Twists and turns: a tale of two shikimate-pathway enzymes

2003 ◽  
Vol 31 (3) ◽  
pp. 543-547 ◽  
Author(s):  
K.A. Brown ◽  
E.P. Carpenter ◽  
K.A. Watson ◽  
J.R. Coggins ◽  
A.R. Hawkins ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Shikimate Pathway ◽  
Structural Features ◽  
Side Chain ◽  
Computational Techniques ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Presence And Absence ◽  
Energy Maps

We are studying two enzymes from the shikimate pathway, dehydroquinate synthase (DHQS) and 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Both enzymes have been the subject of numerous studies to elucidate their reaction mechanisms. Crystal structures of DHQS and EPSPS in the presence and absence of substrates, cofactors and/or inhibitors are now available. These structures reveal movements of domains, rearrangements of loops and changes in side-chain positions necessary for the formation of a catalytically competent active site. The potential for using complementary small-angle X-ray scattering (SAXS) studies to confirm the presence of these structural differences in solution has also been explored. Comparative analysis of crystal structures, in the presence and absence of ligands, has revealed structural features critical for substrate-binding and catalysis. We have also analysed these structures by generating GRID energy maps to detect favourable binding sites. The combination of X-ray crystallography, SAXS and computational techniques provides an enhanced analysis of structural features important for the function of these complex enzymes.

Synthesis of the cyclopropa[c]benzofuran system of mycorrhizin A and of gilmicolin from a benzofuranol. Crystal structure of a 5,8-Methanocyclopropa-[c]naphtho[2,3-b]furan derivative

1982 ◽  
Vol 35 (8) ◽  
pp. 1665 ◽  
Author(s):  
RFC Brown ◽  
GD Fallon ◽  
BM Gatehouse ◽  
CM Jones ◽  
ID Rae
Keyword(s):  
Crystal Structure ◽  
Ultraviolet Irradiation ◽  
Room Temperature ◽  
Cyclopropane Ring ◽  
Structural Features ◽  
Side Chain ◽  
Furan Derivative ◽  
Methoxy Derivative ◽  
X Ray ◽  
X Ray Crystallography

The cyclopropa[c]benzofuran derivative (17), which contains the structural features of methyl ethers of mycorrhizin A and gilmicolin save for the C3 side chain, has been synthesized from the benzofuranol (4) through the benzofuran-4,7-dione (5) and the 7a-methoxy derivative (8). The cyclopropane ring of (17) was introduced by ultraviolet irradiation of a 1-pyrazoline (13) at -78�; irradiation at room temperature gave mainly a profoundly rearranged acidic product for which the methanoindenone structure (18) is proposed. The stereochemistry of the penultimate cyclopropane (16) has been established by X-ray crystallography.

scholarly journals Structure of DnmZ, a nitrososynthase in the Streptomyces peucetius anthracycline biosynthetic pathway

2015 ◽  
Vol 71 (10) ◽  
pp. 1205-1214 ◽  
Author(s):  
Lauren Sartor ◽  
Charmaine Ibarra ◽  
Ahmad Al-Mestarihi ◽  
Brian O. Bachmann ◽  
Jessica L. Vey
Keyword(s):  
Substrate Specificity ◽  
Natural Product ◽  
Crystal Structures ◽  
Conformational Changes ◽  
Biosynthetic Pathway ◽  
Three Dimensional ◽  
Structural Features ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography

The anthracyclines are a class of highly effective natural product chemotherapeutics and are used to treat a range of cancers, including leukemia. The toxicity of the anthracyclines has stimulated efforts to further diversify the scaffold of the natural product, which has led to renewed interest in the biosynthetic pathway responsible for the formation and modification of this family of molecules. DnmZ is an N-hydroxylating flavin monooxygenase (a nitrososynthase) that catalyzes the oxidation of the exocyclic amine of the sugar nucleotide dTDP-L-epi-vancosamine to its nitroso form. Its specific role in the anthracycline biosynthetic pathway involves the synthesis of the seven-carbon acetal moiety attached to C4 of L-daunosamine observed in the anthracycline baumycin. Here, X-ray crystallography was used to elucidate the three-dimensional structure of DnmZ. Two crystal structures of DnmZ were yielded: that of the enzyme alone, solved to 3.00 Å resolution, and that of the enzyme in complex with thymidine diphosphate, the nucleotide carrier portion of the substrate, solved to 2.74 Å resolution. These models add insights into the structural features involved in substrate specificity and conformational changes involved in thymidine diphosphate binding by the nitrososynthases.

scholarly journals Quantum refinement with multiple conformations: application to the P-cluster in nitrogenase

