Mechanisms of the S/CO/Se interchange reactions at FeMo-co, the active site cluster of nitrogenase

2016 ◽  
Vol 45 (36) ◽  
pp. 14285-14300 ◽  
Author(s):  
Ian Dance
Keyword(s):  
Active Site ◽  
Site Cluster ◽  
Interchange Reactions

Mechanisms are developed for the observations of extraordinary substitution of bridging S by CO and Se, and the migration of Se, in the CFe7MoS9cluster at the active site of nitrogenase.

scholarly journals Converting the NiFeS Carbon Monoxide Dehydrogenase to a Hydrogenase and a Hydroxylamine Reductase

2002 ◽  
Vol 184 (21) ◽  
pp. 5894-5897 ◽  
Author(s):  
Jongyun Heo ◽  
Marcus T. Wolfe ◽  
Christopher R. Staples ◽  
Paul W. Ludden
Keyword(s):  
Carbon Monoxide ◽  
Amino Acid ◽  
Active Site ◽  
Reductase Activity ◽  
Carbon Monoxide Dehydrogenase ◽  
Hydrogenase Activity ◽  
Uptake Hydrogenase ◽  
Site Cluster ◽  
Metal Ligand

ABSTRACT Substitution of one amino acid for another at the active site of an enzyme usually diminishes or eliminates the activity of the enzyme. In some cases, however, the specificity of the enzyme is changed. In this study, we report that the changing of a metal ligand at the active site of the NiFeS-containing carbon monoxide dehydrogenase (CODH) converts the enzyme to a hydrogenase or a hydroxylamine reductase. CODH with alanine substituted for Cys531 exhibits substantial uptake hydrogenase activity, and this activity is enhanced by treatment with CO. CODH with valine substituted for His265 exhibits hydroxylamine reductase activity. Both Cys531 and His265 are ligands to the active-site cluster of CODH. Further, CODH with Fe substituted for Ni at the active site acquires hydroxylamine reductase activity.

scholarly journals Interaction of Potassium Cyanide with the [Ni-4Fe-5S] Active Site Cluster of CO Dehydrogenase fromCarboxydothermus hydrogenoformans

2007 ◽  
Vol 282 (14) ◽  
pp. 10639-10646 ◽  
Author(s):  
Seung-Wook Ha ◽  
Malgorzata Korbas ◽  
Mirjam Klepsch ◽  
Wolfram Meyer-Klaucke ◽  
Ortwin Meyer ◽  
...  
Keyword(s):  
Active Site ◽  
Potassium Cyanide ◽  
Co Dehydrogenase ◽  
Site Cluster

scholarly journals Understanding the role of active site residues in CotB2 catalysis using a cluster model

2020 ◽  
Vol 16 ◽  
pp. 50-59 ◽  
Author(s):  
Keren Raz ◽  
Ronja Driller ◽  
Thomas Brück ◽  
Bernhard Loll ◽  
Dan T Major
Keyword(s):  
Gas Phase ◽  
Active Site ◽  
Cluster Model ◽  
Electronic Energy ◽  
Active Site Residues ◽  
Multistep Synthesis ◽  
Site Cluster ◽  
Phase Data ◽  
Streptomyces Melanosporofaciens

Terpene cyclases are responsible for the initial cyclization cascade in the multistep synthesis of a large number of terpenes. CotB2 is a diterpene cyclase from Streptomyces melanosporofaciens, which catalyzes the formation of cycloocta-9-en-7-ol, a precursor to the next-generation anti-inflammatory drug cyclooctatin. In this work, we present evidence for the significant role of the active site's residues in CotB2 on the reaction energetics using quantum mechanical calculations in an active site cluster model. The results revealed the significant effect of the active site residues on the relative electronic energy of the intermediates and transition state structures with respect to gas phase data. A detailed understanding of the role of the enzyme environment on the CotB2 reaction cascade can provide important information towards a biosynthetic strategy for cyclooctatin and the biomanufacturing of related terpene structures.

scholarly journals Understanding the Role of Active Site Residues in CotB2 Catalysis Using a Cluster Model

2019 ◽  
Author(s):  
Keren Raz ◽  
Ronja Driller ◽  
Thomas Brück ◽  
Bernhard Loll ◽  
Dan Thomas Major
Keyword(s):  
Active Site ◽  
Cluster Model ◽  
Electronic Energy ◽  
Active Site Residues ◽  
Site Model ◽  
Multistep Synthesis ◽  
Active Site Model ◽  
Site Cluster ◽  
Phase Data

Terpene cyclases are responsible for the initial cyclization cascade in the multistep synthesis of a large number of terpenes. CotB2 is a diterpene cyclase from Streptomyces melanosporofaciens, which synthesizes the formation of cyclooctat-9-en-7-ol, a precursor to the next-generation anti-inflammatory drug, cyclooctatin. In this work, we present evidence for a significant role of the active site residues in CotB2 on the reaction energetics using quantum mechanics calculations in an active site cluster model. The results using the active site model reveal the significant effect of the active site residues on the relative electronic energy of the intermediates and transition state (TS) structures with respect to gas phase data. A detailed understanding of the role of the enzyme environment on the CotB2 reaction cascade can provide important information towards a biosynthetic strategy for cyclooctatin and the biomanufacturing of related terpene structures.

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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