Analysis of multiple crystal forms ofBacillus subtilisBacB suggests a role for a metal ion as a nucleant for crystallization

2010 ◽  
Vol 66 (5) ◽  
pp. 635-639 ◽  
Author(s):  
M. Rajavel ◽  
B. Gopal
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Crystal Packing ◽  
Crystal Form ◽  
Monoclinic Crystal ◽  
Crystal Forms ◽  
Tetragonal Crystal ◽  
Crystallization Conditions ◽  
Surface Metal ◽  
X Ray Absorption

Bacillus subtilisBacB is an oxidase that is involved in the production of the antibiotic bacilysin. This protein contains two double-stranded β-helix (cupin) domains fused in a compact arrangement. BacB crystallizes in three crystal forms under similar crystallization conditions. An interesting observation was that a slight perturbation of the crystallization droplet resulted in the nucleation of a different crystal form. An X-ray absorption scan of BacB suggested the presence of cobalt and iron in the crystal. Here, a comparative analysis of the different crystal forms of BacB is presented in an effort to identify the basis for the different lattices. It is noted that metal ions mediating interactions across the asymmetric unit dominate the different packing arrangements. Furthermore, a normalizedB-factor analysis of all the crystal structures suggests that the solvent-exposed metal ions decrease the flexibility of a loop segment, perhaps influencing the choice of crystal form. The residues coordinating the surface metal ion are similar in the triclinic and monoclinic crystal forms. The coordinating ligands for the corresponding metal ion in the tetragonal crystal form are different, leading to a tighter packing arrangement. Although BacB is a monomer in solution, a dimer of BacB serves as a template on which higher order symmetrical arrangements are formed. The different crystal forms of BacB thus provide experimental evidence for metal-ion-mediated lattice formation and crystal packing.

Unravelling the chemical basis of the bathochromic shift in the lobster carapace; new crystal structures of unbound astaxanthin, canthaxanthin and zeaxanthin

2007 ◽  
Vol 63 (2) ◽  
pp. 328-337 ◽  
Author(s):  
Giuditta Bartalucci ◽  
Jennifer Coppin ◽  
Stuart Fisher ◽  
Gillian Hall ◽  
John R. Helliwell ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Bathochromic Shift ◽  
Crystal Form ◽  
Crystal Forms ◽  
Bonding Interaction ◽  
Crystallization Conditions ◽  
Intermolecular Distances

The crystal structures of the unbound carotenoids, synthetic astaxanthin (3S,3′S:3R,3′S:3R,3′R in a 1:2:1 ratio), canthaxanthin and (3R,3′S, meso)-zeaxanthin are compared with each other and the protein bound astaxanthin molecule in the carotenoprotein, β-crustacyanin. Three new crystal forms of astaxanthin have been obtained, using different crystallization conditions, comprising a chloroform solvate, a pyridine solvate and an unsolvated form. In each structure, the astaxanthin molecules, which are similar to one another, are centrosymmetric and adopt the 6-s-cis conformation; the end rings are bent out of the plane of the polyene chain by angles of −42.6 (5), −48.9 (5) and −50.4 (3)°, respectively, and are disordered, showing the presence of both R and S configurations (in a 1:1 ratio). In the crystal packing of the chloroform and pyridine solvates, the astaxanthin molecules show pair-wise end-to-end intermolecular hydrogen bonding of the adjacent 3-hydroxyl and 4-keto oxygens, whereas in the unsolvated crystal form, the hydrogen-bonding interaction is intermolecular. In addition, there are intermolecular C—H hydrogen bonds in all three structures. The canthaxanthin structure, measured at 100 and 293 K, also adopts the 6-s-cis conformation, but with disorder of one end ring only. The rotation of the end rings out of the plane of the polyene chains (ca −50 ° for each structure) is similar to that of astaxanthin. A number of possible C—H hydrogen bonds to the keto O atoms are also observed. (3R,3′S, meso)-zeaxanthin is centrosymmetric with a C5—C6—C7—C8 torsion angle of −74.9 (3)°; the molecules show pair-wise hydrogen bonding between the hydroxyl O atoms. In addition, for all the crystal structures the polyene chains were arranged one above the other, with intermolecular distances of 3.61–3.79 Å, indicating the presence of π-stacking interactions. Overall, these six crystal structures provide an ensemble of experimentally derived results that allow several key parameters, thought to influence colour tuning of the bathochromic shift of astaxanthin in crustacyanin, to be varied. The fact that the colour of each of the six crystals remains red, rather than turning blue, is therefore especially significant.

scholarly journals Crystallographic and X-ray absorption spectroscopic characterization of Helicobacter pylori UreE bound to Ni2+ and Zn2+ reveals a role for the disordered C-terminal arm in metal trafficking

