scholarly journals Crystallization behaviour of glyceraldehyde dehydrogenase fromThermoplasma acidophilum

2015 ◽  
Vol 71 (12) ◽  
pp. 1475-1480
Author(s):  
Iuliia Iermak ◽  
Oksana Degtjarik ◽  
Fabian Steffler ◽  
Volker Sieber ◽  
Ivana Kuta Smatanova
Keyword(s):  
Saturation Mutagenesis ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Artificial Enzyme ◽  
Wild Type ◽  
Thermoplasma Acidophilum ◽  
Space Groups ◽  
Enzyme Cascade ◽  
Microbial Enzyme ◽  
Random Approach

The glyceraldehyde dehydrogenase fromThermoplasma acidophilum(TaAlDH) is a microbial enzyme that catalyzes the oxidation of D-glyceraldehyde to D-glycerate in the artificial enzyme cascade designed for the conversion of glucose to the organic solvents isobutanol and ethanol. Various mutants ofTaAlDH were constructed by a random approach followed by site-directed and saturation mutagenesis in order to improve the properties of the enzyme that are essential for its functioning within the cascade. Two enzyme variants, wild-typeTaAlDH (TaAlDHwt) and an F34M+S405N variant (TaAlDH F34M+S405N), were successfully crystallized. Crystals ofTaAlDHwt belonged to the monoclinic space groupP1211 with eight molecules per asymmetric unit and diffracted to a resolution of 1.95 Å.TaAlDH F34M+S405N crystallized in two different space groups: triclinicP1 with 16 molecules per asymmetric unit and monoclinicC121 with four molecules per asymmetric unit. These crystals diffracted to resolutions of 2.14 and 2.10 Å for theP1 andC121 crystals, respectively.

Influence of the position of the methyl substituent and N-oxide formation on the geometry and intermolecular interactions of 1-(phenoxyethyl)piperidin-4-ol derivatives

2020 ◽  
Vol 76 (1) ◽  
pp. 30-36 ◽  
Author(s):  
Ewa Żesławska ◽  
Justyna Kalinowska-Tłuścik ◽  
Wojciech Nitek ◽  
Henryk Marona ◽  
Anna M. Waszkielewicz
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Piperidine Ring ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Methyl Substituent ◽  
X Ray Diffraction ◽  
Oxide Formation ◽  
Space Groups

Aminoalkanol derivatives have attracted much interest in the field of medicinal chemistry as part of the search for new anticonvulsant drugs. In order to study the influence of the methyl substituent and N-oxide formation on the geometry of molecules and intermolecular interactions in their crystals, three new examples have been prepared and their crystal structures determined by X-ray diffraction. 1-[(2,6-Dimethylphenoxy)ethyl]piperidin-4-ol, C15H23NO2, 1, and 1-[(2,3-dimethylphenoxy)ethyl]piperidin-4-ol, C15H23NO2, 2, crystallize in the orthorhombic system (space groups P212121 and Pbca, respectively), with one molecule in the asymmetric unit, whereas the N-oxide 1-[(2,3-dimethylphenoxy)ethyl]piperidin-4-ol N-oxide monohydrate, C15H23NO3·H2O, 3, crystallizes in the monoclinic space group P21/c, with one N-oxide molecule and one water molecule in the asymmetric unit. The geometries of the investigated compounds differ significantly with respect to the conformation of the O—C—C linker, the location of the hydroxy group in the piperidine ring and the nature of the intermolecular interactions, which were investigated by Hirshfeld surface and corresponding fingerprint analyses. The crystal packing of 1 and 2 is dominated by a network of O—H...N hydrogen bonds, while in 3, it is dominated by O—H...O hydrogen bonds and results in the formation of chains.

Studies in aryltin chemistry. Part 6. Crystal and molecular structures of tetra(p-methylsulphonylphenyl)tin(IV) and tetra(p-methylsulphinylphenyl)tin(IV) monohydrate

1990 ◽  
Vol 68 (8) ◽  
pp. 1277-1282 ◽  
Author(s):  
Ivor Wharf ◽  
Michel G. Simard ◽  
Henry Lamparski
Keyword(s):  
Least Squares ◽  
Crystal Structures ◽  
Direct Method ◽  
Molecular Structures ◽  
Water Molecules ◽  
Monoclinic Space Group ◽  
Molecular Symmetry ◽  
Asymmetric Unit ◽  
Full Matrix ◽  
Space Group

