PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (1393940)

Clipboard (0)
None

Related Articles

1.  Crystallization and preliminary X-ray crystallographic analysis of the oxysterol-binding protein Osh3 from Saccharomyces cerevisiae  
The PH domain and ORD of the oxysterol-binding protein Osh3 from S. cerevisae were crystallized and X-ray diffraction data were collected.
Oxysterol-binding protein (OSBP) related proteins (ORPs) are conserved from yeast to humans and are implicated in regulation of sterol homeostasis and in signal transduction pathways. Osh3 of Saccharomyces cerevisiae is a pleckstrin-homology (PH) domain-containing ORP member that regulates phosphoinositide metabolism at endoplasmic reticulum–plasma membrane contact sites. The N-terminal PH domain of Osh3 was purified and crystallized as a lysozyme fusion and the resulting crystal diffracted to 2.3 Å resolution. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 98.03, b = 91.31, c = 84.13 Å, β = 81.41°. With two molecules in the asymmetric unit, the Matthews coefficient was 3.13 Å3 Da−1. Initial attempts to solve the structure by molecular-replacement techniques using T4 lysozyme as a search model were successful. The C-terminal OSBP-related domain (OBD) of Osh3 was crystallized by the vapour-diffusion method and the resulting crystal diffracted to 1.5 Å resolution. The crystal was orthorhombic, belonging to space group P212121, with unit-cell parameters a = 41.57, b = 87.52, c = 100.58 Å. With one molecule in the asymmetric unit, the Matthews coefficient was 2.01 Å3 Da−1. Initial attempts to solve the structure by the single-wavelength anomalous dispersion technique using bromine were successful.
doi:10.1107/S1744309112042510
PMCID: PMC3509973  PMID: 23192032
oxysterol-binding protein; Osh3; Saccharomyces cerevisiae
2.  Crystallization and preliminary X-ray diffraction analysis of the N-terminal domain of Mrs2, a magnesium ion transporter from yeast inner mitochondrial membrane 
Soluble N-terminal domain of yeast magnesium ion transporter Mrs2 was overexpressed in E. coli, purified, crystallized and X-ray diffraction data collected to 1.83 Å resolution.
Mrs2 transporters are distantly related to the major bacterial Mg2+ transporter CorA and to Alr1, which is found in the plasma membranes of lower eukaryotes. Common features of all Mrs2 proteins are the presence of an N-terminal soluble domain followed by two adjacent transmembrane helices (TM1 and TM2) near the C-terminus and of the highly conserved F/Y-G-M-N sequence motif at the end of TM1. The inner mitochondrial domain of the Mrs2 from Saccharomyces cerevisae was overexpressed, purified and crystallized in two different crystal forms corresponding to an orthorhombic and a hexagonal space group. The crystals diffracted X-rays to 1.83 and 4.16 Å resolution, respectively. Matthews volume calculations suggested the presence of one molecule per asymmetric unit in the orthorhombic crystal form and of five or six molecules per asymmetric unit in the hexagonal crystal form. The phase problem was solved for the orthorhombic form by a single-wavelength anomalous dispersion experiment exploiting the sulfur anomalous signal.
doi:10.1107/S1744309110012212
PMCID: PMC2882763  PMID: 20516593
Mrs2; Mg2+ transporters
3.  Crystallization and preliminary X-ray crystallographic analysis of highly thermostable L2 lipase from the newly isolated Bacillus sp. L2 
Thermostable recombinant L2 lipase from thermophilic Bacillus sp. L2 has been crystallized by using counter-diffusion method and diffracted to 2.7 Å resolution. The crystal belongs to the primitive orthorhombic space group P212121 with unit-cell parameters a = 87.44, b = 94.90, c = 126.46 Å.
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 Å resolution using an in-house Bruker X8 PROTEUM single-crystal diffractometer system. The crystal belonged to the primitive ortho­rhombic space group P212121, with unit-cell parameters a = 87.44, b = 94.90, c = 126.46 Å. The asymmetric unit contained one single molecule of protein, with a Matthews coefficient (V M) of 2.85 Å3 Da−1 and a solvent content of 57%.
doi:10.1107/S174430911001482X
PMCID: PMC2882778  PMID: 20516608
lipases; L2 lipase; Bacillus sp. L2; thermostable lipase; counter-diffusion method
4.  Preliminary crystallographic characterization of the Grb2 SH2 domain in complex with a FAK-derived phosphotyrosyl peptide 
Crystals of the Grb2 SH2 domain in complex with a phosphotyrosyl peptide corresponding to residues 921–930 of focal adhesion kinase (FAK) have been obtained using the sitting-drop vapour-diffusion technique. Data have been collected to 2.49 Å resolution.
