scholarly journals Crystal Structure of the Cyclostreptin-Tubulin Adduct: Implications for Tubulin Activation by Taxane-Site Ligands

2019 ◽  
Vol 20 (6) ◽  
pp. 1392 ◽  
Author(s):  
Francisco Balaguer ◽  
Tobias Mühlethaler ◽  
Juan Estévez-Gallego ◽  
Enrique Calvo ◽  
Juan Giménez-Abián ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Drug Resistance ◽  
Covalent Binding ◽  
Helical Structure ◽  
Microtubule Assembly ◽  
Microtubule Stability ◽  
Switch Element ◽  
Insight Into ◽  
Site Binding ◽  
Covalent Inhibitor

It has been proposed that one of the mechanisms of taxane-site ligand-mediated tubulin activation is modulation of the structure of a switch element (the M-loop) from a disordered form in dimeric tubulin to a folded helical structure in microtubules. Here, we used covalent taxane-site ligands, including cyclostreptin, to gain further insight into this mechanism. The crystal structure of cyclostreptin-bound tubulin reveals covalent binding to βHis229, but no stabilization of the M-loop. The capacity of cyclostreptin to induce microtubule assembly compared to other covalent taxane-site agents demonstrates that the induction of tubulin assembly is not strictly dependent on M-loop stabilization. We further demonstrate that most covalent taxane-site ligands are able to partially overcome drug resistance mediated by βIII-tubulin (βIII) overexpression in HeLa cells, and compare their activities to pironetin, an interfacial covalent inhibitor of tubulin assembly that displays invariant growth inhibition in these cells. Our findings suggest a relationship between a diminished interaction of taxane-site ligands with βIII-tubulin and βIII tubulin-mediated drug resistance. This supports the idea that overexpression of βIII increases microtubule dynamicity by counteracting the enhanced microtubule stability promoted by covalent taxane-site binding ligands.

scholarly journals Crystal structure of GCN5 PCAF N-terminal domain reveals atypical ubiquitin ligase structure

2020 ◽  
Vol 295 (43) ◽  
pp. 14630-14639
Author(s):  
Sachiko Toma-Fukai ◽  
Ryota Hibi ◽  
Takao Naganuma ◽  
Mashito Sakai ◽  
Shinya Saijo ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Domain Architecture ◽  
E3 Ligase ◽  
Helical Structure ◽  
New Class ◽  
Ubiquitin E3 Ligase ◽  
Ubiquitin Conjugating Enzyme ◽  
Acetyltransferase Domain ◽  
Insight Into ◽  
Structural Aspects

General control nonderepressible 5 (GCN5, also known as Kat2a) and p300/CBP-associated factor (PCAF, also known as Kat2b) are two homologous acetyltransferases. Both proteins share similar domain architecture consisting of a PCAF N-terminal (PCAF_N) domain, acetyltransferase domain, and a bromodomain. PCAF also acts as a ubiquitin E3 ligase whose activity is attributable to the PCAF_N domain, but its structural aspects are largely unknown. Here, we demonstrated that GCN5 exhibited ubiquitination activity in a similar manner to PCAF and its activity was supported by the ubiquitin-conjugating enzyme UbcH5. Moreover, we determined the crystal structure of the PCAF_N domain at 1.8 Å resolution and found that PCAF_N domain folds into a helical structure with a characteristic binuclear zinc region, which was not predicted from sequence analyses. The zinc region is distinct from known E3 ligase structures, suggesting this region may form a new class of E3 ligase. Our biochemical and structural study provides new insight into not only the functional significance of GCN5 but also into ubiquitin biology.