2012 ◽  
Vol 441 (3) ◽  
pp. 1017-1035 ◽  
Author(s):  
Katarzyna Banaszak ◽  
Vlad Martin-Diaconescu ◽  
Matteo Bellucci ◽  
Barbara Zambelli ◽  
Wojciech Rypniewski ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Metal Ions ◽  
Metal Binding ◽  
Metal Ion ◽  
Mutual Influence ◽  
Accurate Information ◽  
Metal Ion Binding ◽  
X Ray ◽  
X Ray Absorption

The survival and growth of the pathogen Helicobacter pylori in the gastric acidic environment is ensured by the activity of urease, an enzyme containing two essential Ni2+ ions in the active site. The metallo-chaperone UreE facilitates in vivo Ni2+ insertion into the apoenzyme. Crystals of apo-HpUreE (H. pylori UreE) and its Ni2+- and Zn2+-bound forms were obtained from protein solutions in the absence and presence of the metal ions. The crystal structures of the homodimeric protein, determined at 2.00 Å (apo), 1.59 Å (Ni2+) and 2.52 Å (Zn2+) resolution, show the conserved proximal and solvent-exposed His102 residues from two adjacent monomers invariably involved in metal binding. The C-terminal regions of the apoprotein are disordered in the crystal, but acquire significant ordering in the presence of the metal ions due to the binding of His152. The analysis of X-ray absorption spectral data obtained using solutions of Ni2+- and Zn2+-bound HpUreE provided accurate information of the metal-ion environment in the absence of solid-state effects. These results reveal the role of the histidine residues at the protein C-terminus in metal-ion binding, and the mutual influence of protein framework and metal-ion stereo-electronic properties in establishing co-ordination number and geometry leading to metal selectivity.

Crystallization and preliminary diffraction studies of the RNA polymerase subunit RPB5 from Saccharomyces cerevisiae

1999 ◽  
Vol 55 (7) ◽  
pp. 1373-1374 ◽  
Author(s):  
Meredith Hodach ◽  
Flavia Todone ◽  
Jyrki J. Eloranta ◽  
Silvia Onesti ◽  
Robert O. J. Weinzierl
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Crystal Form ◽  
Bacterial Cells ◽  
Glutathione S Transferase ◽  
Unit Cell Parameters ◽  
Monoclinic Crystal ◽  
Crystal Forms ◽  
Cell Parameters ◽  
Vapour Diffusion

Crystals of the RNA polymerase subunit RPB5 from Saccharomyces cerevisiae have been obtained by vapour-diffusion techniques. The protein has been overexpressed in bacterial cells as a fusion with glutathione S-transferase. Two monoclinic crystal forms can be grown under different sets of conditions. In both cases, the diffraction is consistent with space group P21, with unit-cell parameters a = 45.3, b = 135.3, c = 47.3 Å, β = 118.6° for crystal form I and a = 48.4, b = 137.1, c = 47.1 Å, β = 118.6° for crystal form II.

scholarly journals Structures ofEscherichia colitryptophanase in holo and `semi-holo' forms

2015 ◽  
Vol 71 (3) ◽  
pp. 286-290 ◽  
Author(s):  
Anna Kogan ◽  
Leah Raznov ◽  
Garik Y. Gdalevsky ◽  
Rivka Cohen-Luria ◽  
Orna Almog ◽  
...  
Keyword(s):  
Pyridoxal Phosphate ◽  
Crystal Form ◽  
Asymmetric Unit ◽  
Sulfate Ions ◽  
Crystal Forms ◽  
Cell Parameters ◽  
Open Conformation ◽  
Crystallization Conditions ◽  
Tyrosine Phenol Lyase ◽  
Polypeptide Chains

Two crystal forms ofEscherichia colitryptophanase (tryptophan indole-lyase, Trpase) were obtained under the same crystallization conditions. Both forms belonged to the same space groupP43212 but had slightly different unit-cell parameters. The holo crystal form, with pyridoxal phosphate (PLP) bound to Lys270 of both polypeptide chains in the asymmetric unit, diffracted to 2.9 Å resolution. The second crystal form diffracted to 3.2 Å resolution. Of the two subunits in the asymmetric unit, one was found in the holo form, while the other appeared to be in the apo form in a wide-open conformation with two sulfate ions bound in the vicinity of the active site. The conformation of all holo subunits is the same in both crystal forms. The structures suggest that Trpase is flexible in the apo form. Its conformation partially closes upon binding of PLP. The closed conformation might correspond to the enzyme in its active state with both cofactor and substrate bound in a similar way as in tyrosine phenol-lyase.

scholarly journals Conformational changes in Apolipoprotein N-acyltransferase (Lnt)

