scholarly journals Crystallization and preliminary X-ray analysis of RabX3, a tandem GTPase fromEntamoeba histolytica

2014 ◽  
Vol 70 (7) ◽  
pp. 933-937 ◽  
Author(s):  
Vijay Kumar Srivastava ◽  
Mintu Chandra ◽  
Sunando Datta
Keyword(s):  
Entamoeba Histolytica ◽  
Conformational Changes ◽  
Membrane Trafficking ◽  
Vital Role ◽  
Diffusion Method ◽  
Monoclinic Space Group ◽  
Rab Gtpases ◽  
Data Set ◽  
Cell Parameters ◽  
Ras Superfamily

Ras superfamily GTPases regulate signalling pathways that control multiple biological processes by modulating the GTP/GDP cycle. Various Rab GTPases, which are the key regulators of vesicular trafficking pathways, play a vital role in the survival and virulence of the enteric parasiteEntamoeba histolytica. The Rab GTPases act as binary molecular switches that utilize the conformational changes associated with the GTP/GDP cycle to elicit responses from target proteins and thereby regulate a broad spectrum of cellular processes including cell proliferation, cytoskeletal assembly, nuclear transport and intracellular membrane trafficking in eukaryotes.Entamoeba histolyticaRabX3 (EhRabX3) is a unique GTPase in the amoebic genome, the only member in the eukaryotic Ras superfamily that harbours tandem G-domains and shares only 8–16% sequence identity with other GTPases. Recent studies suggested thatEhRabX3 binds to a single guanine nucleotide through its N-terminal G-domain (NTD), while the C-terminal G-domain (CTD) plays a potential role in binding of the nucleotide to the NTD. Thus, understanding the intermolecular regulation between the two GTPase domains is expected to reveal valuable information on the overall action ofEhRabX3. To provide structural insights into the inclusive action of this unique GTPase,EhRabX3 was crystallized by successive micro-seeding using the vapour-diffusion method. A complete data set was collected to 3.3 Å resolution using a single nativeEhRabX3 crystal at 100 K on BM14 at the ESRF, Grenoble, France. The crystal belonged to monoclinic space groupC2, with unit-cell parametersa= 198.6,b= 119.3,c= 89.2 Å, β = 103.1°. Preliminary analysis of the data using theMatthews Probability Calculatorsuggested the presence of four to six molecules in the asymmetric unit.

Production, crystallization and preliminary X-ray analysis of the human integrin \alpha_1 I domain

1999 ◽  
Vol 55 (7) ◽  
pp. 1365-1367 ◽  
Author(s):  
Tiina A. Salminen ◽  
Yvonne Nymalm ◽  
Jussi Kankare ◽  
Jarmo Käpylä ◽  
Jyrki Heino ◽  
...  
Keyword(s):  
Large Scale ◽  
Cell Types ◽  
Diffusion Method ◽  
Scale Production ◽  
Data Set ◽  
Cell Parameters ◽  
Collagen Receptors ◽  
Large Scale Production ◽  
Peg 4000 ◽  
Reservoir Solution

Integrin α1β1 is one of the main collagen receptors in many cell types. A fast large-scale production, purification and crystallization method for the integrin α1 I domain is reported here. The α1 I domain was crystallized using the vapour-diffusion method with a reservoir solution containing a mixture of PEG 4000, sodium acetate, glycerol and Tris–HCl buffer. The crystals beong to the C2 space group, with unit-cell parameters a = 74.5, b = 81.9, c = 37.3 Å, α = γ = 90.0, β = 90.8°. The crystals diffract to 2.0 Å and a 94.2% complete data set to 2.2 Å has been collected from a single crystal with an R merge of 5.8%.

