scholarly journals Structural evidence for a dynamic metallocofactor during N2 reduction by Mo-nitrogenase

Science ◽  
2020 ◽  
Vol 368 (6497) ◽  
pp. 1381-1385 ◽  
Author(s):  
Wonchull Kang ◽  
Chi Chung Lee ◽  
Andrew J. Jasniewski ◽  
Markus W. Ribbe ◽  
Yilin Hu
Keyword(s):  
Crystal Structure ◽  
Dynamic Nature ◽  
Protein Ligands ◽  
Mofe Protein

The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N2) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo–O5 (carboxyl) or Mo–O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.

The refined crystal structure of nitrogenase MoFe protein (CP1) at 2.2 Å resolution and its implications for nitrogenase function.

1993 ◽  
Vol 51 (1-2) ◽  
pp. 356
Author(s):  
J.T. Bolin ◽  
N. Campobasso ◽  
S.W. Muchmore ◽  
L.E. Mortenson ◽  
T.V. Morgan
Keyword(s):  
Crystal Structure ◽  
Mofe Protein

The crystal structure of nitrogenase mofe protein from clostridium pasteurianum.

1991 ◽  
Vol 43 (2-3) ◽  
pp. 477 ◽  
Author(s):  
J.T. Bolin ◽  
N. Campobasso ◽  
S.W. Muchmore ◽  
W. Minor ◽  
L.E. Mortenson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Clostridium Pasteurianum ◽  
Mofe Protein

Crystal structure study of a β′-copper vanadium bronze, Cu x V2O5 (x = 0.63), by X-ray and convergent beam electron diffraction

2005 ◽  
Vol 61 (1) ◽  
pp. 17-24 ◽  
Author(s):  
Victor A. Streltsov ◽  
Philip N. H. Nakashima ◽  
Alexandre N. Sobolev ◽  
Ruslan P. Ozerov
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Structure Study ◽  
Convergent Beam Electron Diffraction ◽  
Convincing Evidence ◽  
Dynamic Nature ◽  
Beam Electron ◽  
X Ray ◽  
Structure Changes ◽  
Convergent Beam

The single-crystal structure of a β′-copper vanadium bronze, Cu0.63V2O5, has been studied at room temperature and 9.6 K, and compared with that of the β-sodium vanadium bronze, Na0.33V2O5, structure. No convincing evidence to oppose an assignment of centrosymmetric C2/m symmetry to the structure was identified using the X-ray data. A subsequent convergent beam electron diffraction (CBED) experiment was performed and confirmed the C2/m space group. The oxygen–vanadium atom framework of Cu0.63V2O5 is close to that of Na0.33V2O5. However, in the copper compound the Cu atoms are located in two positions: Cu1 in the 4(i) position with x = 0.541, y = 0 and z = 0.345, and Cu2 in the 8(j) position with x = 0.529, y = 0.038 and z = 0.357. The crystal structure changes little with temperature. Disorder of the Cu ion over two sites is seen at 9.6 K. This suggests that distribution of the Cu atoms over two sites is of a more static than dynamic nature.

Lactoferrin–metal interactions: first crystal structure of a complex of lactoferrin with a lanthanide ion (Sm3+) at 3.4 Å resolution

1999 ◽  
Vol 55 (11) ◽  
pp. 1799-1804 ◽  
Author(s):  
Ashwani K. Sharma ◽  
Tej P. Singh
Keyword(s):  
Crystal Structure ◽  
Characteristic Property ◽  
Crystallographic Analysis ◽  
Large Displacements ◽  
Lanthanide Ion ◽  
Metal Interactions ◽  
Protein Ligands ◽  
Distorted Octahedral Coordination ◽  
Distorted Octahedral ◽  
Binding Cleft

Lactoferrin is an important member of the transferrin family. A characteristic property of transferrins is their ability to bind very tightly (K app ≃ 1020) but reversibly two Fe3+ ions. The structural consequences of binding a metal other than Fe3+ have been examined by crystallographic analysis at 3.4 Å resolution of mare samarium–lactoferrin (Sm2Lf). The structure was refined to an R factor of 0.219 for 8776 reflections in the resolution range 17.0–3.4 Å. The samarium geometry (distorted octahedral coordination) is similar in both lobes. However, the anion interactions are quite different in the two lobes. In the N lobe, the anion is able to form only two hydrogen bonds instead of the four observed in the C lobe of Sm2Lf and the six observed in Fe2Lf. This is because Arg121, Thr117 and Gly124 have moved away from the anion as a consequence of the binding of the Sm3+ ion. The protein ligands in the binding cleft of Sm2Lf show large displacements, but the overall protein structure remains the same. The binding of Sm3+ by lactoferrin shows that the protein is capable of sequestering ions of different sizes and charges, though with reduced affinity. This conclusion should be true of other transferrins also.