2018 ◽  
Author(s):  
Benjamin Wiseman ◽  
Martin Högbom
Keyword(s):  
Conformational Changes ◽  
Crystal Packing ◽  
Cell Envelope ◽  
Crystal Form ◽  
Covalent Attachment ◽  
Gram Negative Bacteria ◽  
Asymmetric Unit ◽  
Cellular Functions ◽  
Crystal Forms ◽  
Potential Mode

SUMMARYIn bacteria, lipoproteins are important components of the cell envelope and are responsible for many essential cellular functions. They are produced by the post-translational covalent attachment of lipids that occurs via a sequential 3-step process controlled by three essential integral membrane enzymes. The last step of this process, unique to Gram negative bacteria, is the N-acylation of the terminal cysteine by Apolipoprotein N-acyltransferase (Lnt) to form the final mature lipoprotein. Here we report 2 crystal forms of this enzyme. In one form the enzyme crystallized with two molecules in the asymmetric unit. In one of those molecules the thioester acyl-intermediate is observed. In the other molecule, the crystal packing suggests one potential mode of apolipoprotein docking to Lnt. In the second crystal form the enzyme crystallized with one molecule in the asymmetric unit in an apparent apo-state remarkably devoid of any bound molecules in the large open substrate entry portal. Taken together, these structures suggest that the movement of the essential W237 is triggered by substrate binding and could help direct and stabilize the interaction between Lnt and the incoming substrate apolipoprotein.Graphical Abstract

scholarly journals New crystal form of human ubiquitin in the presence of magnesium

2016 ◽  
Vol 72 (1) ◽  
pp. 29-35 ◽  
Author(s):  
Ana Camara-Artigas ◽  
Marina Plaza-Garrido ◽  
Sergio Martinez-Rodriguez ◽  
Julio Bacarizo
Keyword(s):  
Metal Ion ◽  
Crystal Packing ◽  
High Surface ◽  
Crystal Form ◽  
Crystallographic Structure ◽  
Native Form ◽  
Triclinic Space Group ◽  
Cell Parameters ◽  
Human Ubiquitin ◽  
Lysine Residues

Ubiquitin is a small globular protein that has a considerable number of lysine residues on its surface. This results in a high surface entropy that precludes the formation of crystal-packing interactions. To date, only a few structures of the native form of ubiquitin have been solved, and most of the crystals that led to these structures were obtained in the presence of different divalent metal cations. In this work, a new crystallographic structure of human ubiquitin solved from crystals grown in the presence of magnesium is presented. The crystals belonged to a triclinic space group, with unit-cell parametersa= 29.96,b = 30.18,c= 41.41 Å, α = 88.52, β = 79.12, γ = 67.37°. The crystal lattice is composed of stacked layers of human ubiquitin molecules with a large hydrophobic interface and a smaller polar interface in which the magnesium ion lies at the junction between adjacent layers in the crystal. The metal ion appears in a hexa-aquo coordination, which is key to facilitating the crystallization of the protein.

A new crystal form of the NSAID dexketoprofen

2019 ◽  
Vol 75 (6) ◽  
pp. 783-792 ◽  
Author(s):  
Patrizia Rossi ◽  
Paola Paoli ◽  
Andrea Ienco ◽  
Diletta Biagi ◽  
Maurizio Valleri ◽  
...  
Keyword(s):  
Single Crystal ◽  
Crystal Packing ◽  
Solid Phase ◽  
Crystal Form ◽  
Interaction Energies ◽  
Scanning Calorimetry ◽  
Short Term Treatment ◽  
Experimental Conditions ◽  
Crystal Forms ◽  
Anti Inflammatory

Dexketoprofen [(2S)-2-(3-benzoylphenyl)propanoic acid], C16H14O3, is the S-enantiomer of ketoprofen, a nonsteroidal anti-inflammatory drug (NSAID) that has analgesic, antipyretic and anti-inflammatory properties, and finds applications for the short-term treatment of mild to moderate pain. A new crystalline phase of dexketoprofen is reported. Its solid-state structure was determined by single-crystal X-ray diffraction (SCXRD). The molecular structure of the two independent molecules found in the asymmetric unit of this new phase (DXKP-β) were compared to those of the already known crystal form of dexketoprofen (DXKP-α) and with the S-enantiomer of the racemic compound. The three different conformers of dexketoprofen found in DXKP-α and DXKP-β were then investigated by computational methods. The optimized structures are very close to the corresponding starting geometries and do not differ significantly in energy. The crystal packing of DXKP-β was studied by means of Hirshfeld surface (HS) analysis; interaction energies were also calculated. A comparison with DXKP-α shows close similarities between the two crystal forms, i.e. in both cases, molecules assemble through the catemer O—H...O synthon of the carboxylic acid stabilized by additional C—H...O contacts and, accordingly, the interaction energies, as well as the contributions to the HS area, are very similar. Finally, the thermal behaviour of the two polymorphs of dexketoprofen was assessed by means of XRD (both from single crystal and microcrystalline powder) and differential scanning calorimetry (DSC); both crystal forms are stable under the experimental conditions adopted (air, 300–350 K for DXKP-α and 300–340 K DXKP-β) and no solid–solid phase transition occurs between the two crystal forms in the investigated temperature range (from 100 K up to ca 350 K).