Growth factor receptor-bound protein 2 (Grb2) is an adaptor protein with a single SH2 domain that specifically binds to focal adhesion kinase (FAK) when residue Tyr925 of FAK is phosphorylated. The Grb2–FAK interaction is associated with cellular integrin-activated signal transduction events leading to the activation of the Ras-MAPK pathway. Crystals of the Grb2 SH2 domain in complex with a phosphopeptide corresponding to residues 921–930 of FAK have been obtained using the sitting-drop vapour-diffusion technique. The crystals belonged to space group P3121, with unit-cell parameters a = b = 102.7, c = 127.6 Å, α = β = 90.0, γ = 120.0°. A diffraction data set was collected from a flash-cooled crystal at 100 K to 2.49 Å resolution using synchrotron radiation. Structure determination by molecular replacement and analysis of the detailed structure of the complex are currently in progress.
doi:10.1107/S1744309109053184
PMCID: PMC2815691  PMID: 20124721
Grb2; SH2 domain; FAK
5.  Crystallization and preliminary X-ray diffraction analysis of a novel type of phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 
A novel type of phosphoserine phosphatase from H. thermophilus TK-6 was heterologously expressed in E. coli, purified and crystallized by the sitting-drop vapour-diffusion method. The crystals obtained belonged to space group P212121 and diffracted X-rays to 1.5 Å resolution.
Two novel-type phosphoserine phosphatases (PSPs) with unique substrate specificity from the thermophilic and hydrogen-oxidizing bacterium Hydrogenobacter thermophilus TK-6 have previously been identified. Here, one of the PSPs (iPSP1) was heterologously expressed in Escherichia coli, purified and crystallized. Diffraction-quality crystals were obtained by the sitting-drop vapour-diffusion method using PEG 4000 as the precipitant. Two diffraction data sets with resolution ranges of 45.0–2.50 and 45.0–1.50 Å were collected from a single crystal and were merged to give a highly complete data set. The space group of the crystal was identified as primitive orthorhombic P212121, with unit-cell parameters a = 49.8, b = 73.6, c = 124.3 Å. The calculated Matthews coefficient (V M = 2.32 Å3 Da−1) indicated that the crystal contained one iPSP1 complex per asymmetric unit.
doi:10.1107/S1744309112025213
PMCID: PMC3412771  PMID: 22869120
phosphoserine phosphatases; Hydrogenobacter thermophilus TK-6
6.  Expression, purification, crystallization and preliminary X-ray diffraction analysis of the dihydroorotase domain of human CAD 
Recombinant dihydroorotase domain of human CAD was expressed in E. coli, purified and crystallized. An X-ray diffraction data set was collected to 1.75 Å resolution.
CAD is a 243 kDa eukaryotic multifunctional polypeptide that catalyzes the first three reactions of de novo pyrimidine biosynthesis: glutamine-dependent carbamyl phosphate synthetase, aspartate transcarbamylase and dihydroorotase (DHO). In prokaryotes, these activities are associated with monofunctional proteins, for which crystal structures are available. However, there is no detailed structural information on the full-length CAD protein or any of its functional domains apart from that it associates to form a homohexamer of ∼1.5 MDa. Here, the expression, purification and crystallization of the DHO domain of human CAD are reported. The DHO domain forms homodimers in solution. Crystallization experiments yielded small crystals that were suitable for X-ray diffraction studies. A diffraction data set was collected to 1.75 Å resolution using synchrotron radiation at the SLS, Villigen, Switzerland. The crystals belonged to the orthorhombic space group C2221, with unit-cell parameters a = 82.1, b = 159.3, c = 61.5 Å. The Matthews coefficient calculation suggested the presence of one protein molecule per asymmetric unit, with a solvent content of 48%.
doi:10.1107/S1744309112038857
PMCID: PMC3515377  PMID: 23143245
human CAD; dihydroorotase domain; pyrimidine biosynthesis
7.  Crystallization and preliminary X-ray analysis of a novel Kunitz-type kallikrein inhibitor from Bauhinia bauhinioides  
Crystallization and preliminary X-ray diffraction studies are reported for a novel Kunitz-type protease inhibitor from B. bauhinioides which contains no disulfide bridges.
A Kunitz-type protease inhibitor (BbKI) found in Bauhinia bauhinioides seeds has been overexpressed in Escherichia coli and crystallized at 293 K using PEG 4000 as the precipitant. X-ray diffraction data have been collected to 1.87 Å resolution using an in-house X-ray generator. The crystals of the recombinant protein (rBbKI) belong to the orthorhombic space group P212121, with unit-cell parameters a = 46.70, b = 64.14, c = 59.24 Å. Calculation of the Matthews coefficient suggests the presence of one monomer of rBbKI in the asymmetric unit, with a corresponding solvent content of 51% (V M = 2.5 Å3 Da−1). Iodinated crystals were prepared and a derivative data set was also collected at 2.1 Å resolution. Crystals soaked for a few seconds in a cryogenic solution containing 0.5 M NaI were found to be reasonably isomorphous to the native crystals. Furthermore, the presence of iodide anions could be confirmed in the NaI-derivatized crystal. Data sets from native and derivative crystals are being evaluated for use in crystal structure determination by means of the SIRAS (single isomorphous replacement with anomalous scattering) method.