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 Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Haixia Su ◽  
Sheng Yao ◽  
Wenfeng Zhao ◽  
Yumin Zhang ◽  
Jia Liu ◽  
...  
Keyword(s):  
Theoretical Calculations ◽  
Cysteine Proteinase ◽  
Covalent Binding ◽  
Food Sources ◽  
Binding Mechanism ◽  
Covalent Inhibitors ◽  
Catalytic Cysteine ◽  
3Cl Protease ◽  
Covalent Ligands ◽  
Covalent Inhibitor

AbstractThe ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) urgently needs an effective cure. 3CL protease (3CLpro) is a highly conserved cysteine proteinase that is indispensable for coronavirus replication, providing an attractive target for developing broad-spectrum antiviral drugs. Here we describe the discovery of myricetin, a flavonoid found in many food sources, as a non-peptidomimetic and covalent inhibitor of the SARS-CoV-2 3CLpro. Crystal structures of the protease bound with myricetin and its derivatives unexpectedly revealed that the pyrogallol group worked as an electrophile to covalently modify the catalytic cysteine. Kinetic and selectivity characterization together with theoretical calculations comprehensively illustrated the covalent binding mechanism of myricetin with the protease and demonstrated that the pyrogallol can serve as an electrophile warhead. Structure-based optimization of myricetin led to the discovery of derivatives with good antiviral activity and the potential of oral administration. These results provide detailed mechanistic insights into the covalent mode of action by pyrogallol-containing natural products and a template for design of non-peptidomimetic covalent inhibitors against 3CLpros, highlighting the potential of pyrogallol as an alternative warhead in design of targeted covalent ligands.

Über einige Beziehungen zwischhen Kristallstrukturen

1956 ◽  
Vol 11 (11) ◽  
pp. 920-934b
Author(s):  
Konrad Schubert
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Spatial Correlation ◽  
Chemical Elements ◽  
Electron Gas ◽  
Lattice Constants ◽  
Hexagonal Close Packed ◽  
Binary Compounds ◽  
Atomic Radii ◽  
Insight Into

In determining structures we use physical propositions in order to find a likely crystal structure. The same propositions are of value for the ordering of known structures into a natural system. The atomic radii form such a proposition. Another proposition is contained in the spatial correlation of electrons in the electron gas. The question is, whether this correlation is of influence on the crystal structure or not. To gain a first insight into this question, it is useful to know whether the crystal structures are physically compatible with a certain spatial correlation of electrons. Some qualitative rules are given to assess the physical possibility of a spatial correlation of electrons in a crystal structure. For the crystal structures of some chemical elements proposals for electron correlation are given. These proposals account for rationalities existing between some lattice constants, e. g. the axial ratios of the hexagonal close packed structures of Co and Zn. The proposals are also applicable to some binary compounds. With regard to these commensurabilities, it seems possible that the examination of the spatial correlation of electrons may lead to a better understanding of the crystal-chemical empiry.

scholarly journals Crystal Structure of the Streptomyces coelicolor Sortase E1 Transpeptidase Provides Insight into the Binding Mode of the Novel Class E Sorting Signal

PLoS ONE ◽  
2016 ◽  
Vol 11 (12) ◽  
pp. e0167763 ◽  
Author(s):  
Michele D. Kattke ◽  
Albert H. Chan ◽  
Andrew Duong ◽  
Danielle L. Sexton ◽  
Michael R. Sawaya ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Streptomyces Coelicolor ◽  
Binding Mode ◽  
The Novel ◽  
Sorting Signal ◽  
Insight Into ◽  
Class E

The Crystal Structure ofBacillus cereusPhosphonoacetaldehyde Hydrolase:  Insight into Catalysis of Phosphorus Bond Cleavage and Catalytic Diversification within the HAD Enzyme Superfamily†,‡

Biochemistry ◽  
2000 ◽  
Vol 39 (34) ◽  
pp. 10385-10396 ◽  
Author(s):  
Marc C. Morais ◽  
Wenhai Zhang ◽  
Angela S. Baker ◽  
Guofeng Zhang ◽  
Debra Dunaway-Mariano ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Bond Cleavage ◽  
Enzyme Superfamily ◽  
Insight Into
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