Models of the active site of dihydroorotase: structure of diaquabis(L-dihydroorotato)zinc(II) reveals an unexpected coordination mode for the L-dihydroorotato ligands

1995 ◽  
Vol 34 (26) ◽  
pp. 6550-6552 ◽  
Author(s):  
Trevor W. Hambley ◽  
Richard I. Christopherson ◽  
Evan S. Zvargulis
Keyword(s):  
Active Site ◽  
Coordination Mode

Influence of key amino acid mutation on the active site structure and on folding in acetyl-CoA synthase: a theoretical perspective

2015 ◽  
Vol 51 (40) ◽  
pp. 8551-8554 ◽  
Author(s):  
Claudio Greco ◽  
Antonella Ciancetta ◽  
Maurizio Bruschi ◽  
Alexander Kulesza ◽  
Giorgio Moro ◽  
...  
Keyword(s):  
Amino Acid ◽  
Active Site ◽  
Coordination Mode ◽  
Theoretical Perspective ◽  
Cluster Structure ◽  
Amino Acid Mutation ◽  
Acetyl Coa ◽  
Site Structure ◽  
Active Site Structure

DFT-based modeling of the A-cluster structure and acetyl-CoA synthase folding highlights an unprecedented coordination mode of histidine to metal-containing cofactors.

Heteroscorpionate complexes based on bis(3,5-di-tert-butylpyrazol-1-yl)dithioacetate

2013 ◽  
Vol 69 (9) ◽  
pp. 981-985 ◽  
Author(s):  
Stefan Tampier ◽  
Nicolai Burzlaff
Keyword(s):  
Zinc Chloride ◽  
Active Site ◽  
Coordination Mode ◽  
Chloride Complex ◽  
Lithium Cation

The heteroscorpionate ligand bis(3,5-di-tert-butylpyrazol-1-yl)dithioacetate (bdtbpzdta) has been synthesized by reacting bis(3,5-di-tert-butylpyrazol-1-yl)methane withn-BuLi and CS2. The ligand was isolated as [bis(3,5-di-tert-butylpyrazol-1-yl)dithioacetato](tetrahydrofuran)lithium(I) tetrahydrofuran monosolvate, [Li(C24H39N4S2)(C4H8O)]·C4H8O or [Li(bdtbpzdta)(THF)]·THF, in which the lithium cation is bound by the κ3N,N′,S-coordinated heteroscorpionate ligand. A similar coordination mode is observed for a zinc chloride complex bearing the bdtbpzdta ligand, namely [bis(3,5-di-tert-butylpyrazol-1-yl)dithioacetato]chloridozinc(II), [Zn(C24H39N4S2)Cl] or [Zn(bdtbpzdta)Cl], which exhibits κ3N,N′,S-coordination and resembles the active site of zinc-containing peptide deformylases (PDFs).

scholarly journals Gold Catalyzed Asymmetric Transformations

2021 ◽  
Author(s):  
Susana Porcel García
Keyword(s):  
Active Site ◽  
Coordination Mode ◽  
Ion Pairing ◽  
The Other ◽  
Chiral Ligands ◽  
Linear Arrangement ◽  
Asymmetric Transformations ◽  
Secondary Interactions ◽  
Square Planar ◽  
Bifunctional Ligands

In this chapter, the strategies developed to attain asymmetric reactions with gold are disclosed. Because of its preferred linear arrangement, to induce asymmetry, gold(I) needs to fulfill one of the following requirements: a) the use of bulky chiral ligands, that create a chiral pocket around the active site, b) the coordination to bifunctional ligands capable to establish secondary interactions with substrates, or c) tight ion pairing with chiral counteranions. On the other hand, gold(III) profits of a square-planar coordination mode, which approaches chiral ligands to substrates. However, its tendency to be reduced leads to difficulties for its applications in catalytic asymmetric transformations. Pioneering works using cyclometaled structures, have found the balance between stability and activity, showing its potential in asymmetric transformations.

Locating Al in the DABCO catalyst before and after Al extraction

1990 ◽  
Vol 48 (4) ◽  
pp. 265-267
Author(s):  
Kathleen B. Reuter
Keyword(s):  
Active Site ◽  
Inverse Relationship ◽  
Transverse Direction ◽  
Reaction Rate ◽  
Acid Phosphate ◽  
Fracture Surfaces ◽  
Al Content ◽  
Before And After ◽  
Relationship Of

The reaction rate and efficiency of piperazine to 1,4-diazabicyclo-octane (DABCO) depends on the Si/Al ratio of the MFI topology catalysts. The Al was shown to be the active site, however, in the Si/Al range of 30-200 the reaction rate increases as the Si/Al ratio increases. The objective of this work was to determine the location and concentration of Al to explain this inverse relationship of Al content with reaction rate.Two silicalite catalysts in the form of 1/16 inch SiO2/Al2O3 bonded extrudates were examined: catalyst A with a Si/Al of 83; and catalyst B, the acid/phosphate Al extracted form of catalyst A, with a Si/Al of 175. Five extrudates from each catalyst were fractured in the transverse direction and particles were obtained from the fracture surfaces near the center of the extrudate diameter. Particles were also obtained from the outside surfaces of five extrudates.

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

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