doi:10.1107/S1744309105028496
PMCID: PMC1991323  PMID: 16511193
Kunitz-type kallikrein inhibitors; disulfide bridges; Bauhinia bauhinioides
8.  Crystallization and preliminary crystallographic study of a trypsin-resistant catalytic domain of human calcineurin 
A trypsin-resistant catalytic domain of human calcineurin α (A subunit, residues 20–347) was crystallized in space group P21212. An X-ray diffraction data set was collected to 2.87 Å resolution and the structure was solved by molecular replacement.
Calcineurin, a Ca2+/calmodulin-dependent serine/threonine protein phosphatase, plays a key role in a number of cellular pathways, including T-cell activation, and is an important molecular target of the immunosuppressive drugs cyclosporin A and FK506. To understand the structural basis underlying the activation of calcineurin by calmodulin, X-ray crystallography was employed to solve the three-dimensional structure of the free calcineurin catalytic domain (residues 20–347 of the A subunit). To accomplish this, a bacterially expressed glutathione S-­transferase (GST) fusion protein of the human calcineurin catalytic domain was first purified by GST-affinity chromatography. After limited digestion by trypsin, the catalytic domain (Cncat) was purified using anion-exchange and size-exclusion chromatography. Crystallization of Cncat was achieved by the hanging-drop vapour-diffusion method at pH 6.5 using PEG 6000 as precipitant. The diffraction results showed that the Cncat crystal belonged to the orthorhombic space group P21212, with unit-cell parameters a = 161.6, b = 87.4, c = 112.0 Å. There are four Cncat molecules in the asymmetric unit, with 49.5% solvent content. An X-ray diffraction data set was collected to 2.87 Å resolution and a clear molecular-replacement solution was obtained. The active site of Cncat is open to the solvent channels in the crystal packing.
doi:10.1107/S1744309112007890
PMCID: PMC3374516  PMID: 22691791
human calcineurin; catalytic domain
9.  Identification of LIM3 as the principal determinant of paxillin focal adhesion localization and characterization of a novel motif on paxillin directing vinculin and focal adhesion kinase binding 
The Journal of Cell Biology  1996;135(4):1109-1123.
Paxillin is a 68-kD focal adhesion phosphoprotein that interacts with several proteins including members of the src family of tyrosine kinases, the transforming protein v-crk, and the cytoskeletal proteins vinculin and the tyrosine kinase, focal adhesion kinase (FAK). This suggests a function for paxillin as a molecular adaptor, responsible for the recruitment of structural and signaling molecules to focal adhesions. The current study defines the vinculin- and FAK-interaction domains on paxillin and identifies the principal paxillin focal adhesion targeting motif. Using truncation and deletion mutagenesis, we have localized the vinculin-binding site on paxillin to a contiguous stretch of 21 amino acids spanning residues 143-164. In contrast, maximal binding of FAK to paxillin requires, in addition to the region of paxillin spanning amino acids 143-164, a carboxyl-terminal domain encompassing residues 265-313. These data demonstrate the presence of a single binding site for vinculin, and at least two binding sites for FAK that are separated by an intervening stretch of 100 amino acids. Vinculin- and FAK-binding activities within amino acids 143-164 were separable since mutation of amino acid 151 from a negatively charged glutamic acid to the uncharged polar residue glutamine (E151Q) reduced binding of vinculin to paxillin by >90%, with no reduction in the binding capacity for FAK. The requirement for focal adhesion targeting of the vinculin- and FAK-binding regions within paxillin was determined by transfection into CHO.K1 fibroblasts. Significantly and surprisingly, paxillin constructs containing both deletion and point mutations that abrogate binding of FAK and/or vinculin were found to target effectively to focal adhesions. Additionally, expression of the amino-terminal 313 amino acids of paxillin containing intact vinculin- and FAK-binding domains failed to target to focal adhesions. This indicated other regions of paxillin were functioning as focal adhesion localization motifs. The carboxyl-terminal half of paxillin (amino acids 313-559) contains four contiguous double zinc finger LIM domains. Transfection analyses of sequential carboxyl-terminal truncations of the four individual LIM motifs and site-directed mutagenesis of LIM domains 1, 2, and 3, as well as deletion mutagenesis, revealed that the principal mechanism of targeting paxillin to focal adhesions is through LIM3. These data demonstrate that paxillin localizes to focal adhesions independent of interactions with vinculin and/or FAK, and represents the first definitive demonstration of LIM domains functioning as a primary determinant of protein subcellular localization to focal adhesions.