Tetrakis(p-methylsulphonylphenyl)tin(IV) and tetrakis(p-methylsulphinylphenyl)tin(IV) n-hydrate have been prepared and their spectra (ir 1350–400 cm−1; nmr, 1H, 13C, 119Sn) and X-ray crystal structures are reported. The first compound is monoclinic, space group C2/c, Z = 4, with a = 21.589(6), b = 6.207(3), c = 22.861(11) Å, β = 93.80(3)° (22 °C); the structure was solved by the direct method and refined by full-matrix least squares calculations to R = 0.043 for 2755 observed reflections. It has 2 molecular symmetry with the methyl group and one oxygen atom completely disordered in both CH3S(O2) groups in the asymmetric unit. The second compound is tetragonal, space group P42/n, Z = 2, with a = b = 15.408(6), c = 6.379(2) Å (−100 °C); the structure was solved by the Patterson method and refined by full-matrix least squares calculations to R = 0.060 for 1209 observed reflections. It has [Formula: see text] molecular symmetry with the whole asymmetric unit disordered. Water molecules occupy positions on parallel 42 axes but molecular packing requirements prevent all sites having 100% occupancy giving n ~ 1 for the hydrate. Keywords: Tetra-aryltins, crystal structures, sulphone, sulphoxide, hydrogen-bonding.

The effect of partial methylation of the glycine amino group on crystal structure inN,N-dimethylglycine and its hemihydrate

2012 ◽  
Vol 68 (8) ◽  
pp. o283-o287 ◽  
Author(s):  
Vasily S. Minkov ◽  
Elena V. Boldyreva
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Water Molecules ◽  
Amino Group ◽  
Asymmetric Unit ◽  
Partial Methylation ◽  
Space Groups ◽  
Carboxylate Groups ◽  
Anhydrous Compound ◽  
Additional Hydrogen

N,N-Dimethylglycine, C4H9NO2, and its hemihydrate, C4H9NO2·0.5H2O, are discussed in order to follow the effect of the methylation of the glycine amino group (and thus its ability to form several hydrogen bonds) on crystal structure, in particular on the possibility of the formation of hydrogen-bonded `head-to-tail' chains, which are typical for the crystal structures of amino acids and essential for considering amino acid crystals as mimics of peptide chains. Both compounds crystallize in centrosymmetric space groups (PbcaandC2/c, respectively) and have twoN,N-dimethylglycine zwitterions in the asymmetric unit. In the anhydrous compound, there are no head-to-tail chains but the zwitterions formR44(20) ring motifs, which are not bonded to each other by any hydrogen bonds. In contrast, in the crystal structure ofN,N-dimethylglycinium hemihydrate, the zwitterions are linked to each other by N—H...O hydrogen bonds into infiniteC22(10) head-to-tail chains, while the water molecules outside the chains provide additional hydrogen bonds to the carboxylate groups.

Cellulose organic solvents: V. Conformational aspects of N,N-dimethyl ethanolamine N-oxide in its crystalline and diluted states

1984 ◽  
Vol 62 (1) ◽  
pp. 6-10 ◽  
Author(s):  
E. R. Maia ◽  
A. Péguy ◽  
S. Pérez
Keyword(s):  
Tertiary Amine ◽  
Amine Oxide ◽  
Direct Methods ◽  
Monoclinic Space Group ◽  
Cyclic Form ◽  
Asymmetric Unit ◽  
Ir And Nmr Spectroscopy ◽  
Conformational Investigation ◽  
Intramolecular Hydrogen ◽  
Strong Intramolecular Hydrogen Bond

N,N-Dimethyl ethanolamine N-oxide (DMEAO) belongs to the class of tertiary amine oxide molecules that are good solvents for cellulose, although not being cyclic. Crystallographic investigation shows that anhydrous DMEAO is monoclinic, space group Cc, a = 25.725(9), b = 7.023(4), c = 9.483(5) Å, β = 101.16(10)°, Z = 12. The crystal structure has been solved by direct methods and refined to a final R value of 0.063 for 575 observed reflexions. Three independent molecules are found within the asymmetric unit; one of these displays a pseudo-cyclic form dictated by the occurrence of a strong intramolecular hydrogen bond. Conformational investigation of DMEAO in solution, using ir and nmr spectroscopy shows that this pseudo-cyclic form is more likely to occur in diluted states. These findings are related to the ability of this tertiary amine oxide to act as a good solvent, up to a water content of one water molecule per DMEAO molecule.

