scholarly journals Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor

2014 ◽  
Vol 70 (12) ◽  
pp. 1584-1590 ◽  
Author(s):  
Michael C. Thompson ◽  
Christopher S. Crowley ◽  
Jeffrey Kopstein ◽  
Thomas A. Bobik ◽  
Todd O. Yeates
Keyword(s):  
Crystal Structure ◽  
Transport Phenomena ◽  
Molecular Transport ◽  
Vitamin B ◽  
Ligand Interaction ◽  
X Ray ◽  
Shell Protein ◽  
Bacterial Microcompartment ◽  
Selective Diffusion ◽  
Protein Ligand Interaction

The EutL shell protein is a key component of the ethanolamine-utilization microcompartment, which serves to compartmentalize ethanolamine degradation in diverse bacteria. The apparent function of this shell protein is to facilitate the selective diffusion of large cofactor molecules between the cytoplasm and the lumen of the microcompartment. While EutL is implicated in molecular-transport phenomena, the details of its function, including the identity of its transport substrate, remain unknown. Here, the 2.1 Å resolution X-ray crystal structure of a EutL shell protein bound to cobalamin (vitamin B12) is presented and the potential relevance of the observed protein–ligand interaction is briefly discussed. This work represents the first structure of a bacterial microcompartment shell protein bound to a potentially relevant cofactor molecule.

Theoretical and experimental (113 K) electron-density study of lithium bis(tetramethylammonium) hexanitrocobaltate(III)

1996 ◽  
Vol 52 (3) ◽  
pp. 471-478 ◽  
Author(s):  
R. Bianchi ◽  
C. Gatti ◽  
V. Adovasio ◽  
M. Nardelli
Keyword(s):  
Crystal Structure ◽  
Model Description ◽  
Topological Properties ◽  
Ligand Interaction ◽  
X Ray ◽  
Hartree Fock ◽  
Laplacian Distribution ◽  
Density Study ◽  
Metal Ligand ◽  
Close Parallel

This paper presents an analysis of the crystal structure and the charge density, ρ(r), for lithium bis(tetramethylammonium) hexanitrocobaltate(III) determined by the rigid pseudoatom model from accurate X-ray data measured at 113 K. This compound has also been investigated by an ab initio Hartree–Fock fully periodic approach. A comparison of the topological properties between the experimentally and theoretically derived density is also given. A notable agreement between experiment and theory is observed in the topological properties of the metal-ligand interaction and a close parallel between the orbital model description and the shape of the Laplacian distribution around the Co atom is outlined. The results confirm the typical 3d-electron distribution of octahedral CoIII complexes in a low-spin state and the presence of four C—H...O hydrogen bonds in the crystal structure. Important differences between experiment and theory remain for the Laplacian and the parallel curvature (λ 3) values at the C—N and N—O bond critical points. The atomic charges derived from the Quantum Theory of Atoms in Molecules are remarkably close to the formal values.

The structure of vitamin B 12 . II. The crystal structure of a hexacarboxylic acid obtained by the degradation of vitamin B 12

1959 ◽  
Vol 251 (1266) ◽  
pp. 306-352 ◽  
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Cobalt Atom ◽  
Side Chain ◽  
Vitamin B ◽  
X Ray ◽  
Structure Factors ◽  
Lactam Ring ◽  
Vitamin B 12 ◽  
Made In

A hexacarboxylic acid, obtained by the degradation of vitamin B 12 by Cannon, Johnson & Todd in 1953 has been examined by X-ray analytical methods. These lead to a solution of both the crystal and chemical structure of the acid. The crystals are orthorhombic, a = 24·58, b = 15·52, c = 13·32 Å, space group, P 2 1 2 1 2 1 , n = 4. The asymmetric unit is found to consist essentially of one molecule of hexacarboxylic acid, C 46 H 58 O 13 N 6 . CoCl, two molecules of water and one of acetone. The hexacarboxylic acid molecule has a central cobalt atom in approximately octahedral co-ordination attached to one cyanide group, one chlorine atom and four nitrogen atoms of the corrin nucleus. The nucleus itself is substituted by acetic and propionic acid groups, a lactam ring and a number of methyl groups. The position of the cobalt atom in the crystal structure was first found from Patterson projections and the remaining atomic positions then derived from a series of calculated approximations to the three-dimensional electron density distribution. For these calculations, phases were derived from structure factors calculated on gradually increasing numbers of selected atomic positions from the stage of ρ 1, where only the cobalt atom sites were known, to ρ 10 where 73 atoms, not counting hydrogen, had been placed. The process was not quite straightforward; particular difficulty was experienced in finding the positions of the atoms of one side-chain which may be affected by disorder. The parameters of the atoms have been refined by two cycles of least-squares calculations. A number of observations were made in the course of the analysis which bear on the further use of non-centrosymmetric Fourier syntheses in the study of complex structures. An appendix by A. Vos deals with intensity anomalies observed on the X-ray photographs of the hexacarboxylic acid which provide evidence of its absolute configuration. An appendix by K. N. Trueblood summarizes various aspects of the analysis of the hexacarboxylic acid, seen as a whole.