PMCID: PMC2133378  PMID: 8922390
10.  Crystallization and preliminary X-ray diffraction studies on the human Plk1 Polo-box domain in complex with an unphosphorylated and a phosphorylated target peptide from Cdc25C 
Crystals of the human Plk1 Polo-box domain in complex with a Cdc25C target peptide in an unphosphorylated and a phosphorylated state have been obtained in orthorhombic and monoclinic forms that diffract to 2.1 and 2.85 Å, respectively, using synchrotron radiation.
Polo-like kinase (Plk1) is crucial for cell-cycle progression via mitosis. Members of the Polo-like kinase family are characterized by the presence of a C-terminal domain termed the Polo-box domain (PBD) in addition to the N-terminal kinase domain. The PBD of Plk1 was cloned and overexpressed in Escherichia coli. Crystallization experiments of the protein in complex with an unphosphorylated and a phosphorylated target peptide from Cdc25C yield crystals suitable for X-­ray diffraction analysis. Crystals of the PBD in complex with the phosphorylated peptide belong to the orthorhombic space group P212121, with unit-cell parameters a = 38.23, b = 67.35, c = 88.25 Å, α = γ = β = 90°, and contain one molecule per asymmetric unit. Crystals of the PBD in complex with the unphosphorylated peptide belong to the monoclinic space group P21, with unit-cell parameters a = 40.18, b = 49.17, c = 56.23 Å, α = γ = 90, β = 109.48°, and contain one molecule per asymmetric unit. The crystals diffracted to resolution limits of 2.1 and 2.85 Å using synchrotron radiation at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS), respectively.
doi:10.1107/S1744309106007494
PMCID: PMC2222578  PMID: 16582488
Polo-like kinase; Polo-box domain; Cdc25C
11.  Cloning, expression, purification, crystallization and preliminary X-ray diffraction studies of a major group 7 allergen, Der f 7, from the dust mite Dermatophagoides farinae  
The major group 7 allergen, Der f 7, from the dust mite Dermatophagoides farinae has been crystallized and diffracted X-rays to a resolution of 2.24 Å.
Der f 7 is a major group 7 allergen from the dust mite Dermatophagoides farinae that shows 86% sequence identity to the homologous allergen Der p 7 from D. pteronyssinus. Der f 7 was successfully overexpressed in an Escherichia coli expression system and purified to homogeneity using Ni–NTA affinity and size-exclusion column chromatography. SeMet-labelled Der f 7 was crystallized by the hanging-drop vapour-diffusion method using a reservoir solution consisting of 0.1 M bis-tris pH 7.4 and 28% polyethylene glycol monomethyl ether 2000 at 293 K. X-ray diffraction data were collected to 2.24 Å resolution using synchrotron radiation. The crystals belonged to the orthorhombic system, space group P212121, with unit-cell parameters a = 50.19, b = 58.67, c = 123.81 Å. Based on the estimated Matthews coefficient (2.16 Å3 Da−1), two molecules of Der f 7 could be present in the asymmetric unit of the crystal lattice.
doi:10.1107/S174430911103836X
PMCID: PMC3232152  PMID: 22139179
group 7 allergens; Der f 7; Dermatophagoides farinae
12.  Crystallization and initial X-ray diffraction studies of scaffolding protein (gp7) of bacteriophage ϕ29 
ϕ29 bacteriophage scaffolding protein (gp7) has been overproduced in E. coli, purified, crystallized and characterized by X-ray diffraction. Two distinct crystal forms were obtained and a diffraction data set was collected to 1.8 Å resolution.
The Bacillus subtilis bacteriophage ϕ29 scaffolding protein (gp7) has been crystallized by the hanging-drop vapour-diffusion method at 293 K. Two new distinct crystal forms that both differed from a previously crystallized and solved scaffolding protein were grown under the same conditions. Form I belongs to the primitive tetragonal space group P41212, with unit-cell parameters a = b = 77.13, c = 37.12 Å. Form II crystals exhibit an orthorhombic crystal form, with space group C222 and unit-cell parameters a = 107.50, b = 107. 80, c = 37.34 Å. Complete data sets have been collected to 1.78 and 1.80 Å for forms I and II, respectively, at 100 K using Cu Kα X-rays from a rotating-anode generator. Calculation of a V M value of 2.46 Å3 Da−1 for form I suggests the presence of one molecule in the asymmetric unit, corresponding to a solvent content of 50.90%, whereas form II has a V M of 4.80 Å3 Da−1 with a solvent content of 48.76% and two molecules in the asymmetric unit. The structures of both crystal forms are being determined by the molecular-replacement method using the coordinates of the published crystal structure of gp7.
doi:10.1107/S1744309105008511
PMCID: PMC1952437  PMID: 16511059
scaffolding protein; bacteriophage ϕ29
13.  Crystallization and preliminary X-ray analysis of the oxygenase component (HpaB) of 4-hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus HB8 
Crystals of the oxygenase component (HpaB) of 4-hydroxyphenylacetate 3-monooxygenase from T. thermophilus HB8 were obtained which diffracted synchrotron X-rays to a resolution of 1.6 Å.