Absolute configurations of Emycin D, E and F; mimicry of centrosymmetric space groups by mixtures of chiral stereoisomers

1999 ◽  
Vol 55 (4) ◽  
pp. 607-616 ◽  
Author(s):  
Martina Walker ◽  
Ehmke Pohl ◽  
Regine Herbst-Irmer ◽  
Martin Gerlitz ◽  
Jürgen Rohr ◽  
...  
Keyword(s):  
Correct Choice ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
Space Group ◽  
Space Groups ◽  
Centrosymmetric Space Group ◽  
Distance Restraints ◽  
Similar Distance ◽  
Triclinic Unit Cell ◽  
R Factors

The crystal structures of Emycin E (1), di-o-bromobenzoyl-Emycin F (2) and o-bromobenzoyl-Emycin D (3) have been determined by X-ray analysis at low temperature. Emycin E and o-bromobenzoyl-Emycin D both crystallize with two molecules in a triclinic unit cell. These two structures can be solved and refined either in the centrosymmetric space group P\bar 1, with apparent disorder localized at or around the expected chiral centre, or in the non-centrosymmetric space group P1 as mixtures of two diastereomers without disorder. Only the latter interpretation is consistent with the chemical and spectroscopic evidence. Refinements in the centrosymmetric and non-centrosymmetric space groups are compared in this paper and are shown to favour the chemically correct interpretation, more decisively so in the case of the bromo derivative as a result of the anomalous dispersion of bromine. Structures (1) and (3) provide a dramatic warning of the dangers inherent in the conventional wisdom that if a structure can be refined satisfactorarily in both centrosymmetric and non-centrosymmetric space groups, the former should always be chosen. In these two cases, despite apparently acceptable intensity statistics and R factors (5.87 and 3.55%), the choice of the centrosymmetric space group leads to the serious chemical error that the triclinic unit cell contains a racemate rather than two chiral diastereomers! The weakest reflections are shown to be most sensitive to the correct choice of space group, underlining the importance of refining against all data rather than against intensities greater than a specified threshold. The use of similar-distance restraints is shown to be beneficial in both P1 refinements. Di-o-bromobenzoyl-Emycin F crystallizes in the monoclinic space group P21 with one molecule in the asymmetric unit and so does not give rise to these problems of interpretation. The absolute configuration of the two bromo derivatives, and hence the Emycins in general, was determined unambiguously as S at the chiral centre C3.

scholarly journals An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants

2021 ◽  
Vol 7 (8) ◽  
pp. eabf1738 ◽  
Author(s):  
Kui K. Chan ◽  
Timothy J. C. Tan ◽  
Krishna K. Narayanan ◽  
Erik Procko
Keyword(s):  
In Vitro Selection ◽  
Protein S ◽  
Saturation Mutagenesis ◽  
Wild Type ◽  
Host Cell Membrane ◽  
Decoy Receptor ◽  
Decoy Receptors ◽  
Binding Surface ◽  
Type Receptor

The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, because of close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find that an engineered decoy receptor, sACE22.v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain followed by in vitro selection, with wild-type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild-type receptor. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.

Structural studies of complexes of kallikrein 4 with wild-type and mutated forms of the Kunitz-type inhibitor BbKI

2021 ◽  
Vol 77 (8) ◽  
Author(s):  
Mi Li ◽  
Jaroslav Srp ◽  
Michael Mareš ◽  
Alexander Wlodawer ◽  
Alla Gustchina
Keyword(s):  
Serine Proteases ◽  
Structural Studies ◽  
Wild Type ◽  
Inhibitory Potency ◽  
Crystal Forms ◽  
Space Groups ◽  
Bovine Trypsin ◽  
Kallikrein 4 ◽  
Kunitz Type ◽  
Resolution Structure

Structures of BbKI, a recombinant Kunitz-type serine protease inhibitor from Bauhinia bauhinioides, complexed with human kallikrein 4 (KLK4) were determined at medium-to-high resolution in four crystal forms (space groups P3121, P6522, P21 and P61). Although the fold of the protein was virtually identical in all of the crystals, some significant differences were observed in the conformation of Arg64 of BbKI, the residue that occupies the S1 pocket in KLK4. Whereas this residue exhibited two orientations in the highest resolution structure (P3121), making either a canonical trypsin-like interaction with Asp189 of KLK4 or an alternate interaction, only a single alternate orientation was observed in the other three structures. A neighboring disulfide, Cys191–Cys220, was partially or fully broken in all KLK4 structures. Four variants of BbKI in which Arg64 was replaced by Met, Phe, Ala and Asp were expressed and crystallized, and their structures were determined in complex with KLK4. Structures of the Phe and Met variants complexed with bovine trypsin and of the Phe variant complexed with α-chymotrypsin were also determined. Although the inhibitory potency of these variant forms of BbKI was lowered by up to four orders of magnitude, only small changes were seen in the vicinity of the mutated residues. Therefore, a totality of subtle differences in KLK4–BbKI interactions within the fully extended interface in the structures of these variants might be responsible for the observed effect. Screening of the BbKI variants against a panel of serine proteases revealed an altered pattern of inhibitory specificity, which was shifted towards that of chymotrypsin-like proteases for the hydrophobic Phe and Met P1 substitutions. This work reports the first structures of plant Kunitz inhibitors with S1-family serine proteases other than trypsin, as well as new insights into the specificity of inhibition of medically relevant kallikreins.