The structure of vitamin B 12 . VIII. The crystal structure of vitamin B 12 -5'-phosphate

1970 ◽  
Vol 318 (1533) ◽  
pp. 143-167 ◽  
Keyword(s):  
Crystal Structure ◽  
Phosphate Ester ◽  
Water Molecules ◽  
Vitamin B ◽  
X Ray Diffraction ◽  
Fourier Synthesis ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Vitamin B 12 ◽  
Difference Fourier

The crystal structure of vitamin B 12 -5' -phosphate, a biosynthetic precursor of vitamin B 12 , has been determined by X-ray diffraction methods. The air-dried crystals are orthorhombic, space group P 2 1 2 1 2 1 , with a = 23.72 Å, b = 21.74 Å and c = 16.07 Å. The observed density of 1.362 g cm -3 indicates four vitamin B 12 -5' -phosphate and about sixty water molecules in the unit cell. The X-ray diffraction data to 1.2 Å resolution were collected with a PAILRED linear diffractometer using Cu K α radiation from a silicon monochromator. The structure was solved by using Patterson methods in conjunction with the tangent formula and was refined by Fourier and least-squares methods. The final R value for the 2112 observed reflexions is 16.2 %. The structure is very similar to that found by Hodgkin and co-workers for air-dried vitamin B 12 crystals. The difference Fourier synthesis between this compound and vitamin B 12 shows that two water molecules move into phosphate oxygen positions when the phosphate in the precursor is removed, and one acetamide in contact with these water molecules in the vitamin is rotated out of the way in the phosphate. A second acetamide is also differently oriented in the two crystals. The α -glycosidic bond between the ribose and the dimethylbenzimidazole is 16° out of the plane of the base. The ribose conformation is C2'>- exo , and the phosphate ester conformations are similar to those found in other B 12 crystals.

The structure of vitamin B 12 - IV. The X-ray analysis of air-dried crystals of B 12

1962 ◽  
Vol 266 (1327) ◽  
pp. 475-493 ◽  
Keyword(s):  
Crystal Structure ◽  
Density Distribution ◽  
Electron Density Distribution ◽  
Three Dimensional ◽  
Successive Approximations ◽  
Water Molecules ◽  
Vitamin B ◽  
Dimensional Electron ◽  
X Ray ◽  
Vitamin B 12

Measurements were made during 1948-9 of all the intensities of hkl reflexions observable with chromium Koc X-radiation from air-dried crystals of vitamin B 12 . Calculations parallel with those of J. G. White were carried out on these data. The positions of the cobalt atoms in the crystal structure were found from three-dimensional Patterson series and the positions of 90 atoms of the B 12 molecule and 7 water molecules were derived through three successive approximations to the three-dimensional electron density distribution. The choice of atomic positions was checked against superposition maps derived from the original Patterson series, and assisted by comparisons with other B 12 derivatives. Minor differences appear between the positions derived here and in III; some of these may be real differences due to the state of dryness of the crystals.

scholarly journals Structure of a novel 13 nm dodecahedral nanocage assembled from a redesigned bacterial microcompartment shell protein

2016 ◽  
Vol 52 (28) ◽  
pp. 5041-5044 ◽  
Author(s):  
J. Jorda ◽  
D. J. Leibly ◽  
M. C. Thompson ◽  
T. O. Yeates
Keyword(s):  
Crystal Structure ◽  
Self Assembly ◽  
Natural Protein ◽  
Shell Protein ◽  
Bacterial Microcompartment

We report the crystal structure of a novel 60-subunit dodecahedral cage that results from self-assembly of a re-engineered version of a natural protein (PduA) from the Pdu microcompartment shell.