Anion-directed assembly of lanthanide coordination polymers with SMMs properties based on a dihydrazone ligand

2018 ◽  
Vol 233 (1) ◽  
pp. 51-59
Author(s):  
Lina Zhang ◽  
Peigao Duan ◽  
Yang Liu ◽  
Jingxian Sun ◽  
Dan Zhao ◽  
...  
Keyword(s):  
Coordination Polymers ◽  
Single Molecule ◽  
Variable Temperature ◽  
Ac Susceptibility ◽  
Directed Assembly ◽  
Magnetization Measurement ◽  
Vital Role ◽  
Diffusion Method ◽  
Monoclinic Space Group ◽  
Space Group

AbstractFour new Ln(III)-based coordination polymers (CPs), [Eu(HL)Cl2(DMF)2]·(H2L) (1), [Dy(HL)Cl2(DMF)2]·(H2L) (2), [Er(HL)Cl2(DMF)(CH3OH)]·(DMF) (3) and [Yb(HL)Cl2(DMF)(H2O)]·(DMF) (4) (H2L=2,6-bis[(3-methoxysalicylidene)hydrazinocarbonyl]pyridine) have been synthesized through the reaction of Ln(III) chloride and H2L by using the vapour diffusion method. Interestingly, Cl−as a template agent plays a vital role in the formation of the target complexes. Single-crystal X-ray diffraction studies indicate that1and2are isostructural and crystallize in triclinic space groupP1̅, while complexes3and4are isostructural and crystallize in monoclinic space groupC2/c. Variable temperature magnetization measurement (χMT–T) demonstrates possible antiferromagnetic interactions in complex2. Alternating-current (ac) susceptibility measurement furthermore indicated frequency dependence for both the in-phase (χ′) and out-of-phase (χ″) components in2, suggesting that there is a slow relaxation behavior of the magnetization, which is typical of single-molecule magnets (SMMs). This is the first time that Ln(III) CPs based on such a dihydrazone ligand has been reported so far.

Crystal structure of the GTP-binding protein-like domain of AGAP1

2021 ◽  
Vol 77 (4) ◽  
Author(s):  
Nuo Cheng ◽  
Hao Zhang ◽  
Shiyan Zhang ◽  
Xiaodan Ma ◽  
Guoyu Meng
Keyword(s):  
Membrane Trafficking ◽  
Protein Transport ◽  
Structural Information ◽  
Binding Protein ◽  
Lymphoblastic Leukemia ◽  
Diffusion Method ◽  
Gtp Binding Protein ◽  
Aberrant Expression ◽  
Cell Parameters ◽  
Gtp Binding

AGAP1 is often considered to regulate membrane trafficking, protein transport and actin cytoskeleton dynamics. Recent studies have shown that aberrant expression of AGAP1 is associated with many diseases, including neurodevelopmental disorders and acute lymphoblastic leukemia. It has been proposed that the GTP-binding protein-like domain (GLD) is involved in the binding of cofactors and thus regulates the catalytic activity of AGAP1. To obtain a better understanding of the pathogenic mechanism underpinning AGAP1-related diseases, it is essential to obtain structural information. Here, the GLD (residues 70–235) of AGAP1 was overexpressed in Escherichia coli BL21 (DE3) cells. Affinity and gel-filtration chromatography were used to obtain AGAP1GLD with high purity for crystallization. Using the hanging-drop vapor-diffusion method with the protein at a final concentration of 20 mg ml−1, AGAP1GLD protein crystals of suitable size were obtained. The crystals were found to diffract to 3.0 Å resolution and belonged to space group I4, with unit-cell parameters a = 100.39, b = 100.39, c = 48.08 Å. The structure of AGAP1GLD exhibits the highly conserved functional G1–G5 loops and is generally similar to other characterized ADP-ribosylation factor (Arf) GTPase-activating proteins (GAPs), implying an analogous function to Arf GAPs. Additionally, this study indicates that AGAP1 could be classified as a type of NTPase, the activity of which might be regulated by protein partners or by its other domains. Taken together, these results provide insight into the regulatory mechanisms of AGAP1 in cell signaling.

scholarly journals Production, crystallization and preliminary crystallographic analysis ofAllochromatium vinosumthiosulfate dehydrogenase TsdA, an unusual acidophilicc-type cytochrome