scholarly journals Preliminary crystallographic analysis of the N-terminal domain of FILIA, a protein essential for embryogenesis

2010 ◽  
Vol 66 (9) ◽  
pp. 1111-1114
Author(s):  
Juke Wang ◽  
Tong-Cun Zhang ◽  
Xinqi Liu
Keyword(s):  
Diffraction Data ◽  
Early Stage ◽  
Crystal Form ◽  
Crystallographic Analysis ◽  
Orthorhombic Crystal ◽  
Crystal Forms ◽  
Terminal Domain ◽  
Peg 4000 ◽  
Tetragonal Crystals ◽  
Crystallization Conditions

FILIA is a component of the subcortical maternal complex that is essential for early stage embryogenesis. Its 6×His-tagged N-terminal domain was expressed inEscherichia coliand purified to homogeneity. Two types of crystals formed under different crystallization conditions during screening. Orthorhombic crystals appeared in a solution containing 1.4 Mammonium sulfate, 0.1 MTris pH 8.2 and 12% glycerol, while tetragonal crystals were obtained using 15% PEG 4000 mixed with 0.1 MHEPES pH 7.5 and 15% 2-propanol. High-quality diffraction data were collected from the two crystal forms to resolutions of 1.8 and 2.2 Å, respectively, using synchrotron radiation. The Matthews coefficients indicated that theP212121andP41212 crystals contained two molecules and one molecule per asymmetric unit, respectively. A selenomethionine-substituted sample failed to crystallize under the native conditions, but another orthorhombic crystal form was obtained under different conditions and anomalous diffraction data were collected.

The structure of dihydrodipicolinate reductase (DapB) fromMycobacterium tuberculosisin three crystal forms

2009 ◽  
Vol 66 (1) ◽  
pp. 61-72 ◽  
Author(s):  
Robert Janowski ◽  
Georgia Kefala ◽  
Manfred S. Weiss
Keyword(s):  
Conformational Change ◽  
Normal Modes ◽  
Low Frequency ◽  
Pyridine Nucleotide ◽  
Crystal Form ◽  
Orthorhombic Crystal ◽  
Monoclinic Crystal ◽  
Crystal Forms ◽  
Comparison Of The Results ◽  
Unstable Product

Dihydrodipicolinate reductase (DHDPR, DapB) is an enzyme that belongs to the L-lysine biosynthetic pathway. DHDPR reduces the α,β-unsaturated cyclic imine 2,3-dihydrodipicolinic acid to yield the compound 2,3,4,5-tetrahydrodipicolinic acid in a pyridine nucleotide-dependent reaction. The substrate of this reaction is the unstable product of the preceding enzyme dihydrodipicolinate synthase (DHDPS, DapA). Here, the structure of apo-DHDPR fromMycobacterium tuberculosisis reported in two orthorhombic crystal forms, as well as the structure of DHDPR fromM. tuberculosisin complex with NADH in a monoclinic crystal form. A comparison of the results with previously solved structures of this enzyme shows that DHDPR undergoes a major conformational change upon binding of its cofactor. This conformational change can be interpreted as one of the low-frequency normal modes of the structure.

scholarly journals A new crystal form of Lys48-linked diubiquitin

2010 ◽  
Vol 66 (9) ◽  
pp. 994-998 ◽  
Author(s):  
Jean-François Trempe ◽  
Nicholas R. Brown ◽  
Martin E. M. Noble ◽  
Jane A. Endicott
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Crystal Form ◽  
Asymmetric Unit ◽  
Polyubiquitin Chains ◽  
Isopeptide Bond ◽  
Closed Conformation ◽  
Crystallization Conditions

Lys48-linked polyubiquitin chains are recognized by the proteasome as a tag for the degradation of the attached substrates. Here, a new crystal form of Lys48-linked diubiquitin (Ub2) was obtained and the crystal structure was refined to 1.6 Å resolution. The structure reveals an ordered isopeptide bond in atransconfiguration. All three molecules in the asymmetric unit were in the same closed conformation, in which the hydrophobic patches of both the distal and the proximal moieties interact with each other. Despite the different crystallization conditions and different crystal packing, the new crystal structure of Ub2is similar to the previously published structure of diubiquitin, but differences are observed in the conformation of the flexible isopeptide linkage.

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