scholarly journals Oxo-iron clusters in a bacterial iron-trafficking protein: new roles for a conserved motif

2003 ◽  
Vol 376 (1) ◽  
pp. 35-41 ◽  
Author(s):  
Haizhong ZHU ◽  
Dmitriy ALEXEEV ◽  
Dominic J. B. HUNTER ◽  
Dominic J. CAMPOPIANO ◽  
Peter J. SADLER
Keyword(s):  
Iron Acquisition ◽  
Ion Binding ◽  
Binding Motif ◽  
Iron Cluster ◽  
X Ray ◽  
Iron Trafficking ◽  
Organic Mineral ◽  
Unit Cells ◽  
Independent Molecules ◽  
Mineral Interfaces

We report a set of three 1.8–1.9 Å resolution X-ray crystal structures of Neisseria gonorrhoeae Fbp (ferric-ion binding protein): (i) open-cleft apo-Fbp containing bound phosphate, (ii) open-cleft mono-Fe Fbp capped by nitrilotriacetate, and (iii) open-cleft trinuclear oxo-iron Fbp, the first structure of an iron-cluster adduct of a transferrin. The nine independent molecules in the unit cells provide ‘snapshots’ of the versatile dynamic structural roles of the conserved dityrosyl iron-binding motif (Tyr195-Tyr196) which control the capture and, possibly, processing of iron. These findings have implications for understanding bacterial iron acquisition and dissimilation, and organic/mineral interfaces.

Crystal Forms of Semisynthetic Ergot Alkaloid Terguride

2002 ◽  
Vol 67 (4) ◽  
pp. 479-489 ◽  
Author(s):  
Michal Hušák ◽  
Bohumil Kratochvíl ◽  
Ivana Císařová ◽  
Ladislav Cvak ◽  
Alexandr Jegorov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ergot Alkaloid ◽  
Simplified Model ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray Diffraction ◽  
Torsion Angles ◽  
Crystal Forms ◽  
X Ray ◽  
Independent Molecules

Two new structures of semisynthetic ergot alkaloid terguride created by unusual number of symmetry-independent molecules were determined by X-ray diffraction methods at 150 K. Form A (monoclinic, P212121, Z = 12) contains three symmetry-independent terguride molecules and two molecules of water in the asymmetric part of the unit cell. The form CA (monoclinic, P21, Z = 8) is an anhydrate remarkable by the presence of four symmetry-independent molecules in the crystal structure. Conformations of twelve symmetry-independent molecules that were found in four already described terguride structures are compared with torsion angles obtained by ab initio quantum-mechanical calculations for the simplified model of N-cyclohexyl-N'-diethylurea.

scholarly journals Snapshots of a Non-Canonical RdRP in Action

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1260
Author(s):  
Diego S. Ferrero ◽  
Michela Falqui ◽  
Nuria Verdaguer
Keyword(s):  
Metal Ion ◽  
Rna Viruses ◽  
Ion Binding ◽  
Genome Replication ◽  
Metal Ion Binding ◽  
Insect Virus ◽  
X Ray ◽  
Template Strand ◽  
Nucleotide Incorporation ◽  
Elongation Process

RNA viruses typically encode their own RNA-dependent RNA polymerase (RdRP) to ensure genome replication and transcription. The closed “right hand” architecture of RdRPs encircles seven conserved structural motifs (A to G) that regulate the polymerization activity. The four palm motifs, arranged in the sequential order A to D, are common to all known template dependent polynucleotide polymerases, with motifs A and C containing the catalytic aspartic acid residues. Exceptions to this design have been reported in members of the Permutotetraviridae and Birnaviridae families of positive single stranded (+ss) and double-stranded (ds) RNA viruses, respectively. In these enzymes, motif C is located upstream of motif A, displaying a permuted C–A–B–D connectivity. Here we study the details of the replication elongation process in the non-canonical RdRP of the Thosea asigna virus (TaV), an insect virus from the Permutatetraviridae family. We report the X-ray structures of three replicative complexes of the TaV polymerase obtained with an RNA template-primer in the absence and in the presence of incoming rNTPs. The structures captured different replication events and allowed to define the critical interactions involved in: (i) the positioning of the acceptor base of the template strand, (ii) the positioning of the 3’-OH group of the primer nucleotide during RNA replication and (iii) the recognition and positioning of the incoming nucleotide. Structural comparisons unveiled a closure of the active site on the RNA template-primer binding, before rNTP entry. This conformational rearrangement that also includes the repositioning of the motif A aspartate for the catalytic reaction to take place is maintained on rNTP and metal ion binding and after nucleotide incorporation, before translocation.