2014 ◽  
Vol 70 (10) ◽  
pp. 1424-1427 ◽  
Author(s):  
José A. Brito ◽  
André Gutierres ◽  
Kevin Denkmann ◽  
Christiane Dahl ◽  
Margarida Archer
Keyword(s):  
Crystallographic Analysis ◽  
Sulfur Cycle ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Oxidative Condensation ◽  
Unit Cell Parameters ◽  
Allochromatium Vinosum ◽  
Data Set ◽  
Purple Sulfur Bacterium ◽  
Cell Parameters

The ability to perform the very simple oxidation of two molecules of thiosulfate to tetrathionate is widespread among prokaryotes. Despite the prevalent occurrence of tetrathionate formation and its well documented significance within the sulfur cycle, little is known about the enzymes that catalyze the oxidative condensation of two thiosulfate anions. To fill this gap, the thiosulfate dehydrogenase (TsdA) enzyme from the purple sulfur bacteriumAllochromatium vinosumwas recombinantly expressed inEscherichia coli, purified and crystallized, and a crystallographic data set was collected. The crystals belonged to the monoclinic space groupC2, with unit-cell parametersa= 79.2,b= 69.9,c= 57.9 Å, β = 129.3°, contained one monomer per asymmetric unit and diffracted to a resolution of 1.98 Å.

scholarly journals Crystallization and preliminary X-ray diffraction studies of the C-terminal domain ofChlamydia trachomatisCdsD

2014 ◽  
Vol 70 (10) ◽  
pp. 1431-1433 ◽  
Author(s):  
Gitte Meriläinen ◽  
Rik K. Wierenga
Keyword(s):  
Amino Acids ◽  
Type Iii Secretion ◽  
Type Iii Secretion System ◽  
Secretion System ◽  
Size Exclusion ◽  
Diffusion Method ◽  
Data Set ◽  
Cell Parameters ◽  
Type Iii ◽  
Terminal Domain

The inner membrane ring of the bacterial type III secretion system (TTSS) is composed of two proteins. InChlamydia trachomatisthis ring is formed by CdsD (gene nameCT_664) and CdsJ (gene nameCTA_0609). CdsD consists of 829 amino acids. The last 400 amino acids at its C-terminal end relate it to the type III secretion system YscD/HrpQ protein family. The C-terminal domain, consisting of amino acids 558–771, ofC. trachomatisCdsD was overexpressed inEscherichia coliand purified using immobilized metal-affinity chromatography (IMAC) and size-exclusion chromatography. The protein was crystallized using the vapour-diffusion method. A data set was collected to 2.26 Å resolution. The crystals have the symmetry of space groupC2, with unit-cell parametersa= 106.60,b= 23.91,c= 118.65 Å, β = 104.95°. According to the data analysis there is expected to be one molecule in the asymmetric unit, with a Matthews coefficient of 3.0 Å3 Da−1.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of AntE, a crotonyl-CoA carboxylase/reductase fromStreptomycessp. NRRL 2288

2014 ◽  
Vol 70 (6) ◽  
pp. 734-737 ◽  
Author(s):  
Lihan Zhang ◽  
Jing Chen ◽  
Takahiro Mori ◽  
Yan Yan ◽  
Wen Liu ◽  
...  
Keyword(s):  
Diffusion Method ◽  
Antimycin A ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters ◽  
Vapour Diffusion ◽  
Unsaturated Acyl ◽  
Reductive Carboxylation

AntE fromStreptomycessp. NRRL 2288 is a crotonyl-CoA carboxylase/reductase that catalyzes the reductive carboxylation of various α,β-unsaturated acyl-CoAs to provide the building block at the C7 position for antimycin A biosynthesis. Recombinant AntE expressed inEscherichia coliwas crystallized by the sitting-drop vapour-diffusion method. The crystals belonged to space groupI222 orI212121, with unit-cell parametersa= 76.4,b= 96.7,c= 129.6 Å, α = β = γ = 90.0°. A diffraction data set was collected at the KEK Photon Factory to 2.29 Å resolution.

