High-pressure x-ray diffraction study of SrMoO4 and pressure-induced structural changes

SrMoO4 was studied under compression up to 25 GPa by angle-dispersive x-ray diffraction. A phase transition was observed from the scheelite-structured ambient phase to a monoclinic fergusonite phase at 12.2(9) GPa with cell parameters a = 5.265(9) A, b = 11.191(9) A, c = 5.195 (5) A, and beta = 90.9, Z = 4 at 13.1 GPa. There is no significant volume collapse at the phase transition. No additional phase transitions were observed and on release of pressure the initial phase is recovered, implying that the observed structural modifications are reversible. The reported transition appeared to be a ferroelastic second-order transformation producing a structure that is a monoclinic distortion of the low-pressure phase and was previously observed in compounds isostructural to SrMoO4. A possible mechanism for the transition is proposed and its character is discussed in terms of the present data and the Landau theory. Finally, the EOS is reported and the anisotropic compressibility of the studied crystal is discussed in terms of the compression of the Sr-O and Mo-O bonds.Comment: 36 pages, 9 figures, 1 tabl

DFT study of pressure induced phase transitions in LiYF4

An investigation of the pressure induced phase transition from the scheelite phase (I41/a, Z=4) to the fergusonite-like phase (I2/a, Z=4)/LaTaO(P21/c, Z=4) of LiYF4 is presented. Employing density functional theory (DFT) within the generalized gradient approximation, the internal degrees of freedom were relaxed for a pressure range of 0 GPa to 20 Gpa. The influence of pressure on the lattice vibration spectrum of the scheelite phase (I41/a, Z=4) was evaluated using the direct approach, i.e. using force constants calculated from atomic displacements. The transition volume is in good agreement with experiment, while the transition pressure is overestimated of 6 GPa. At 20 GPa, a P21/c structure with apentacoordinated lithium cation is found to be the most stable phase. This structure is compatible with a transition driven by a Bg zone-center soft optic mode linked to a soft-acoustic mode along the [11-1] direction as observed for the proper ferroelastic transition of BiVO4

The PolyA tail length of yeast histone mRNAs varies during the cell cycle and is influenced by Sen1p and Rrp6p

Yeast histone mRNAs are polyadenylated, yet factors such as Rrp6p and Trf4p, required for the 3′-end processing of non-polyadenylated RNAs, contribute to the cell cycle regulation of these transcripts. Here, we investigated the role of other known 3′-end processing/transcription termination factors of non-polyadenylated RNA in the biogenesis of histone mRNAs, specifically the Nab3p/Nrd1p/Sen1p complex. We also re-evaluated the polyadenylation status of these mRNAs during the cell cycle. Our analysis reveals that yeast histone mRNAs have shorter than average PolyA tails and the length of the PolyA tail varies during the cell cycle; S-phase histone mRNAs possess very short PolyA tails while in G1, the tail length is relatively longer. Inactivation of either Sen1p or Rrp6p leads to a decrease in the PolyA tail length of histone mRNAs. Our data also show that Sen1p contributes to 3′-end processing of histone primary transcripts. Thus, histone mRNAs are distinct from the general pool of yeast mRNAs and 3′-end processing and polyadenylation contribute to the cell cycle regulation of these transcripts

Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.

The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity

Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases.

Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D-glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site

The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function.

Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to β-lactamase inhibitor protein, PepSY and SmpA_OmlA proteins and hence are likely to function as inhibitory proteins

A germanate transparent conductive oxide

Wide bandgap conductors such as In2O3 and ZnO are used as transparent conducting oxides (TCOs). To date, TCOs are realized using post transition metal cations with largely spread s-orbitals such as In3+, Sn4+, Zn2+ and Cd2+. On the other hand, no good electronic conductor has been realized in oxides of Al, Si and Ge. Here we report the conversion of an oxide of Ge into a good electronic conductor by employing the concept of superdegeneracy. We find that cubic SrGeO3, synthesized under high pressure, displays a direct bandgap of 3.5 eV, a carrier mobility of 12 cm2(Vs)−1, and conductivities of 3 Scm−1 (DC) and 400 Scm−1 (optical conductivity). This is the first Ge-based electronic conductive oxide, and expands the family of TCOs from ionic oxides to covalent oxides

The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45 Å resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator

The crystal structure of the first representative of the Pfam PF07336 (DUF1470) family reveals a two-domain organization that contains a new fold, termed the ABATE domain, at the N-terminus and a treble-clef zinc finger that is likely to bind DNA at the C-terminus

Substrate specificity of the TRAMP nuclear surveillance complexes

During nuclear surveillance in yeast and human cells, the RNA exosome functions together with the TRAMP complexes. Here, the authors defined the protein composition of the TRAMP complexes and identified specific RNA binding sites for the different TRAMP components