X-ray Photoelectron Spectroscopy of Fast-Frozen Hematite Colloids in Aqueous Solutions. 6. Sodium Halide (F–, Cl–, Br–, I–) Ion Binding on Microparticles

Langmuir ◽  
2018 ◽  
Vol 34 (45) ◽  
pp. 13497-13504
Author(s):  
Marie Lucas ◽  
Merve Yeşilbaş ◽  
Andrey Shchukarev ◽  
Jean-François Boily
Keyword(s):  
Aqueous Solutions ◽  
Photoelectron Spectroscopy ◽  
Ion Binding ◽  
X Ray

scholarly journals Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family

eLife ◽  
2022 ◽  
Vol 11 ◽  
Author(s):  
Karthik Ramanadane ◽  
Monique S Straub ◽  
Raimund Dutzler ◽  
Cristina Manatschal
Keyword(s):  
Hydration Shell ◽  
Transition Metal Ions ◽  
Ion Binding ◽  
X Ray ◽  
X Ray Crystallography ◽  
Protein Architecture ◽  
Large Pool ◽  
Structural And Functional Properties ◽  
The Family ◽  
Magnesium Transporter

Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca2+ and Mg2+, which are both orders of magnitude more abundant, and to concentrate them in the cytoplasm aided by the cotransport of H+ serving as energy source. In the present study, we have characterized a member of a distant clade of the family found in prokaryotes, termed NRMTs, that were proposed to function as transporters of Mg2+. The protein transports Mg2+ and Mn2+ but not Ca2+ by a mechanism that is not coupled to H+. Structures determined by cryo-EM and X-ray crystallography revealed a generally similar protein architecture compared to classical NRAMPs, with a restructured ion binding site whose increased volume provides suitable interactions with ions that likely have retained much of their hydration shell.

scholarly journals Structural basis for the coiled-coil architecture of human CtIP

2021 ◽  
Author(s):  
C. R. Morton ◽  
N. J. Rzechorzek ◽  
J. D. Maman ◽  
M. Kuramochi ◽  
H. Sekiguchi ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Strand Break ◽  
Structural Basis ◽  
Binding Motif ◽  
Chromosomal Dna ◽  
Dsb Repair ◽  
Critical Function ◽  
X Ray

AbstractThe DNA repair factor CtIP has a critical function in Double-Strand Break (DSB) repair by Homologous Recombination, promoting the assembly of the repair apparatus at DNA ends and participating in DNA-end resection. However, the molecular mechanisms of CtIP function in DSB repair remain unclear. Here we present an atomic model for the three-dimensional architecture of human CtIP, derived from a multi-disciplinary approach that includes X-ray crystallography, Small-angle X-ray Scattering (SAXS) and Diffracted X-ray Tracking (DXT). Our data show that CtIP adopts an extended dimer-of-dimers structure, in agreement with a role in bridging distant sites on chromosomal DNA during recombinational repair. The zinc-binding motif in CtIP’s N-terminus alters dynamically the coiled coil structure, with functional implications for the long-range interactions of CtIP with DNA. Our results provide a structural basis for the three-dimensional arrangement of chains in the CtIP tetramer, a key aspect of CtIP function in DNA DSB repair.

scholarly journals Synthesis of heterovalently substituted slab perovskites Sr2–xLnxBIV1–xBxIIIO4 (BIV= Sn, Ti, BIII= Sc, In)

