scholarly journals Crystallization and preliminary X-ray diffraction studies of the family 54 carbohydrate-binding module from laminarinase (β-1,3-glucanase) Lic16A ofClostridium thermocellum

2015 ◽  
Vol 71 (2) ◽  
pp. 217-220 ◽  
Author(s):  
Yury A. Kislitsyn ◽  
Valeriya R. Samygina ◽  
Igor A. Dvortsov ◽  
Nataliya A. Lunina ◽  
Inna P. Kuranova ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Diffusion Method ◽  
Carbohydrate Binding ◽  
Carbohydrate Binding Module ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
The Family ◽  
Overexpression System

The crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding module (CBM) from laminarinase Lic16A of the hyperthermophilic anaerobic bacteriumClostridium thermocellum(ctCBM54) are reported. Recombinant ctCBM54 was prepared using anEscherichia coli/pQE30 overexpression system and was crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.1 Å resolution using synchrotron radiation. The crystals belonged to space groupP6322, with unit-cell parametersa=b= 130.15,c= 131.05 Å. The three-dimensional structure of ctCBM54 will provide valuable information about the structure–function relation of the laminarinase Lic16A and will allow the exploitation of this binding module in biotechnological applications.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of a single variable domain of the immunoglobulin superfamily in amphioxus,Amphi-IgSF-V

2014 ◽  
Vol 70 (8) ◽  
pp. 1072-1075 ◽  
Author(s):  
Bo Jiang ◽  
Yanjie Liu ◽  
Rong Chen ◽  
Zhenbao Wang ◽  
Mansoor Tariq ◽  
...  
Keyword(s):  
Immune System ◽  
Structural Information ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Immunoglobulin Superfamily ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
System A ◽  
Human Immunoglobulins

Amphioxus is regarded as an essential animal model for the study of immune evolution. Discovery of new molecules with the immunoglobulin superfamily (IgSF) variable (V) domain in amphioxus would help in studying the evolution of IgSF V molecules in the immune system. A protein was found which just contains only one IgSF V domain in amphioxus, termedAmphi-IgSF-V; it has over 30% sequence identity to the V domains of human immunoglobulins and mammalian T-cell receptors. In order to clarify the three-dimensional structure of this new molecule in amphioxus,Amphi-IgSF-V was expressed, purified and crystallized, and diffraction data were collected to a resolution of 1.95 Å. The crystal belonged to space groupP3221, with unit-cell parametersa=b= 53.9,c= 135.5 Å. The Matthews coefficient and solvent content were calculated to be 2.58 Å3 Da−1and 52.38%, respectively. The results will provide structural information to study the evolution of IgSF V molecules in the immune system.

scholarly journals Cloning, purification, crystallization and preliminary X-ray studies of a carbohydrate-binding module (CBM_E1) derived from sugarcane soil metagenome

2014 ◽  
Vol 70 (9) ◽  
pp. 1232-1235 ◽  
Author(s):  
Bruna Medeia Campos ◽  
Thabata Maria Alvarez ◽  
Marcelo Vizona Liberato ◽  
Igor Polikarpov ◽  
Harry J. Gilbert ◽  
...  
Keyword(s):  
Fossil Fuels ◽  
Plant Biomass ◽  
Metagenomic Library ◽  
Glycoside Hydrolases ◽  
Diffusion Method ◽  
Carbohydrate Binding ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Carbohydrate Binding Modules

In recent years, owing to the growing global demand for energy, dependence on fossil fuels, limited natural resources and environmental pollution, biofuels have attracted great interest as a source of renewable energy. However, the production of biofuels from plant biomass is still considered to be an expensive technology. In this context, the study of carbohydrate-binding modules (CBMs), which are involved in guiding the catalytic domains of glycoside hydrolases for polysaccharide degradation, is attracting growing attention. Aiming at the identification of new CBMs, a sugarcane soil metagenomic library was analyzed and an uncharacterized CBM (CBM_E1) was identified. In this study, CBM_E1 was expressed, purified and crystallized. X-ray diffraction data were collected to 1.95 Å resolution. The crystals, which were obtained by the sitting-drop vapour-diffusion method, belonged to space groupI23, with unit-cell parametersa=b=c= 88.07 Å.

scholarly journals PicW2 fromPicea wilsonii: preparation, purification, crystallization and X-ray diffraction analysis

2018 ◽  
Vol 74 (6) ◽  
pp. 363-366 ◽  
Author(s):  
Bei Zhang ◽  
Gangxing Guo ◽  
Fang Lu ◽  
Ying Song ◽  
Yong Liu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Gel Filtration ◽  
Three Dimensional ◽  
Temperature Tolerance ◽  
Diffusion Method ◽  
Limiting Factor ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters

Low temperature is a major limiting factor for plant growth and development. Dehydrin proteins are generally induced in response to low-temperature stress. In previous research, a full-length dehydrin gene,PicW2, was isolated fromPicea wilsoniiand its expression was associated with hardiness to cold. In order to gain insight into the mechanism of low-temperature tolerance by studying its three-dimensional crystal structure, prokaryotically expressed PicW2 dehydrin protein was purified using chitosan-affinity chromatography and gel filtration, and crystallized using the vapour-diffusion method. The crystal grew in a condition consisting of 0.1 MHEPES pH 8.0, 25%(w/v) PEG 3350 using 4 mg ml−1protein solution at 289 K. X-ray diffraction data were collected from a crystal at 100 K to 2.82 Å resolution. The crystal belonged to space groupC121, with unit-cell parametersa= 121.55,b= 33.26,c= 73.39 Å, α = γ = 90.00, β = 109.01°. The asymmetric unit contained one molecule of the protein, with a corresponding Matthews coefficient of 2.87 Å3 Da−1and a solvent content of 57.20%. Owing to a lack of structures of homologous dehydrin proteins, molecular-replacement trials failed. Data collection for selenium derivatization of PicW2 and crystal structure determination is currently in progress.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of theEscherichia colicommon pilus chaperone EcpB

2015 ◽  
Vol 71 (6) ◽  
pp. 676-679 ◽  
Author(s):  
James A. Garnett ◽  
Mamou Diallo ◽  
Steve J. Matthews
Keyword(s):  
Heavy Atom ◽  
Three Dimensional ◽  
Solid Surfaces ◽  
Dimensional Structure ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
The Common ◽  
First Time

Pili are key cell-surface components that allow the attachment of bacteria to both biological and abiotic solid surfaces, whilst also mediating interactions between themselves. InEscherichia coli, the common pilus (Ecp) belongs to an alternative chaperone–usher (CU) pathway that plays a major role in both early biofilm formation and host-cell adhesion. The chaperone EcpB is involved in the biogenesis of the filament, which is composed of EcpA and EcpD. Initial attempts at crystallizing EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under denaturing conditions and subsequent refolding, crystals were obtained at pH 8.0 using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.4 Å resolution. These crystals belonged to the trigonal space groupP3121 orP3221, with unit-cell parametersa=b= 62.65,c= 121.14 Å and one monomer in the asymmetric unit. Molecular replacement was unsuccessful, but selenomethionine-substituted protein and heavy-atom derivatives are being prepared for phasing. The three-dimensional structure of EcpB will provide invaluable information on the subtle mechanistic differences in biogenesis between the alternative and classical CU pathways. Furthermore, this is the first time that this refolding strategy has been used to purify CU chaperones, and it could be implemented in similar systems where it has not been possible to obtain highly ordered crystals.

scholarly journals Purification, crystallization and preliminary X-ray crystallographic analysis of glycosyltransferase-1 fromBacillus cereus

2014 ◽  
Vol 70 (9) ◽  
pp. 1228-1231 ◽  
Author(s):  
Yin-Cheng Hsieh ◽  
Hsi-Ho Chiu ◽  
Yen-Chieh Huang ◽  
Hoong-Kun Fun ◽  
Chia-Yu Lu ◽  
...  
Keyword(s):  
Small Molecules ◽  
Crystallographic Analysis ◽  
Diffusion Method ◽  
Uridine Diphosphate ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Biological Compounds ◽  
The Family ◽  
Diphosphate Glucose

Glycosyltransferases (GTs), which are distributed widely in various organisms, including bacteria, fungi, plants and animals, play a role in synthesizing biological compounds. Glycosyltransferase-1 fromBacillus cereus(BcGT-1), which is capable of transferring glucose to small molecules such as kaempferol and quercetin, has been identified as a member of the family 1 glycosyltransferases which utilize uridine diphosphate glucose (UDP-glucose) as the sugar donor.BcGT-1 (molecular mass 45.5 kDa) has been overexpressed, purified and crystallized using the hanging-drop vapour-diffusion method. According to X-ray diffraction ofBcGT-1 crystals to 2.10 Å resolution, the crystal belonged to space groupP1, with unit-cell parametersa= 54.56,b= 84.81,c= 100.12 Å, α = 78.36, β = 84.66, γ = 84.84°. Preliminary analysis indicates the presence of fourBcGT-1 molecules in the asymmetric unit with a solvent content of 50.27%.

scholarly journals Crystallization and preliminary X-ray diffraction studies of La1 fromLiocheles australasiae

2014 ◽  
Vol 70 (7) ◽  
pp. 915-917 ◽  
Author(s):  
Saori Kamachi ◽  
Junya Nagao ◽  
Masahiro Miyashita ◽  
Yoshiaki Nakagawa ◽  
Hisashi Miyagawa ◽  
...  
Keyword(s):  
Biological Function ◽  
Three Dimensional ◽  
Scorpion Venom ◽  
Dimensional Structure ◽  
Diffusion Method ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Cell Parameters ◽  
Factor Type ◽  
Von Willebrand

A novel scorpion venom peptide, La1 fromLiocheles australasiae, with a molecular weight of 7.8 kDa, is presumed to possess a single von Willebrand factor type C (VWC) domain, a common protein module, based on the position of eight Cys residues in its sequence. The biological function of La1 is still unknown. Deciphering its three-dimensional structure will be helpful in understanding its biological function. La1 was crystallized by the sitting-drop vapour-diffusion method using magnesium sulfate as a precipitant. The crystals belonged to the monoclinic space groupC2, with unit-cell parametersa= 63.0,b= 30.2,c= 32.3 Å, β = 108.5°, and diffracted to 1.9 Å resolution. The calculatedVMbased on one molecule per asymmetric unit was 1.87 Å3 Da−1. The solvent content was 34.1%.