The 4-hydroxyphenylacetate (4HPA) 3-monooxygenase enzyme catalyzes the hydroxylation of 4HPA to 3,4-dihydroxyphenylacetate in the initial step of the degradation pathway of 4HPA. This enzyme consists of two components: an oxygenase (HpaB) and a reductase (HpaC). HpaB hydroxylates 4HPA using an oxygen molecule and a reduced flavin, which is supplied by HpaC. HpaB from Thermus thermophilus HB8 was overexpressed in Escherichia coli and crystallized. Crystals of HpaB were grown in 0.4 M 1,6-hexanediol, 0.1 M sodium acetate pH 5.0 and 25%(v/v) glycerol and diffracted X-rays to a resolution of 1.60 Å. The crystals belong to the orthorhombic space group I222, with unit-cell parameters a = 91.8, b = 99.6, c = 131.1 Å. The asymmetric unit volume provides space for only one subunit of the tetrameric HpaB molecule, giving a Matthews coefficient V M of 2.8 Å3 Da−1 and a solvent content of 55.1%. Platinum-derivatized crystals of HpaB were prepared by soaking native crystals in a solution containing 1 mM ammonium tetrachloroplatinate(II) for 1 d and diffracted X-rays to a resolution of 2.50 Å. MAD data were successfully collected for structural determination using these crystals.
doi:10.1107/S174430910702492X
PMCID: PMC2335138  PMID: 17620709
4-hydroxyphenylacetate 3-monooxygenase; oxygenase component; Thermus thermophilus HB8
14.  Cloning, overexpression, purification, crystallization, and preliminary X-ray studies of SP_0149, the substrate binding protein of an ABC transporter from Streptococcus pneumoniae  
The substrate binding protein (SP_0149) of an ABC transporter from Streptococcus pneumoniae was molecularly cloned, overexpressed and purified. Diffraction quality crystals were grown using the hanging-drop vapour-diffusion technique.
A truncated (29 residues from the N-terminus) and N-terminal His-tagged form of SP_0149 from pneumococcal strain ATCC BAA-334 was overexpressed and purified to homogeneity using affinity and gel-filtration chromatography. Diffraction quality crystals were grown at 293 K using the hanging-drop vapour-diffusion technique. X-ray diffraction data were collected to 2.3 Å resolution from a single-crystal that belonged to the orthorhombic space group P212121 with the unit-cell parameters a = 54.56, b = 75.61, c = 75.52 Å. The calculated values of the Matthews coefficient assuming one molecule (with calculated molecular weight of 30 400 Da) in the crystal asymmetric unit and the corresponding solvent content were 2.56 Å3 Da−1 and 52.0%, respectively.
doi:10.1107/S1744309111018422
PMCID: PMC3144799  PMID: 21795797
ABC transporter; Streptococcus pneumoniae; SP_0149; ATCC BAA-334
15.  Expression, purification and preliminary crystallographic analysis of the recombinant β-­glucosidase (BglA) from the halothermophile Halothermothrix orenii  
A β-glucosidase A (BglA) from the thermophile Halothermothrix orenii has been cloned, purified and crystallized in an orthorhombic space group. X-ray diffraction data have been collected to 3.5 Å resolution, and the structure was solved by molecular replacement, revealing the presence of two molecules in the asymmetric unit.
The β-glucosidase A gene (bglA) has been cloned from the halothermophilic bacterium Halothermothrix orenii and the recombinant enzyme (BglA; EC 3.2.1.21) was bacterially expressed, purified using metal ion-affinity chromatography and subsequently crystallized. Orthorhombic crystals were obtained that diffracted to a resolution limit of 3.5 Å. The crystal structure with two molecules in the asymmetric unit was solved by molecular replacement using a library of known glucosidase structures. Attempts to collect higher resolution diffraction data from crystals grown under different conditions and structure refinement are currently in progress.
doi:10.1107/S1744309110046981
PMCID: PMC3079986  PMID: 21206038
β-glucosidases; halothermophiles; Halothermothrix orenii; BglA
16.  X-ray diffraction analysis of a crystal of HscA from Escherichia coli  
A truncated form of HscA (52 kDa) containing both nucleotide- and substrate-binding domains has been crystallized and analyzed by X-ray diffraction. The crystal belongs to space group P212121 and diffracts to 2.9 Å.