scholarly journals Elimination of 2-keto-3-deoxy-D-glycero-D-galacto-nonulosonic acid 9-phosphate synthase activity from human N-acetylneuraminic acid 9-phosphate synthase by a single mutation

2006 ◽  
Vol 397 (1) ◽  
pp. 195-201 ◽  
Author(s):  
Jijun Hao ◽  
Willie F. Vann ◽  
Stephan Hinderlich ◽  
Munirathinam Sundaramoorthy
Keyword(s):  
Aldol Condensation ◽  
Saturation Mutagenesis ◽  
Single Mutation ◽  
Wild Type ◽  
Wild Type Enzyme ◽  
High Sequence Identity ◽  
Acetylneuraminic Acid ◽  
Nonulosonic Acid ◽  
The Impact ◽  
Phosphate Synthase

The most commonly occurring sialic acid Neu5Ac (N-acetylneuraminic acid) and its deaminated form, KDN (2-keto-3-deoxy-D-glycero-D-galacto-nonulosonic acid), participate in many biological functions. The human Neu5Ac-9-P (Neu5Ac 9-phosphate) synthase has the unique ability to catalyse the synthesis of not only Neu5Ac-9-P but also KDN-9-P (KDN 9-phosphate). Both reactions are catalysed by the mechanism of aldol condensation of PEP (phosphoenolpyruvate) with sugar substrates, ManNAc-6-P (N-acetylmannosamine 6-phosphate) or Man-6-P (mannose 6-phosphate). Mouse and putative rat Neu5Ac-9-P synthases, however, do not show KDN-9-P synthase activity, despite sharing high sequence identity (>95%) with the human enzyme. Here, we demonstrate that a single mutation, M42T, in human Neu5Ac-9-P synthase can abolish the KDN-9-P synthase activity completely without compromising the Neu5Ac-9-P synthase activity. Saturation mutagenesis of Met42 of the human Neu5Ac-9-P synthase showed that the substitution with all amino acids except leucine retains only the Neu5Ac-9-P synthase activity at levels comparable with the wild-type enzyme. The M42L mutant, like the wild-type enzyme, showed the additional KDN-9-P synthase activity. In the homology model of human Neu5Ac-9-P synthase, Met42 is located 22 Å (1 Å=0.1 nm) away from the substrate-binding site and the impact of this distant residue on the enzyme functions is discussed.

Studies on Crown Ether Complexes. XXXI. Synthesis, Properties and Structure of the Complexes of Lighter Lanthanide Nitrates With (Z)-2,3-Diphenyl-1,4,7,10,13-pentaoxacyclopentadec-2-ene (Stilbeno-15-crown-5)

1993 ◽  
Vol 46 (11) ◽  
pp. 1817 ◽  
Author(s):  
TB Lu ◽  
N Tang ◽  
MY Tan ◽  
Y Liu ◽  
KB Yu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Conductivity Measurements ◽  
X Ray ◽  
Elemental Analyses ◽  
Crown Ether Complexes ◽  
Synthesis Properties ◽  
Lanthanide Nitrates ◽  
Ray Methods

Complexes of the lighter lanthanide nitrates with stilbeno-15-crown-5 (L) have been prepared in ethyl acetate. These new complexes with the general formula Ln (NO3)3.L.H2O ( Ln = La, Ce , Pr, Nd ) have been characterized by means of elemental analyses, i.r . spectra, 1H n.m.r. spectra and conductivity measurements. The crystal structure of La(NO3)3.L has been determined by X-ray methods, and refined to a residual R 0.0513 for 4937 independent reflections with I ≥ 1.5σ(I). It crystallizes in the monoclinic space group P21/a with a 16.090(5), b 15.654(8), c 22.687(2) Ǻ, β 93.96(4)°, V 5700(4)Ǻ3, and Z 8. There are two independent La(NO3)3.L monomers in one asymmetric unit; in each the coordination number is 11.

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.

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