scholarly journals Cloning, purification, crystallization and preliminary X-ray diffraction crystallographic study of acyl-protein thioesterase 1 fromSaccharomyces cerevisiae

2012 ◽  
Vol 68 (7) ◽  
pp. 775-777
Author(s):  
Ye Yuan ◽  
Xiao Wang ◽  
Xu Li ◽  
Maikun Teng ◽  
Liwen Niu ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Modification ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Preliminary Model

Palmitoylation/depalmitoylation plays an important role in protein modification. yApt1 is the only enzyme inSaccharomyces cerevisiaethat catalyses depalmitoylation. In the present study, recombinant full-length yApt1 was cloned, expressed, purified and crystallized. The crystals diffracted to 2.40 Å resolution and belonged to space groupP42212, with unit-cell parametersa = b = 146.43,c = 93.29 Å. A preliminary model of the three-dimensional structure has been built and further refinement is ongoing.

scholarly journals Crystal Structure of a Putative Modulator of Gyrase (TldE) from Thermococcus kodakarensis

Crystals ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 107 ◽  
Author(s):  
Xin Zhang ◽  
Zhengqun Li ◽  
Yanxiang Zhao ◽  
Xilan Cheng ◽  
Yang Liu ◽  
...  
Keyword(s):  
Metal Ion ◽  
Structural Information ◽  
Sequence Similarity ◽  
Dimensional Structure ◽  
Structural Basis ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
Thermococcus Kodakarensis

TldD and TldE proteins interact and form a complex to degrade unfolded peptides. The gene Tk0499 from Thermococcus kodakarensis encoded a putative modulator of gyrase (TkTldE). Although TldE genes were common in bacteria and archaea, the structural basis on the evolution of proteins remained largely unknown. Here, the three-dimensional structure of TkTldE was determined by X-ray diffraction. Crystals were acquired by the sitting-drop vapor-diffusion method. X-ray diffraction data from crystals were collected at 2.35 Å. The space group and unit-cell parameters suggested that there were two molecules in the asymmetric unit. Our results showed that TkTldE forms a homodimer, which contained anti-parallel β-strands and a pair of α-helices. Comparison of the structures of TldE and TldD showed that despite their high sequence similarity, TldE lacked the conserved HExxxH and GxC motif in which two His and a Cys residues bound a metal ion. Taken together, these results provided insight into the structural information of this class of TldE/TldD.

scholarly journals Crystallization and preliminary X-ray diffraction data for a purple acid phosphatase from sweet potato

1999 ◽  
Vol 55 (12) ◽  
pp. 2051-2052 ◽  
Author(s):  
Gerhard Schenk ◽  
Lyle E. Carrington ◽  
Susan E. Hamilton ◽  
John de Jersey ◽  
Luke W. Guddat
Keyword(s):  
Acid Phosphatase ◽  
Sweet Potato ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Purple Acid Phosphatase ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
The Subject

Purple acid phosphatase from sweet potato is a homodimer of 110 kDa. Two forms of the enzyme have been characterized. One contains an Fe–Zn centre similar to that previously reported for red kidney bean purple acid phosphatase. Another isoform, the subject of this work, is the first confirmed example of an Fe–Mn-containing enzyme. Crystals of this protein have been grown from PEG 6000. They have unit-cell parameters a = b = 118.4, c = 287.4 Å and have the symmetry of space group P6522, with one dimer per asymmetric unit. Diffraction data collected using a conventional X-ray source from a cryocooled crystal extend to 2.90 Å resolution. The three-dimensional structure of the enzyme will provide insight into the coordination of this novel binuclear metal centre.

scholarly journals Crystallization and preliminary X-ray diffraction studies of mammalian purple acid phosphatase

1999 ◽  
Vol 55 (8) ◽  
pp. 1462-1464 ◽  
Author(s):  
Luke W. Guddat ◽  
Alan S. McAlpine ◽  
David Hume ◽  
John de Jersey ◽  
Susan Hamilton ◽  
...  
Keyword(s):  
Acid Phosphatase ◽  
Rational Design ◽  
Three Dimensional ◽  
Allantoic Fluid ◽  
Bone Diseases ◽  
Purple Acid Phosphatase ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters

The oxidized form of purple acid phosphatase from pig allantoic fluid has been crystallized in the presence of phosphate using the hanging-drop technique. The crystals belong to the space group P212121 and have unit-cell parameters a = 66.8, b = 70.3, c = 78.7 Å. Diffraction data collected from a cryocooled crystal using a conventional X-ray source extend to 1.55 Å resolution. A knowledge of the three-dimensional structure of mammalian purple acid phosphatase will aid in understanding the substrate specificity of the enzyme and will be important in the rational design of inhibitors, with potential in the treatment of bone diseases.

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