2020 ◽  
Vol 76 (11) ◽  
pp. 1145-1156
Author(s):  
Lili Cao ◽  
Ulf Ryde
Keyword(s):  
Crystal Structures ◽  
Real Space ◽  
Scattering Data ◽  
Original Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Density Maps ◽  
Multiple Conformations ◽  
The One

X-ray crystallography is the main source of atomistic information on the structure of proteins. Normal crystal structures are obtained as a compromise between the X-ray scattering data and a set of empirical restraints that ensure chemically reasonable bond lengths and angles. However, such restraints are not always available or accurate for nonstandard parts of the structure, for example substrates, inhibitors and metal sites. The method of quantum refinement, in which these empirical restraints are replaced by quantum-mechanical (QM) calculations, has previously been suggested for small but interesting parts of the protein. Here, this approach is extended to allow for multiple conformations in the QM region by performing separate QM calculations for each conformation. This approach is shown to work properly and leads to improved structures in terms of electron-density maps and real-space difference density Z-scores. It is also shown that the quality of the structures can be gauged using QM strain energies. The approach, called ComQumX-2QM, is applied to the P-cluster in two different crystal structures of the enzyme nitrogenase, i.e. an Fe8S7Cys6 cluster, used for electron transfer. One structure is at a very high resolution (1.0 Å) and shows a mixture of two different oxidation states, the fully reduced PN state (Fe8 2+, 20%) and the doubly oxidized P2+ state (80%). In the original crystal structure the coordinates differed for only two iron ions, but here it is shown that the two states also show differences in other atoms of up to 0.7 Å. The second structure is at a more modest resolution, 2.1 Å, and was originally suggested to show only the one-electron oxidized state, P1+. Here, it is shown that it is rather a 50/50% mixture of the P1+ and P2+ states and that many of the Fe—Fe and Fe—S distances in the original structure were quite inaccurate (by up to 0.8 Å). This shows that the new ComQumX-2QM approach can be used to sort out what is actually seen in crystal structures with dual conformations and to give locally improved coordinates.

scholarly journals A mixed chirality α-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography

2021 ◽  
Author(s):  
Stéphane Baeriswyl ◽  
Hippolyte Personne ◽  
Ivan Di Bonaventura ◽  
Thilo Köhler ◽  
Christian van Delden ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Antimicrobial Peptide ◽  
Crystal Structures ◽  
X Ray ◽  
X Ray Crystallography ◽  
Α Helix

We report the first X-ray crystal structures of mixed chirality α-helices comprising only natural residues as the example of bicyclic and linear membrane disruptive amphiphilic antimicrobial peptides containing seven l- and four d-residues.

Bis(1-phenyl-1-propyne) complexes of tungsten(II): crystal structures of [WI2(CO)(NCR)(η2-MeC2Ph)2] (R = Me, Et, or Ph)

2001 ◽  
Vol 79 (3) ◽  
pp. 263-271
Author(s):  
Paul K Baker ◽  
Michael GB Drew ◽  
Deborah S Evans
Keyword(s):  
Carbon Monoxide ◽  
Solid State ◽  
Crystal Structures ◽  
Octahedral Geometry ◽  
X Ray ◽  
X Ray Crystallography ◽  
Alkyne Complexes ◽  
First Time

Reaction of [WI2(CO)3(NCMe)2] with two equivalents of 1-phenyl-1-propyne (MeC2Ph) in CH2Cl2, and in the absence of light, gave the bis(1-phenyl-1-propyne) complex [WI2(CO)(NCMe)(η2-MeC2Ph)2] (1) in 77% yield. Treatment of equimolar quantities of 1 and NCR (R = Et, i-Pr, t-Bu, Ph) in CH2Cl2 afforded the nitrile-exchanged products, [WI2(CO)(NCR)(η2-MeC2Ph)2] (2-5) (R = Et (2), i-Pr (3), t-Bu (4), Ph (5)). Complexes 1, 2, and 5 were structurally characterized by X-ray crystallography. All three structures have the same pseudo-octahedral geometry, with the equatorial sites being occupied by cis and parallel alkyne groups, which are trans to the cis-iodo groups. The trans carbon monoxide and acetonitrile ligands occupy the axial sites. In structures 1 and 2, the methyl and phenyl substituents of the 1-phenyl-1-propyne ligands are cis to each other, whereas for the bulkier NCPh complex (5), the methyl and phenyl groups are trans to one another. This is the first time that this arrangement has been observed in the solid state in bis(alkyne) complexes of this type.Key words: bis(1-phenyl-1-propyne), carbonyl, nitrile, diiodo, tungsten(II), crystal structures.