Crystal Structure of Cs2Zn(NO2)4: Influence of Steric Crowding on Nitrite Coordination

2005 ◽  
Vol 58 (3) ◽  
pp. 224 ◽  
Author(s):  
Susan G. Oates ◽  
Michael A. Hitchman ◽  
Brian W. Skelton ◽  
Robert Stranger ◽  
Horst Stratemeier ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Energy Curve ◽  
X Ray Diffraction ◽  
Nitrite Ion ◽  
Ligand Interaction ◽  
Functional Theory ◽  
X Ray ◽  
Steric Crowding

The crystal structure of Cs2[Zn(NO2)4] has been determined by X-ray diffraction. Each nitrite ion in the Zn(NO2)42− group forms one short [2.080(3) Å] and one long [2.516(3) Å] Zn–O bond, the metal–ligand interaction being intermediate between symmetrical chelation and syn-unidentate nitrito coordination. It seems likely that this unsymmetrical geometry is adopted in order to minimize ligand–ligand repulsions, though density functional theory calculations suggest a very shallow potential energy curve for the complex.

scholarly journals Selective molecular transport through the protein shell of a bacterial microcompartment organelle

2015 ◽  
Vol 112 (10) ◽  
pp. 2990-2995 ◽  
Author(s):  
Chiranjit Chowdhury ◽  
Sunny Chun ◽  
Allan Pang ◽  
Michael R. Sawaya ◽  
Sharmistha Sinha ◽  
...  
Keyword(s):  
Small Molecules ◽  
Carbon Fixation ◽  
Molecular Diffusion ◽  
Molecular Transport ◽  
Phenotypic Data ◽  
Bacterial Microcompartments ◽  
Shell Protein ◽  
Bacterial Microcompartment ◽  
Selective Permeability ◽  
Protein Shell

Bacterial microcompartments are widespread prokaryotic organelles that have important and diverse roles ranging from carbon fixation to enteric pathogenesis. Current models for microcompartment function propose that their outer protein shell is selectively permeable to small molecules, but whether a protein shell can mediate selective permeability and how this occurs are unresolved questions. Here, biochemical and physiological studies of structure-guided mutants are used to show that the hexameric PduA shell protein of the 1,2-propanediol utilization (Pdu) microcompartment forms a selectively permeable pore tailored for the influx of 1,2-propanediol (the substrate of the Pdu microcompartment) while restricting the efflux of propionaldehyde, a toxic intermediate of 1,2-propanediol catabolism. Crystal structures of various PduA mutants provide a foundation for interpreting the observed biochemical and phenotypic data in terms of molecular diffusion across the shell. Overall, these studies provide a basis for understanding a class of selectively permeable channels formed by nonmembrane proteins.

A study on α-RuCl3 crystal structure by scanning tunneling microscopy

1989 ◽  
Vol 47 ◽  
pp. 30-31
Author(s):  
H.-J. Cantow ◽  
H. Hillebrecht ◽  
S. Magonov ◽  
H. W. Rotter ◽  
G. Thiele
Keyword(s):  
Crystal Structure ◽  
Density Distribution ◽  
Scanning Tunneling Microscopy ◽  
Electron Density ◽  
Structure Determination ◽  
Electron Density Distribution ◽  
Scanning Tunneling ◽  
Monoclinic Space Group ◽  
Tunneling Microscopy ◽  
X Ray

From X-ray analysis, the conclusions are drawn from averaged molecular informations. Thus, limitations are caused when analyzing systems whose symmetry is reduced due to interatomic interactions. In contrast, scanning tunneling microscopy (STM) directly images atomic scale surface electron density distribution, with a resolution up to fractions of Angstrom units. The crucial point is the correlation between the electron density distribution and the localization of individual atoms, which is reasonable in many cases. Thus, the use of STM images for crystal structure determination may be permitted. We tried to apply RuCl3 - a layered material with semiconductive properties - for such STM studies. From the X-ray analysis it has been assumed that α-form of this compound crystallizes in the monoclinic space group C2/m (AICI3 type). The chlorine atoms form an almost undistorted cubic closed package while Ru occupies 2/3 of the octahedral holes in every second layer building up a plane hexagon net (graphite net). Idealizing the arrangement of the chlorines a hexagonal symmetry would be expected. X-ray structure determination of isotypic compounds e.g. IrBr3 leads only to averaged positions of the metal atoms as there exist extended stacking faults of the metal layers.

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