HscA is a constitutively expressed Hsp70 that interacts with the iron–sulfur cluster assembly protein IscU. Crystals of a truncated form of HscA (52 kDa; residues 17–505) grown in the presence of an IscU-recognition peptide, WELPPVKI, have been obtained by hanging-drop vapor diffusion using ammonium sulfate as the precipitant. A complete native X-ray diffraction data set was collected from a single crystal at 100 K to a resolution of 2.9 Å. The crystal belongs to the orthorhombic space group P212121, with unit-cell parameters a = 158.35, b = 166.15, c = 168.26 Å, and contains six molecules per asymmetric unit. Phases were determined by molecular replacement using the nucleotide-binding domain from DnaK and the substrate-binding domain from HscA as models. This is the first reported crystallization of an Hsp70 containing both nucleotide- and substrate-binding domains.
doi:10.1107/S1744309105019251
PMCID: PMC1952449  PMID: 16511138
HscA; molecular chaperones
17.  Purification, crystallization and preliminary X-ray analysis of Enterococcus casseliflavus aminoglycoside-2′′-phosphotransferase-IVa 
Aminoglycoside-2′′-phosphotransferase-IVa [APH(2′′)-IVa] is an enzyme that is responsible for high-level gentamicin resistance in E. casseliflavus isolates. Three different crystals of wild-type substrate-free APH(2′′)-IVa have been prepared and preliminary X-ray diffraction experiments have been undertaken on all three crystal forms.
The deactivation of aminoglycoside antibiotics by chemical modification is one of the major sources of bacterial resistance to this family of therapeutic compounds, which includes the clinically relevant drugs streptomycin, kanamycin and gentamicin. The aminoglycoside phosphotransferases (APHs) form one such family of enzymes responsible for this resistance. The gene encoding one of these enzymes, aminoglycoside-2′′-phosphotransferase-IVa [APH(2′′)-IVa] from Enterococcus casseliflavus, has been cloned and the protein (comprising 306 amino-acid residues) has been expressed in Escherichia coli and purified. The enzyme was crystallized in three substrate-free forms. Two of the crystal forms belonged to the orthorhombic space group P212121 with similar unit-cell parameters, although one of the crystal forms had a unit-cell volume that was approximately 13% smaller than the other and a very low solvent content of around 38%. The third crystal form belonged to the monoclinic space group P21 and preliminary X-ray diffraction analysis was consistent with the presence of two molecules in the asymmetric unit. The orthorhombic crystal forms of apo APH(2′′)-IVa both diffracted to 2.2 Å resolution and the monoclinic crystal form diffracted to 2.4 Å resolution; synchrotron diffraction data were collected from these crystals at SSRL (Stanford, California, USA). Structure determination by molecular replacement using the structure of the related enzyme APH(2′′)-IIa is proceeding.
doi:10.1107/S1744309109050039
PMCID: PMC2805544  PMID: 20057078
aminoglycoside-2′′-phosphotransferase-IVa; Enterococcus casseliflavus; antibiotic resistance
18.  Purification, crystallization and preliminary X-ray crystallographic analysis of 3-ketosteroid Δ1-dehydrogenase from Rhodococcus erythropolis SQ1 
3-Ketosteroid Δ1-dehydrogenase from Rhodococcus erythropolis SQ1 was successfully crystallized and its initial structure was solved.
3-Ketosteroid Δ1-dehydrogenase plays a crucial role in the early steps of steroid degradation by introducing a double bond between the C1 and C2 atoms of the A-ring of its 3-ketosteroid substrates. The 3-ketosteroid Δ1-dehydrogenase from Rhodococcus erythropolis SQ1, a 56 kDa flavoprotein, was crystallized using the sitting-drop vapour-diffusion method at room temperature. The crystals grew in various buffers over a wide pH range (from pH 5.5 to 10.5), but the best crystallization condition consisted of 2%(v/v) PEG 400, 0.1 M HEPES pH 7.5, 2.0 M ammonium sulfate. A native crystal diffracted X-rays to 2.0 Å resolution. It belonged to the primitive orthorhombic space group P212121, with unit-cell parameters a = 107.4, b = 131.6, c = 363.2 Å, and contained eight molecules in the asymmetric unit. The initial structure of the enzyme was solved using multi-wavelength anomalous dispersion (MAD) data collected from a Pt-derivatized crystal.
doi:10.1107/S1744309112011025
PMCID: PMC3374511  PMID: 22691786
3-ketosteroid Δ1-dehydrogenase; Rhodococcus erythropolis SQ1
19.  Crystallization and preliminary crystallographic analysis of cyanide-insensitive alternative oxidase from Trypanosoma brucei brucei  
Cyanide-insensitive alternative oxidase from T. brucei brucei has been purified and crystallized for X-ray structure analysis.
