-glycosidic linkages within xylan, a major hemicellulose component in the biosphere. The extracellular endoxylanase (XylnA) from the alkalophilic Bacillus sp. strain NG-27 belongs to family 10 of the glycoside hydrolases. It is active at 343 K and pH 8.4. Moreover, it has attractive features from the point of view of utilization in the paper pulp, animal feed and baking industries since it is an alkali-thermostable protein. In this study, ...[more]

PMID: 16511146

Similar Datasets

Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions.

Project description:Crystal structures are known for several glycosyl hydrolase family 10 (GH10) xylanases. However, none of them is from an alkalophilic organism that can grow in alkaline conditions. We have determined the crystal structures at 2.2 Angstroms of a GH10 extracellular endoxylanase (BSX) from an alkalophilic Bacillus sp. NG-27, for the native and the complex enzyme with xylosaccharides. The industrially important enzyme is optimally active and stable at 343 K and at a pH of 8.4. Comparison of the structure of BSX with those of other thermostable GH10 xylanases optimally active at acidic or close to neutral pH showed that the solvent-exposed acidic amino acids, Asp and Glu, are markedly enhanced in BSX, while solvent-exposed Asn was noticeably depleted. The BSX crystal structure when compared with putative three-dimensional homology models of other extracellular alkalophilic GH10 xylanases from alkalophilic organisms suggests that a protein surface rich in acidic residues may be an important feature common to these alkali thermostable enzymes. A comparison of the surface features of BSX and of halophilic proteins allowed us to predict the activity of BSX at high salt concentrations, which we verified through experiments. This offered us important lessons in the polyextremophilicity of proteins, where understanding the structural features of a protein stable in one set of extreme conditions provided clues about the activity of the protein in other extreme conditions. The work brings to the fore the role of the nature and composition of solvent-exposed residues in the adaptation of enzymes to polyextreme conditions, as in BSX.

| S-EPMC2242578 | biostudies-literature

Bleach enhancement of mixed wood pulp by mixture of thermo-alkali-stable xylanase and mannanase derived through co-culturing of Alkalophilic <i>Bacillus</i> sp. NG-27 and <i>Bacillus nealsonii</i> PN-11.

Project description:The Application of a combination of enzymes is the best alternative to reduce the use of chemicals in the paper industry. Bacillus sp. NG-27 and Bacillus nealsonii PN-11 are known to produce thermoalkali stable xylanse (X) and mannanase (M) respectively having potential for pulp biobleaching. The Present study, reports the production of a mixture of X + M by co-culturing of strains in SSF and standardizing its application for pulp biobleaching. Production of enzymes by co-cultivation in SSF was optimized by statistical methods. Substantial increase in the yield of enzymes; 3.61 fold of xylanase and 37.71 fold of mannanase was achieved. Application of enzyme cocktail for pulp biobleaching resulted in a 45.64% reduction of kappa number with 55 IU g-1odp of enzyme dose (xylanase:mannanase; 3:1) at pH 8.0 in 1h at 65 °C along with significant increase in brightness (11%) and whiteness (75%). The Same quality of paper as made up from chemical treated pulp can be made from enzyme-treated pulp with 30% less use of chlorine. Structural analysis of enzyme-treated pulp showed dissolution of hemicellulose as indicated by pores, cracks and increased roughness all over the surface. Cocktail of X + M produced economically in a single fermentation having all the requisite characteristics for pulp biobleaching is a highly suitable candidate for application in the pulp and paper industry.

| S-EPMC7855340 | biostudies-literature

Expression, crystallization and preliminary X-ray diffraction studies of thermostable ?-1,3-xylanase from Thermotoga neapolitana strain DSM?4359.

Project description:Crystals of ?-1,3-xylanase (1,3-?-D-xylan xylanohydrolase; EC 3.2.1.32) from Thermotoga neapolitana strain DSM?4359 with maximum dimensions of 0.2×0.1×0.02?mm were grown using the sitting-drop vapour-diffusion method at 293?K over 24?h. The crystals diffracted to a resolution of 1.82?Å, allowing structure determination. The crystals belonged to space group P2(1), with unit-cell parameters a=39.061, b=75.828, c=52.140?Å; each asymmetric unit cell contained a single molecule.

| S-EPMC3144794 | biostudies-literature

Preliminary X-ray diffraction analysis of thermostable β-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

Crystallization and preliminary X-ray crystallographic analysis of a thermostable organic solvent-tolerant lipase from Bacillus sp. strain 42.