2021 ◽  
pp. 77-83
Author(s):  
Y.A. Titov ◽  
◽  
M.S. Slobodyanik ◽  
V.V. Chumak ◽  
M.V. Tymoshenko ◽  
...  
Keyword(s):  
Layer Structure ◽  
Single Layer ◽  
Continuous Phase ◽  
Phase Region ◽  
Heterovalent Substitution ◽  
Linear Type ◽  
X Ray ◽  
Unit Cells ◽  
Pseudobinary Systems ◽  
New Compounds

The possibility of the heterovalent substitution of A- and B-positions atoms in a single-layer slab perovskite-like structure of strontium titanate and stannate Sr2BIVO4 (BIV= Ti, Sn) by type Sr2–xLnxBIV1–xBxIIIO4 (Ln == La – Tb, BIV= Ti, Sn, BIII= Sc, In) has been established by X-ray powder diffraction methods. The bounda-ries of the heterovalent substitution of A- and B-positions atoms and the crystallographic parameters of the synthesized Sr2–xLnxBIV1–xBxIIIO4 phases with a single-layer structure are determined. The continuous phase area formation with a single-layer structure has been observed in 10 systems: Sr2–xLnxTi1–xScxO4 (Ln = La, Pr, Nd, Sm, Eu), Sr2–xLnxTi1–xInxO4 (Ln = La, Pr), Sr2–xLaxSn1–xScxO4, Sr2–xLnxSn1–xInxO4 (Ln = La, Pr). In-creasing the degree of heterovalent substitution of atoms in these systems leads to a reduction of the sym metry of the crystal lattice of phases from the tetragonal (space group I4/mmm) to the interconnected rhombic one. In the rest of the studied Sr2–xLnxBIV1–xBxIIIO4 systems, the existence of a narrow (x value significantly less than 1) phase region with a single-layer structure based on Sr3BIVO7 is observed. The character of the phase relations in the Sr2–xLnxBIV1–xBxIIIO4 systems (Ln = La – Tb, BIII= Sc, In) (BIV= Sn, Ti) and the linear type of concentra-tion dependences of the parameters of the reduced tetragonal unit cells of Sr2–xLnxBIV1–xBxIIIO4 phases with a single-layer structure indicate that, by their nature, these phases are series of solid solutions in the pseudobinary systems Sr2BIVO4 – SrLnBIIIO4 (BIV= Ti, Sn, BIII = Sc, In). The obtained data can be used to regulate the functional properties of titanates and stannates Sr2BIVO4 and materials based on them, as well as to solve the problem of a purposeful search for new compounds of the type An+1BnO3n+1 with a slab perovskite-like structure.

Sur la structure cristalline des dimethyl-1,1 germa-1 (et sila-1) cycloundécanediols-6,7

1975 ◽  
Vol 53 (23) ◽  
pp. 3596-3598 ◽  
Author(s):  
François Brisse ◽  
Aviva Battat ◽  
Jean-Claude Richer ◽  
Pierre Mazerolles ◽  
Alfreda Faucher
Keyword(s):  
Asymmetric Unit ◽  
Space Group ◽  
X Ray ◽  
Independent Molecules

1,1-Dimethyl-1-germa (and-1-sila) -6,7-cycloundecanediol (C12H26O2Ge and C12H26O2Si) are isostructural as established by their X-ray powder patterns. The dimensions of the triclinic cells are as follows: for the silicon derivative, a = 10.53, b = 12.45, and c = 12.43 Å, α = 81.5°, β = 67.0°, and γ = 76.3°; for the germanium derivative, a = 10.56, b = 12.50, and c = 12.58 Å, α = 82.1°, β = 67.8°, and γ = 76.1°. If the space group is [Formula: see text] there will be two independent molecules in each asymmetric unit.

scholarly journals Structures of mono-unsaturated triacylglycerols. IV. The highest melting β′-2 polymorphs of trans-mono-unsaturated triacylglycerols and related saturated TAGs and their polymorphic stability

