scholarly journals Mechanistic pathways of mercury removal from the organomercurial lyase active site

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1127 ◽  
Author(s):  
Pedro J. Silva ◽  
Viviana Rodrigues
Keyword(s):  
Active Site ◽  
Mercury Removal ◽  
Organomercurial Lyase

scholarly journals Mechanistic pathways of mercury removal from the organomercurial lyase active site

2015 ◽  
Author(s):  
Pedro J Silva ◽  
Viviana Rodrigues
Keyword(s):  
Active Site ◽  
Resistance Mechanism ◽  
Initial Reaction ◽  
Bacterial Populations ◽  
Mercury Compounds ◽  
Active Site Cysteine ◽  
Rate Determining Step ◽  
Related Enzyme ◽  
The One ◽  
Organomercurial Lyase

Bacterial populations present in Hg-rich environments have evolved biological mechanisms to detoxify methylmercury and other organometallic mercury compounds. The most common resistance mechanism relies on the H+-assisted cleavage of the Hg-C bond of methylmercury by the organomercurial lyase MerB. Although the initial reaction steps which lead to the loss of methane from methylmercury have already been studied experimentally and computationally, the reaction steps leading to the removal of Hg2+ from MerB and regeneration of the active site for a new round of catalysis have not yet been elucidated. In this paper, we describe an MP2/CBS//B3PW91/6-31G(d) study of the final steps of the reaction catalyzed by MerB. While conceptually simple, these reaction steps occur in a complex potential energy surface where several distinct pathways are accessible and may operate concurrently. The only pathway which clearly emerges as forbidden in our analysis is the one arising from the sequential addition of two thiolates to the metal atom, due to the accumulation of negative charges in the active site. Addition of two thiols, in contrast, leads to two feasible mechanistic possibilities. The most straightforward pathway proceeds through proton transfer from the attacking thiol to Cys159 , leading to its removal from the mercury coordination sphere, followed by a slower attack of a second thiol, which removes Cys96. The other pathway involves Asp99 in an accessory role similar to the one observed earlier for the initial stages of the reaction and affords a lower activation enthalpy, around 14 kcal.mol-1, determined solely by the cysteine removal step rather than by the thiol ligation step. Addition of one thiolate to the intermediates arising from either thiol attack occurs without a barrier and produces an intermediate bound to one active site cysteine and from which Hg(SCH3)2 may be removed only after protonation by solvent-provided H3O+. Thiolate addition to the active site (prior to any attack by thiols) leads to pathways where the removal of the first cysteine becomes the rate-determining step, irrespective of whether Cys159 or Cys96 leaves first. Comparisons with the recently computed mechanism of the related enzyme MerA further underline the important role of Asp99 in the energetics of the MerB reaction.

scholarly journals Mechanistic pathways of mercury removal from the organomercurial lyase active site

2015 ◽  
Author(s):  
Pedro J Silva ◽  
Viviana Rodrigues
Keyword(s):  
Active Site ◽  
Resistance Mechanism ◽  
Initial Reaction ◽  
Bacterial Populations ◽  
Mercury Compounds ◽  
Active Site Cysteine ◽  
Rate Determining Step ◽  
Related Enzyme ◽  
The One ◽  
Organomercurial Lyase

Bacterial populations present in Hg-rich environments have evolved biological mechanisms to detoxify methylmercury and other organometallic mercury compounds. The most common resistance mechanism relies on the H+-assisted cleavage of the Hg-C bond of methylmercury by the organomercurial lyase MerB. Although the initial reaction steps which lead to the loss of methane from methylmercury have already been studied experimentally and computationally, the reaction steps leading to the removal of Hg2+ from MerB and regeneration of the active site for a new round of catalysis have not yet been elucidated. In this paper, we describe an MP2/CBS//B3PW91/6-31G(d) study of the final steps of the reaction catalyzed by MerB. While conceptually simple, these reaction steps occur in a complex potential energy surface where several distinct pathways are accessible and may operate concurrently. The only pathway which clearly emerges as forbidden in our analysis is the one arising from the sequential addition of two thiolates to the metal atom, due to the accumulation of negative charges in the active site. Addition of two thiols, in contrast, leads to two feasible mechanistic possibilities. The most straightforward pathway proceeds through proton transfer from the attacking thiol to Cys159 , leading to its removal from the mercury coordination sphere, followed by a slower attack of a second thiol, which removes Cys96. The other pathway involves Asp99 in an accessory role similar to the one observed earlier for the initial stages of the reaction and affords a lower activation enthalpy, around 14 kcal.mol-1, determined solely by the cysteine removal step rather than by the thiol ligation step. Addition of one thiolate to the intermediates arising from either thiol attack occurs without a barrier and produces an intermediate bound to one active site cysteine and from which Hg(SCH3)2 may be removed only after protonation by solvent-provided H3O+. Thiolate addition to the active site (prior to any attack by thiols) leads to pathways where the removal of the first cysteine becomes the rate-determining step, irrespective of whether Cys159 or Cys96 leaves first. Comparisons with the recently computed mechanism of the related enzyme MerA further underline the important role of Asp99 in the energetics of the MerB reaction.

MERCURY ADSORPTION ON SULFURIC ACID-IMPREGNATED CARBONACEOUS SURFACE: THEORETICAL STUDY

2014 ◽  
Vol 21 (01) ◽  
pp. 1450018 ◽  
Author(s):  
PING HE ◽  
JIANG WU ◽  
XIUMIN JIANG ◽  
WEIGUO PAN ◽  
JIANXING REN
Keyword(s):  
Sulfuric Acid ◽  
Adsorption Capacity ◽  
Active Site ◽  
Active Sites ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Mercury Removal ◽  
Mercury Adsorption ◽  
Acid Effect ◽  
Negative Effect

Density functional theory calculations are performed to provide a molecular-level understanding of the mechanism of mercury adsorption on sulfuric acid-impregnated carbonaceous surface. The carbonaceous surface is modeled by a nine-fused benzene ring in which its edge carbon atoms on the upper side are unsaturated to simulate the active sites for reaction. SO 4 clusters with and without charge are examined to act as the representative species to model the sulfuric acid absorbed on the carbonaceous surface. All of the possible approaches of SO 4 clusters with and without charge on the carbonaceous surface are conduced to study their effects on mercury adsorption. The results suggest that sulfuric acid effect on the mercury adsorption capacity of the carbonaceous surface is very complicated, and it depends on a combination of concentration and charge of SO 4 cluster. SO 4 cluster presents a positive effect on mercury adsorption on the carbonaceous surface, but higher concentration of SO 4 cluster decreases the adsorption capacity of the carbonaceous surface for mercury removal because there is considerable competition for active sites between Hg and SO 4 cluster. Since all of the possible approaches of mercury on the carbonaceous surface with [Formula: see text] cluster, excluding one that mercury is adsorbed at bridge active site, can lead to the decrease in the adsorption energies of mercury on the carbonaceous surface, [Formula: see text] cluster presents a negative effect on the capacity of the carbonaceous surface for mercury adsorption regardless of the concentration of [Formula: see text] cluster. The results also indicate that SO 2 cluster and surface oxygen complex can be formed from SO 4 cluster with or without charge if mercury is adsorbed at bridge active site, which facilitates the mercury removal for the carbonaceous surface.

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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