Project description:An organic solvent-tolerant lipase from Bacillus sp. strain 42 was crystallized using the capillary-tube method. The purpose of studying this enzyme was in order to better understand its folding and to characterize its properties in organic solvents. By initially solving its structure in the native state, further studies on protein-solvent interactions could be performed. X-ray data were collected at 2.0?Å resolution using an in-house diffractometer. The estimated crystal dimensions were 0.09×0.19×0.08?mm. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a=117.41, b=80.85, c=99.44?Å, ?=96.40°.

| S-EPMC3053172 | biostudies-literature

Crystallization and preliminary X-ray crystallographic analysis of highly thermostable L2 lipase from the newly isolated Bacillus sp. L2.

Project description:Purified thermostable recombinant L2 lipase from Bacillus sp. L2 was crystallized by the counter-diffusion method using 20% PEG 6000, 50 mM MES pH 6.5 and 50 mM NaCl as precipitant. X-ray diffraction data were collected to 2.7 A resolution using an in-house Bruker X8 PROTEUM single-crystal diffractometer system. The crystal belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 87.44, b = 94.90, c = 126.46 A. The asymmetric unit contained one single molecule of protein, with a Matthews coefficient (V(M)) of 2.85 A(3) Da(-1) and a solvent content of 57%.

| S-EPMC2882778 | biostudies-literature

Studies on an alkali-thermostable xylanase from Aspergillus fumigatus MA28.

Project description:An alkalitolerant fungus, Aspergillus fumigatus strain MA28 produced significant amounts of cellulase-free xylanase when grown on a variety of agro-wastes. Wheat bran as the sole carbon source supported higher xylanase production (8,450 U/L) than xylan (7,500 U/L). Soybean meal was observed to be the best nitrogen source for xylanase production (9,000 U/L). Optimum medium pH for xylanase production was 8 (9,800 U/L), though, significant quantities of the enzyme was also produced at pH 7 (8,500 U/L), 9 (8,200 U/L) and 10 (4,600 U/L). The xylanase was purified by ammonium sulphate precipitation and carboxymethyl cellulose chromatography, and was found to have a molecular weight of 14.4 kDa with a V(max) of 980 μmol/min/mg of protein and a K(m) of approximately 4.9 mg/mL. The optimum temperature and pH for enzyme activity was 50 °C and pH 8, respectively. However, the enzyme also showed substantial residual activity at 60-70 °C (53-75%) and at alkaline pH 8-9 (56-88%).

| S-EPMC3339620 | biostudies-literature

Crystallization and preliminary X-ray study of a thermostable alanine racemase from Thermoanaerobacter tengcongensis MB4.

Project description:Alanine racemase (Alr(MB4)), a dimeric PLP-dependent thermostable enzyme from the anaerobic eubacterium Thermoanaerobacter tengcongensis MB4, was expressed and purified with a His(6) tag in a form suitable for X-ray crystallographic analysis. Crystals were grown by the hanging-drop vapour-diffusion method at 289 K using a solution consisting of 0.1 M bis-tris pH 7.0, 22%(w/v) polyethylene glycol 4000. X-ray diffraction data were collected to 2.6 Å resolution. The crystal belonged to the orthorhombic space group P2(1)2(1)2(1), with two protein molecules in an asymmetric unit.

| S-EPMC3668588 | 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 a phosphopentomutase from Bacillus cereus.

Project description:Phosphopentomutases (PPMs) interconvert D-ribose 5-phosphate and alpha-D-ribose 1-phosphate to link glucose and nucleotide metabolism. PPM from Bacillus cereus was overexpressed in Escherichia coli, purified to homogeneity and crystallized. Bacterial PPMs are predicted to contain a di-metal reaction center, but the catalytically relevant metal has not previously been identified. Sparse-matrix crystallization screening was performed in the presence or absence of 50 mM MnCl(2). This strategy resulted in the formation of two crystal forms from two chemically distinct conditions. The crystals that formed with 50 mM MnCl(2) were more easily manipulated and diffracted to higher resolution. These results suggest that even if the catalytically relevant metal is not known, the crystallization of putative metalloproteins may still benefit from supplementation of the crystallization screens with potential catalytic metals.

| S-EPMC2898468 | 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