2008 ◽  
Vol 64 (2) ◽  
pp. 249-259 ◽  
Author(s):  
Jan B. van Mechelen ◽  
Rene Peschar ◽  
Henk Schenk
Keyword(s):  
Powder Diffraction Data ◽  
Asymmetric Unit ◽  
Double Chain ◽  
Molecular Conformations ◽  
X Ray ◽  
Acyl Chains ◽  
Independent Molecules ◽  
The Difference ◽  
Polymorphic Stability ◽  
Prime 2

The β_1^{\prime}-2 crystal structures of a series of mixed-chain saturated and trans-mono-unsaturated triacylglycerols containing palmitoyl, stearoyl and elaidoyl acyl chains have been solved from high-resolution powder diffraction data, from synchrotron as well as laboratory X-ray sources. The structures crystallized in the space group I2 with two independent molecules forming a dimer in the asymmetric unit, and packed in double-chain length layers. Unlike the corresponding β-2 structures the solved β_1^{\prime}-2 structures have different molecular conformations for the symmetric and the asymmetric mixed triacylglycerols, both with the sn-2 chain in a leg position of the chair-shaped conformation. A transformation to the β-2 structure with the sn-2 chain in the back position is complicated and unlikely to take place in the solid state. A novel β′-2 polymorph of PSS has been crystallized and its structure has been solved. The melting point (239 K) of this so-called β_0^{\prime}-2 polymorph is 2 K above that of the β_1^{\prime}-2 polymorph and almost equal to that of the β-2 polymorph of PSS. The difference in packing of the β_0^{\prime}-2 versus β_1^{\prime}-2 structure explains the slow β_1^{\prime}-2 to β_0^{\prime}-2 phase transition. The transition is strikingly similar to the β2-3 to β1-3 transition in cis-mono-unsaturated triacylglycerols.

X-ray and neutron structure of 1,8-(3,6,9-trioxaundecane-1,11-diyldioxy)-9,10-dihydro-10,10-dimethylanthracene-9-ol (P326); some pitfalls of automatic data collection

2001 ◽  
Vol 57 (3) ◽  
pp. 339-345 ◽  
Author(s):  
Rex A. Palmer ◽  
Brian S. Potter ◽  
John N. Lisgarten ◽  
Ruth H. Fenn ◽  
Sax A. Mason ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecule ◽  
Parent Compound ◽  
Ring Structure ◽  
Automatic Data ◽  
X Ray ◽  
Planar Structures ◽  
Unit Cells ◽  
Automatic Data Collection ◽  
O 18

The structure of the crown ether 1,8-(3,6,9-trioxaundecane-1,11-diyldioxy)-9,10-dihydro-10,10-dimethylanthracene-9-ol, C24H30O6·H2O (1), code name P326, the parent compound for a series of derivatives, has been determined by both X-ray diffraction at room temperature and neutron diffraction at very low temperature. The unit cells are very similar at both temperatures and in both cases the crystals exhibit P21 symmetry with Z = 4 (two molecules, A and B, respectively, per asymmetric unit) and pseudosymmetry P21/c. The higher symmetry is broken mainly by the two independent water molecules in the unit cell, some reflections which would be absent in P21/c having strong intensities in both the X-ray and neutron data. In both molecules A and B hydrogen bonds involving the water molecule stabilize the macrocyclic ring structure, one involving the macrocyclic O(9) as a donor. Close contacts between the water and macrocyclic O atoms in each molecule also suggest the presence of two bifurcated hydrogen bonds, involving water HW2 to both O(16) and O(18), and water HW1 to both O(18) and O(20), respectively, with considerable variation in the geometry being present. Both molecules A and B exhibit very close pseudosymmetry across a plane perpendicular to the molecular plane and through atoms C(9) and O(18), and in addition are predominantly planar structures. The X-ray analysis failed to reveal one H atom per water molecule, each being subsequently included after location and refinement in the neutron analysis.

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