scholarly journals Cloning, purification and preliminary crystallographic analysis of theHelicobacter pyloripseudaminic acid biosynthesisN-acetyltransferase PseH

2014 ◽  
Vol 70 (9) ◽  
pp. 1276-1279 ◽  
Author(s):  
Yu C. Liu ◽  
Abu I. Ud-Din ◽  
Anna Roujeinikova
Keyword(s):  
Crystallographic Analysis ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
Data Set ◽  
Cell Parameters ◽  
Nonulosonic Acid ◽  
Pseudaminic Acid ◽  
The Common ◽  
H Pylori ◽  
Development Of Gastric Cancer

Helicobacter pyloriinfection is the common cause of gastritis and duodenal and stomach ulcers, which have been linked to a higher risk of the development of gastric cancer. The motility that facilitates persistent infection requires functional flagella that are heavily glycosylated with 5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-L-manno-nonulosonic acid (pseudaminic acid). Pseudaminic acid biosynthesis protein H (PseH) catalyzes the third step in its biosynthetic pathway, producing UDP-2,4-diacetamido-2,4,6-trideoxy-β-L-altropyranose. Crystals ofH. pyloriPseH have been grown by the hanging-drop vapour-diffusion method using diammonium tartrate as a precipitating agent. The crystals belonged to space groupI222 orI212121, with unit-cell parametersa= 107.8,b= 145.4,c= 166.3 Å. A complete X-ray diffraction data set has been collected to 2.5 Å resolution using cryocooling conditions and synchrotron radiation.

Crystallization and preliminary X-ray diffraction studies on the N-utilizing substance-B (NusB) from Mycobacterium tuberculosis

2000 ◽  
Vol 56 (1) ◽  
pp. 64-66 ◽  
Author(s):  
B. Gopal ◽  
R. A. Cox ◽  
M. J. Colston ◽  
G. G. Dodson ◽  
S. J. Smerdon ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Ribosomal Rna ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Core Complex ◽  
Unit Cell Parameters ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters

N-utilizing substance B (NusB) is a protein which forms part of a complex assembly in transcriptional antitermination in Mycobacterium tuberculosis. It forms a heterodimer with the product of the NusE gene (identical to the ribosomal protein S10) and mediates the process of transcriptional antitermination by forming the core complex with the nut site of the ribosomal RNA along with other protein factors. NusB has been cloned and overexpressed in Escherichia coli and crystallized using the hanging-drop vapour-diffusion method. The space group is P212121, with unit-cell parameters a = 46.6, b = 64.2, c = 90.1 Å. A native data set complete to 1.6 Å resolution has been collected from a single crystal.

Crystal Structure of the Interaction of Human Urokinase Plasminogen Activitor with Its Receptor.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 683-683 ◽  
Author(s):  
Qing Huai ◽  
Andrew P. Mazar ◽  
Graham Parry ◽  
Alice Kuo ◽  
Douglas B. Cines ◽  
...  
Keyword(s):  
Ternary Complex ◽  
Hydrophobic Interactions ◽  
Structural Basis ◽  
Diffusion Method ◽  
Monoclinic Space Group ◽  
Fab Fragment ◽  
Data Set ◽  
Kringle Domain ◽  
Amino Terminal ◽  
High Affinity

