Crystal structure of the pyrimidine 5′-nucleotidase SDT1 from Saccharomyces cerevisiae complexed with uridine 5′-monophosphate provides further insight into ligand binding

2011 ◽  
Vol 79 (4) ◽  
pp. 1358-1362 ◽  
Author(s):  
Nuo Shi ◽  
Yu-Jie Zhang ◽  
Hong-Kai Chen ◽  
Yongxiang Gao ◽  
Maikun Teng ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Saccharomyces Cerevisiae ◽  
Ligand Binding ◽  
Insight Into

scholarly journals Structure of the 14-3-3ζ–LKB1 fusion protein provides insight into a novel ligand-binding mode of 14-3-3

2015 ◽  
Vol 71 (9) ◽  
pp. 1114-1119 ◽  
Author(s):  
Sheng Ding ◽  
Ruiqing Zhou ◽  
Yaqin Zhu
Keyword(s):  
Crystal Structure ◽  
Energy Metabolism ◽  
Cell Growth ◽  
Fusion Protein ◽  
Ligand Binding ◽  
Cell Polarity ◽  
Binding Mode ◽  
Cellular Processes ◽  
Potential Binding ◽  
Insight Into

The 14-3-3 proteins are a family of highly conserved proteins that play key roles in many cellular processes. The tumour suppressor LKB1 regulates cell polarity, cell growth and energy metabolism. 14-3-3 proteins bind to LKB1 and suppress its functions. Previously, preliminary crystallographic data for the 14-3-3ζ–LKB1 fusion protein have been reported. Here, the crystal structure of this fusion protein was solved and a novel potential binding mode of 14-3-3 to its ligands was found.

Crystal structure of KBSi3O8 isostructural with danburite

1993 ◽  
Vol 57 (386) ◽  
pp. 157-164 ◽  
Author(s):  
Mitsuyoshi Kimata
Keyword(s):  
Crystal Structure ◽  
Direct Method ◽  
Crystal Chemical ◽  
Chemical Formula ◽  
Crystal Chemical Formula ◽  
3 Dimensional ◽  
Tetrahedral Sites ◽  
Structural Types ◽  
Coupled Substitution ◽  
Insight Into

AbstractThe crystal structure of KBSi3O8 (orthorhombic, Pnam, with a = 8.683(1), b = 9.253(1), c = 8.272(1) Å,, V = 664.4(1) Å3, Z = 4) has been determined by the direct method applied to 3- dimensional rcflection data. The structure of a microcrystal with the dimensions 20 × 29 × 37 μm was refined to an unweightcd residual of R = 0.031 using 386 non-zero structure amplitudes. KBSi3O8 adopts a structure essentially different from recdmergneritc NaBSi3O8, with the low albite (NaAlSi3O8) structure, and isotypic with danburite CaB2Si2Os which has the same topology as paracelsian BaAl2Si2O8. The chenfical relationship between this sample and danburitc gives insight into a new coupled substitution; K+ + Si4+ = Ca2+ + B3+ in the extraframework and tetrahedral sites. The present occupancy refinement revealed partial disordering of B and Si atoms which jointly reside in two kinds of general equivalent points, T(1) and T(2) sites. Thus the expanded crystal-chemical formula can be written in the form K(B0.44Si0.56)2(B0.06Si0.94)2O8The systematic trend among crystalline compounds with the M+T3+T4+3O8 formula suggests that they exist in one of four structural types; the feldspar structures with T3+/T4+ ordered and/or disordered forms, and the paracelsian and the hollandite structures.

Insight into the physics of the 5f -band antiferromagnet U2Ni2Sn from the pressure dependence of crystal structure and electrical resistivity

2021 ◽  
Vol 103 (3) ◽  
Author(s):  
Silvie Maskova-Cerna ◽  
Alexandre Kolomiets ◽  
Jiri Prchal ◽  
Itzhak Halevy ◽  
Volodymyr Buturlim ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Electrical Resistivity ◽  
Pressure Dependence ◽  
Insight Into

scholarly journals Putative ligand binding sites of two functionally characterized bark beetle odorant receptors

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Jothi K. Yuvaraj ◽  
Rebecca E. Roberts ◽  
Yonathan Sonntag ◽  
Xiao-Qing Hou ◽  
Ewald Grosse-Wilde ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Bark Beetle ◽  
Pest Control ◽  
Binding Sites ◽  
Functional Characterization ◽  
Site Directed Mutagenesis ◽  
Odorant Receptors ◽  
Functional Evolution ◽  
General Importance ◽  
Insight Into

Abstract Background Bark beetles are major pests of conifer forests, and their behavior is primarily mediated via olfaction. Targeting the odorant receptors (ORs) may thus provide avenues towards improved pest control. Such an approach requires information on the function of ORs and their interactions with ligands, which is also essential for understanding the functional evolution of these receptors. Hence, we aimed to identify a high-quality complement of ORs from the destructive spruce bark beetle Ips typographus (Coleoptera, Curculionidae, Scolytinae) and analyze their antennal expression and phylogenetic relationships with ORs from other beetles. Using 68 biologically relevant test compounds, we next aimed to functionally characterize ecologically important ORs, using two systems for heterologous expression. Our final aim was to gain insight into the ligand-OR interaction of the functionally characterized ORs, using a combination of computational and experimental methods. Results We annotated 73 ORs from an antennal transcriptome of I. typographus and report the functional characterization of two ORs (ItypOR46 and ItypOR49), which are responsive to single enantiomers of the common bark beetle pheromone compounds ipsenol and ipsdienol, respectively. Their responses and antennal expression correlate with the specificities, localizations, and/or abundances of olfactory sensory neurons detecting these enantiomers. We use homology modeling and molecular docking to predict their binding sites. Our models reveal a likely binding cleft lined with residues that previously have been shown to affect the responses of insect ORs. Within this cleft, the active ligands are predicted to specifically interact with residues Tyr84 and Thr205 in ItypOR46. The suggested importance of these residues in the activation by ipsenol is experimentally supported through site-directed mutagenesis and functional testing, and hydrogen bonding appears key in pheromone binding. Conclusions The emerging insight into ligand binding in the two characterized ItypORs has a general importance for our understanding of the molecular and functional evolution of the insect OR gene family. Due to the ecological importance of the characterized receptors and widespread use of ipsenol and ipsdienol in bark beetle chemical communication, these ORs should be evaluated for their potential use in pest control and biosensors to detect bark beetle infestations.

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