Cyanide-insensitive alternative oxidase (AOX) is a mitochondrial membrane protein and a non-proton-pumping ubiquinol oxidase that catalyzes the four-electron reduction of dioxygen to water. In the African trypanosomes, tryp­anosome alternative oxidase (TAO) functions as a cytochrome-independent terminal oxidase that is essential for survival in the mammalian host; hence, the enzyme is considered to be a promising drug target for the treatment of trypanosomiasis. In the present study, recombinant TAO (rTAO) overexpressed in haem-deficient Escherichia coli was purified and crystallized at 293 K by the hanging-drop vapour-diffusion method using polyethylene glycol 400 as a precipitant. X-ray diffraction data were collected at 100 K and were processed to 2.9 Å resolution with 93.1% completeness and an overall R merge of 9.5%. The TAO crystals belonged to the orthorhombic space group I222 or I212121, with unit-cell parameters a = 63.11, b = 136.44, c = 223.06 Å. Assuming the presence of two rTAO molecules in the asymmetric unit (2 × 38 kDa), the calculated Matthews coefficient (V M) was 3.2 Å3 Da−1, which corresponds to a solvent content of 61.0%. This is the first report of a crystal of the membrane-bound diiron proteins, which include AOXs.
doi:10.1107/S1744309109054062
PMCID: PMC2833035  PMID: 20208159
alternative oxidases; membrane proteins; Trypanosoma brucei brucei; ascofuranone
20.  Expression, purification, crystallization and preliminary X-ray crystallographic analysis of a novel plant-type ferredoxin/thioredoxin reductase-like protein from Methanosarcina acetivorans  
A novel ferredoxin/thioredoxin reductase-like protein from M. acetivorans was heterologously expressed in E. coli, purified and then subjected to crystallization. Preliminary X-ray diffraction studies revealed that the crystal belonged to a primitive cubic space group, with unit-cell parameters a = b = c = 92.72 Å.
The genome of Methanosarcina acetivorans contains a gene (ma1659) that is predicted to encode an uncharacterized chimeric protein containing a plant-type ferredoxin/thioredoxin reductase-like catalytic domain in the N-terminal region and a bacterial-like rubredoxin domain in the C-terminal region. To understand the structural and functional properties of the protein, the ma1659 gene was cloned and overexpressed in Escherichia coli. Crystals of the MA1659 protein were grown by the sitting-drop method using 2 M ammonium sulfate, 0.1 M HEPES buffer pH 7.5 and 0.1 M urea. Diffraction data were collected to 2.8 Å resolution using the remote data-collection feature of the Advanced Light Source, Lawrence Berkeley National Laboratory. The crystal belonged to the primitive cubic space group P23 or P213, with unit-cell parameters a = b = c = 92.72 Å. Assuming the presence of one molecule in the asymmetric unit gave a Matthews coefficient (V M) of 3.55 Å3 Da−1, corresponding to a solvent content of 65%.
doi:10.1107/S1744309111017234
PMCID: PMC3144793  PMID: 21795791
ferredoxin/thioredoxin reductase-like proteins; rubredoxin; Methanosarcina acetivorans; archaea
21.  Crystallization and preliminary X-ray analysis of crustacean hyperglycaemic hormone from the kuruma prawn Marsupenaeus japonicus in its weakly active precursor form 
Crustacean hyperglycaemic hormone from the kuruma prawn M. japonicus was crystallized by the sitting-drop vapour-diffusion method in its weakly active precursor form which has an extra glycine residue at the C-terminus. The crystals belonged to the orthorhombic space group P212121 and diffracted to 1.95 Å resolution.
Crustacean hyperglycaemic hormone (CHH) plays a pivotal role in the regulation of glucose metabolism in crustaceans. Pej-SGP-I, one of the six known CHHs in the kuruma prawn Marsupenaeus japonicus, was heterolo­gously expressed in Escherichia coli as an N-terminally His-tagged and Nus-tagged protein in its weakly active precursor form, Pej-SGP-I-Gly, which has an extra glycine residue at the C-terminus. The recombinant peptide was subjected to affinity purification, tag removal, further purification and crystallization by the sitting-drop vapour-diffusion method using NaCl as the main precipitant. The crystals diffracted to 1.95 Å resolution and the space group was assigned as primitive orthorhombic P212121, with unit-cell parameters a = 40.19, b = 53.65, c = 53.63 Å. The Matthews coefficient (V M = 1.73 Å3 Da−1) indicated that the crystal contained two Pej-SGP-I-Gly molecules per asymmetric unit, with a solvent content of 29.0%.
doi:10.1107/S1744309111040140
PMCID: PMC3232146  PMID: 22139173
Marsupenaeus japonicus; crustacean hyperglycaemic hormone
22.  Crystallization and preliminary X-ray diffraction analysis of the dimerization domain of the tumour suppressor ING4 
The N-terminal domain of ING4 was overexpressed in Escherichia coli and purified to homogeneity. Crystallization experiments yielded crystals that were suitable for high-resolution X-ray diffraction analysis.