XAFS studies of nitrogenase: the MoFe and VFe proteins and the use of crystallographic coordinates in three-dimensional EXAFS data analysis

2002 ◽  
Vol 10 (1) ◽  
pp. 71-75 ◽  
Author(s):  
Richard W. Strange ◽  
Robert R. Eady ◽  
David Lawson ◽  
S. Samar Hasnain
Keyword(s):  
Crystal Structure ◽  
Data Analysis ◽  
Klebsiella Pneumoniae ◽  
Crystal Structures ◽  
Excellent Agreement ◽  
Coordination Sphere ◽  
Three Dimensional ◽  
Protein Crystal ◽  
Mofe Protein ◽  
Distance Restraints

This paper reports a three-dimensional EXAFS refinement of the Mo coordination sphere of the FeMoco cluster of the dithionite-reduced MoFe protein fromKlebsiella pneumoniaenitrogenase (Kp1) using the 1.6 Å-resolution crystallographic coordinates. At this resolution, the positions of the heavy (Fe and S) atoms of the cluster are well determined and there is excellent agreement between the crystallographic and EXAFS models. However, the lighter homocitrate and histidine ligands are poorly determined in the crystal structure, and it is shown that the application of EXAFS-derived distance restraints during the early stages of crystallographic refinement provides a means of substantially improving (by ∼0.1 Å) the final crystallographic model. The consistency of the EXAFS analysis with the crystallographic information in this case justifies applications of EXAFS to cases where protein crystal structures are absent. Thus, the VFe protein of V-nitrogenase has been shown by EXAFS to possess a V-atom site catalytically similar to the well characterized MoFe-nitrogenases, with V replacing Mo.

Crystal Structure Determination of Glycerol-Containing Lipids from Electron Diffraction Data. Use of Analog Compounds Based upon Configurational Isomers of Cyclopentane-1, 2, 3-TRIOL

1977 ◽  
Vol 35 ◽  
pp. 24-25
Author(s):  
Douglas L. Dorset ◽  
Anthony J. Hancock
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Crystal Surface ◽  
Coherent Scattering ◽  
Crystal Structure Determination ◽  
Electron Diffraction Data ◽  
Polar Group ◽  
Axis Orientation

Lipids containing long polymethylene chains were among the first compounds subjected to electron diffraction structure analysis. It was only recently realized, however, that various distortions of thin lipid microcrystal plates, e.g. bends, polar group and methyl end plane disorders, etc. (1-3), restrict coherent scattering to the methylene subcell alone, particularly if undistorted molecular layers have well-defined end planes. Thus, ab initio crystal structure determination on a given single uncharacterized natural lipid using electron diffraction data can only hope to identify the subcell packing and the chain axis orientation with respect to the crystal surface. In lipids based on glycerol, for example, conformations of long chains and polar groups about the C-C bonds of this moiety still would remain unknown.One possible means of surmounting this difficulty is to investigate structural analogs of the material of interest in conjunction with the natural compound itself. Suitable analogs to the glycerol lipids are compounds based on the three configurational isomers of cyclopentane-1,2,3-triol shown in Fig. 1, in which three rotameric forms of the natural glycerol derivatives are fixed by the ring structure (4-7).

Spherulitic crystal growth in the prodissoconch larval of Crassostrea virginica

1983 ◽  
Vol 41 ◽  
pp. 518-519
Author(s):  
George G. Cocks ◽  
Louis Leibovitz ◽  
DoSuk D. Lee
Keyword(s):  
Crystal Structure ◽  
Crassostrea Virginica ◽  
Crystal Orientation ◽  
Developmental Changes ◽  
Gastrula Stage ◽  
Orthorhombic Crystal ◽  
Orthorhombic Crystal Structure ◽  
Stages Of Growth ◽  
Early Stages ◽  
Initial Deposition

Our understanding of the structure and the formation of inorganic minerals in the bivalve shells has been considerably advanced by the use of electron microscope. However, very little is known about the ultrastructure of valves in the larval stage of the oysters. The present study examines the developmental changes which occur between the time of conception to the early stages of Dissoconch in the Crassostrea virginica(Gmelin), focusing on the initial deposition of inorganic crystals by the oysters.The spawning was induced by elevating the temperature of the seawater where the adult oysters were conditioned. The eggs and sperm were collected separately, then immediately mixed for the fertilizations to occur. Fertilized animals were kept in the incubator where various stages of development were stopped and observed. The detailed analysis of the early stages of growth showed that CaCO3 crystals(aragonite), with orthorhombic crystal structure, are deposited as early as gastrula stage(Figuresla-b). The next stage in development, the prodissoconch, revealed that the crystal orientation is in the form of spherulites.

Transmission Electron Microscopy studies of the vacancy ordering in YSI2-X thin films

1991 ◽  
Vol 49 ◽  
pp. 562-563
Author(s):  
F.-R. Chen ◽  
T. L. Lee ◽  
L. J. Chen
Keyword(s):  
Crystal Structure ◽  
Electron Microscopy ◽  
Thin Films ◽  
Diffraction Pattern ◽  
Annealing Temperature ◽  
Lattice Mismatch ◽  
Si Substrate ◽  
Metal Thin Films ◽  
Transmission Electron ◽  
Vacancy Ordering

YSi2-x thin films were grown by depositing the yttrium metal thin films on (111)Si substrate followed by a rapid thermal annealing (RTA) at 450 to 1100°C. The x value of the YSi2-x films ranges from 0 to 0.3. The (0001) plane of the YSi2-x films have an ideal zero lattice mismatch relative to (111)Si surface lattice. The YSi2 has the hexagonal AlB2 crystal structure. The orientation relationship with Si was determined from the diffraction pattern shown in figure 1(a) to be and . The diffraction pattern in figure 1(a) was taken from a specimen annealed at 500°C for 15 second. As the annealing temperature was increased to 600°C, superlattice diffraction spots appear at position as seen in figure 1(b) which may be due to vacancy ordering in the YSi2-x films. The ordered vacancies in YSi2-x form a mesh in Si plane suggested by a LEED experiment.

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