scholarly journals Structure of the Lassa Virus Nucleoprotein Revealed by X-ray Crystallography, Small-angle X-ray Scattering, and Electron Microscopy

2011 ◽  
Vol 286 (44) ◽  
pp. 38748-38756 ◽  
Author(s):  
Linda Brunotte ◽  
Romy Kerber ◽  
Weifeng Shang ◽  
Florian Hauer ◽  
Meike Hass ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Small Angle ◽  
Lassa Virus ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Ray Scattering

Phosphate tungsten bronze series: crystallographic and structural properties of low-dimensional conductors

2001 ◽  
Vol 57 (5) ◽  
pp. 603-632 ◽  
Author(s):  
P. Roussel ◽  
O. Pérez ◽  
Ph. Labbé
Keyword(s):  
Crystal Structures ◽  
Structural Properties ◽  
Tungsten Bronze ◽  
Structural Description ◽  
X Ray ◽  
X Ray Scattering ◽  
Modulated Structures ◽  
Low Dimensionality ◽  
Low Dimensional ◽  
Thickness Function

Phosphate tungsten bronzes have been shown to be conductors of low dimensionality. A review of the crystallographic and structural properties of this huge series of compounds is given here, corresponding to the present knowledge of the different X-ray studies and electron microscopy investigations. Three main families are described, monophosphate tungsten bronzes, Ax (PO2)4(WO3)2m , either with pentagonal tunnels (MPTBp) or with hexagonal tunnels (MPTBh), and diphosphate tungsten bronzes, Ax (P2O4)2(WO3)2m , mainly with hexagonal tunnels (DPTBh). The general aspect of these crystal structures may be described as a building of polyhedra sharing oxygen corners made of regular stacking of WO3-type slabs with a thickness function of m, joined by slices of tetrahedral PO4 phosphate or P2O7 diphosphate groups. The relations of the different slabs with respect to the basic perovskite structure are mentioned. The structural description is focused on the tilt phenomenon of the WO6 octahedra inside a slab of WO3-type. In this respect, a comparison with the different phases of the WO3 crystal structures is established. The various modes of tilting and the different possible connections between two adjacent WO3-type slabs involve a great variety of structures with different symmetries, as well as the existence of numerous twins in MPTBp's. Several phase transitions, with the appearance of diffuse scattering and modulation phenomena, were analysed by X-ray scattering measurements and through the temperature dependence of various physical properties for the MPTBp's. The role of the W displacements within the WO3-type slabs, in two modulated structures (m = 4 and m = 10), already solved, is discussed. Finally, the complexity of the structural aspects of DPTBh's is explained on the basis of the average structures which are the only ones solved.

scholarly journals NMR and X-ray studies of apetalic acid isolated from Calophyllum brasiliense and of its chiral amides

2021 ◽  
Author(s):  
Marie-Rose Van Calsteren ◽  
Ricardo Reyes-Chilpa ◽  
Chistopher K Jankowski ◽  
Fleur Gagnon ◽  
Simón Hernández-Ortega ◽  
...  
Keyword(s):  
Antimycobacterial Activity ◽  
Side Chain ◽  
Carboxyl Group ◽  
X Ray Diffraction ◽  
Rain Forests ◽  
X Ray ◽  
X Ray Crystallography ◽  
Calophyllum Brasiliense ◽  
Derivatives Of

The tropical tree Calophyllum brasiliense (Clusiaceae) grows in the rain forests from Brazil to Mexico. Its leaves, as well as those of other Calophyllum species, are rich sources of chromanone acids, such as apetalic acid, isoapetalic acid, and their derivatives. Apetalic acid has shown significant antimycobacterial activity. The biological activity of apetalic acid has been related to the configuration of three asymmetric centers and the stereochemistry of the molecule; however, the C-19 configuration in the acidic side chain has not been fully resolved. For this reason, the unequivocal determination of the absolute configuration by means of X-ray crystallography in a sample of unique homogeneous apetalic acid stereoisomer was the most important point to start this study. We prepared some chiral amides using the carboxyl group. We determined the C-19 stereochemistry of apetalic acid, and its specific chiral derivatives, using NMR, X-ray diffraction methods, and molecular mechanics. Finally, we observed that steric hindrance in the side chain of apetalic acid leads to restriction of rotation around the pivotal link C-10 and C-19 establishing chiral centers at C2(R), C3(S), and C19(R). We were able to separate derivatives of these two high-rotatory-barrier conformers of apetalic acid by forming diastereoisomeric amides with phenylglycine methyl ester having a chiral center at C-2’. Our results allowed the conclusion of the existence of atropisomerism in the apetalic acid molecule.

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