Inhibitor of growth protein 4 (ING4) belongs to the ING family of tumour suppressors and is involved in chromatin remodelling, in growth arrest and, in cooperation with p53, in senescence and apoptosis. Whereas the structure and histone H3-binding properties of the C-terminal PHD domains of the ING proteins are known, no structural information is available for the N-terminal domains. This domain contains a putative oligomerization site rich in helical structure in the ING2–5 members of the family. The N-terminal domain of ING4 was overexpressed in Escherichia coli and purified to homogeneity. Crystallization experiments yielded crystals that were suitable for high-resolution X-ray diffraction analysis. The crystals belonged to the orthorhombic space group C222, with unit-cell parameters a = 129.7, b = 188.3, c = 62.7 Å. The self-rotation function and the Matthews coefficient suggested the presence of three protein dimers per asymmetric unit. The crystals diffracted to a resolution of 2.3 Å using synchrotron radiation at the Swiss Light Source (SLS) and the European Synchrotron Radiation Facility (ESRF).
doi:10.1107/S1744309110010080
PMCID: PMC2864694  PMID: 20445261
ING4; tumour suppressors; dimerization domain
23.  Purification, crystallization and preliminary X-ray characterization of the human GTP fucose pyrophosphorylase 
The human GTP fucose pyrophosphohydrolase protein has been crystallized via the hanging-drop technique over a reservoir of polyethylene glycol (MW 8000) and ethylene glycol. The orthorhombic crystals diffract to 2.8 Å resolution.
The human nucleotide-sugar metabolizing enzyme GTP fucose pyrophosphorylase (GFPP) has been purified to homogeneity by an affinity chromatographic procedure that utilizes a novel nucleoside analog. This new purification regime results in a protein preparation that produces significantly better crystals than traditional purification methods. The purified 66.6 kDa monomeric protein has been crystallized via hanging-drop vapor diffusion at 293 K. Crystals of the native enzyme diffract to 2.8 Å and belong to the orthorhombic space group P212121. There is a single GFPP monomer in the asymmetric unit, giving a Matthews coefficient of 2.38 Å3 Da−1 and a solvent content of 48.2%. A complete native data set has been collected as a first step in determining the three-dimensional structure of this enzyme.
doi:10.1107/S1744309106008529
PMCID: PMC2222559  PMID: 16582493
GTP fucose pyrophosphohydrolase
24.  Crystallization and preliminary X-ray diffraction anaylsis of the LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana  
Crystals of the LOV1 domains of phototropin 1 and 2 from A. thaliana were obtained which diffracted X-rays to a resolution of at least 2.1 Å.
Phototropin is a blue-light receptor protein in plants that is responsible for phototropic responses, stomata opening and photo-induced relocation of chloroplasts. Higher plants such as Arabidopsis thaliana have two isoforms of phototropin: phototropin 1 and phototropin 2. Both isoforms comprise a tandem pair of blue-light-absorbing light–oxygen–voltage domains named LOV1 and LOV2 in the N-terminal half and a serine/threonine kinase domain in the C-­terminal half. The LOV1 domain is thought to function as a dimerization site. In the present study, recombinant LOV1 domains of A. thaliana phototropin 1 and phototropin 2 were crystallized. The crystal of the LOV1 domain of phototropin 1 belonged to the orthorhombic space group P212121, with unit-cell parameters a = 61.2, b = 64.9, c = 70.8 Å, and diffracted X-rays to a resolution of 2.1 Å. The crystal of the LOV1 domain of phototropin 2 belonged to space group P21, with unit-cell parameters a = 32.5, b = 66.5, c = 56.7 Å, β = 92.4°, and diffracted X-rays to beyond 2.0 Å resolution. In both crystals, two LOV1 domains occupied the crystallographic asymmetric unit.
doi:10.1107/S1744309108015534
PMCID: PMC2443956  PMID: 18607090
phototropins; LOV domains; blue-light receptors
25.  Crystallization and preliminary X-ray crystallographic study of a putative aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 
A putative nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon S. tokodaii strain 7 has been recombinantly expressed, purified and crystallized. The crystal structure has been preliminarily solved at 2.3 Å resolution by the molecular-replacement method.
Genome analysis suggests that the aspartyl-tRNA synthetase of the crenarchaeon Sulfolobus tokodaii strain 7 belongs to the nondiscriminating type that is believed to catalyze aspartylation of tRNAAsp and tRNAAsn. This protein has been overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method from 100 mM sodium HEPES buffer pH 7.5 containing 100 mM NaCl and 1.6 M (NH4)2SO4 as the crystallizing reagent. Diffraction data were collected to 2.3 Å resolution using synchrotron radiation. The crystal belongs to the orthorhombic space group P21212, with unit-cell parameters a = 116.0, b = 139.3, c = 75.3 Å. The estimated Matthews coefficient (3.10 Å3 Da−1; 60.3% solvent content) suggests the presence of two subunits in the asymmetric unit. The structure has been successfully solved by the molecular-replacement method. Full refinement of the structure may reveal it to be the original ancestor of the nondiscriminating AspRS.
doi:10.1107/S1744309107026905
PMCID: PMC2335148  PMID: 17620724
aspartyl-tRNA synthetases; Sulfolobus tokodaii strain 7

Results 1-25 (1393940)