Abstract Urokinase-type plasminogen activator (uPA) and its cellular receptor (uPAR) mediate plasminogen activation. The uPA binds to uPAR with high affinity (Kd 0.1–1nM), thus localizing the generation of plasmin from plasminogen on the surface of a variety of cells. uPA-uPAR binding is also involved in other cellular functions and diverse pathophysiological processes such as tissue remodeling during wound healing, atherosclerosis, angiogenesis and tumor metastasis. We have determined the structure of uPAR complexed with the amino terminal fragment (amino acid residues 1–143) of uPA (ATF), which contains the uPAR binding domain, at 1.9 Å resolution by X-ray crystallography. Soluble uPAR (suPAR) and the ATF were expressed separately in stably transfected Drosophila Schneider 2 (S2) cells. The suPAR-ATF complex was crystallized by the sitting-drop vapor diffusion method. However, the diffraction of this crystal was limited to 3.1 Å resolution. Therefore, the Fab fragment of an antibody raised against suPAR, ATN-615, was used to facilitate suPAR-ATF crystallization. Crystals of the suPAR-ATF-ATN615 ternary complex were generated by microdialysis with 4% PEG4K, 5% ethylene glycol, 5% methanol, 0.05% sodium azide, 50 mM cacodylate pH 6.5. A complete data set of the ternary complex to 1.9 Å was collected using synchrotron radiation at the Advanced Photon Source (APS), Argonne National Laboratory. The crystals belong to the monoclinic space group, with unit cell parameters a=51.79 Å, b=86.81 Å, c=124.69 Å and β=94.54°. uPAR is comprised of three consecutive domains (D1, D2 and D3) that form the shape of a thick-walled teacup with a diameter of about 52 Å and a height of 27 Å. At the center of teacup and surrounded by three suPAR domains is a cone shape cavity with a wide opening (25 Å) and large depth (14 Å). ATF consists of a growth factor domain (GFD) and a kringle domain. Both domains pack more tightly in the complex structure compared with their unbound state. The GFD domain of uPA occupies part of the uPAR cavity and is primarily responsible for uPAR binding. The D1 domain of uPAR forms three hydrogen bonds and many hydrophobic interactions with the GFD domain of uPA, thus playing an important role in the binding of uPA. However, D2 and D3 of uPAR also have direct interactions with the GFD domain of uPA. The kringle domain of uPA sits outside the uPAR pocket, but forms some direct contacts with the D1 domain of uPAR. Therefore, the three domains of uPAR and two domains of uPA form a complementary interaction, which describes the structural basis for the high affinity binding of uPA to uPAR. This structure presents the first high resolution view of uPA-uPAR interaction, and may provide a new platform to design de novo uPA-uPAR antagonists.

scholarly journals Crystallization and preliminary X-ray crystallographic analysis of the ArsM arsenic(III)S-adenosylmethionine methyltransferase

2010 ◽  
Vol 66 (9) ◽  
pp. 1050-1052 ◽  
Author(s):  
Kavitha Marapakala ◽  
A. Abdul Ajees ◽  
Jie Qin ◽  
Banumathi Sankaran ◽  
Barry P. Rosen
Keyword(s):  
Crystallographic Analysis ◽  
Hazardous Substances ◽  
Diffusion Method ◽  
Monoclinic Space Group ◽  
Hanging Drop ◽  
Unit Cell Parameters ◽  
Priority List ◽  
X Ray ◽  
Cell Parameters ◽  
Environmental Toxin

Arsenic is the most ubiquitous environmental toxin and carcinogen and consequently ranks first on the Environmental Protection Agency's Superfund Priority List of Hazardous Substances. It is introduced primarily from geochemical sources and is acted on biologically, creating an arsenic biogeocycle. A common biotransformation is methylation to monomethylated, dimethylated and trimethylated species. Methylation is catalyzed by the ArsM (or AS3MT) arsenic(III)S-adenosylmethionine methyltransferase, an enzyme (EC 2.1.1.137) that is found in members of every kingdom from bacteria to humans. ArsM from the thermophilic algaCyanidioschyzonsp. 5508 was expressed, purified and crystallized. Crystals were obtained by the hanging-drop vapor-diffusion method. The crystals belonged to the monoclinic space groupC2, with unit-cell parametersa= 84.85,b= 46.89,c= 100.35 Å, β = 114.25° and one molecule in the asymmetric unit. Diffraction data were collected at the Advanced Light Source and were processed to a resolution of 1.76 Å.

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