How an Enzyme Tames Reactive Intermediates:  Positioning of the Active-Site Components of Lysine 2,3-Aminomutase during Enzymatic Turnover As Determined by ENDOR Spectroscopy

2006 ◽  
Vol 128 (31) ◽  
pp. 10145-10154 ◽  
Author(s):  
Nicholas S. Lees ◽  
Dawei Chen ◽  
Charles J. Walsby ◽  
Elham Behshad ◽  
Perry A. Frey ◽  
...  
Keyword(s):  
Active Site ◽  
Reactive Intermediates ◽  
Endor Spectroscopy

Exploring the Role of the Central Carbide of the Nitrogenase Active-Site FeMo-cofactor through Targeted 13C Labeling and ENDOR Spectroscopy

2021 ◽  
Author(s):  
Ana Pérez-González ◽  
Zhi-Yong Yang ◽  
Dmitriy A. Lukoyanov ◽  
Dennis R. Dean ◽  
Lance C. Seefeldt ◽  
...  
Keyword(s):  
Active Site ◽  
13C Labeling ◽  
Endor Spectroscopy ◽  
Femo Cofactor

scholarly journals The nature of chemical innovation: new enzymes by evolution

2015 ◽  
Vol 48 (4) ◽  
pp. 404-410 ◽  
Author(s):  
Frances H. Arnold
Keyword(s):  
Cytochrome P450 ◽  
Active Site ◽  
Reactive Intermediates ◽  
Transfer Reactions ◽  
Amino Acid Substitutions ◽  
Chemical Catalysis ◽  
Nitrene Transfer ◽  
Enzyme Systems ◽  
Natural Enzyme ◽  
And Function

AbstractI describe how we direct the evolution of non-natural enzyme activities, using chemical intuition and information on structure and mechanism to guide us to the most promising reaction/enzyme systems. With synthetic reagents to generate new reactive intermediates and just a few amino acid substitutions to tune the active site, a cytochrome P450 can catalyze a variety of carbene and nitrene transfer reactions. The cyclopropanation, N–H insertion, C–H amination, sulfimidation, and aziridination reactions now demonstrated are all well known in chemical catalysis but have no counterparts in nature. The new enzymes are fully genetically encoded, assemble and function inside of cells, and can be optimized for different substrates, activities, and selectivities. We are learning how to use nature's innovation mechanisms to marry some of the synthetic chemists’ favorite transformations with the exquisite selectivity and tunability of enzymes.

Hydrogenases in the "active" state: determination of g-matrix axes and electron spin distribution at the active site by 1H ENDOR spectroscopy

2001 ◽  
Vol 7 (1-2) ◽  
pp. 177-194 ◽  
Author(s):  
Arnd Müller ◽  
Irene Tscherny ◽  
Reinhard Kappl ◽  
Claude E. Hatchikian ◽  
Jürgen Hüttermann ◽  
...  
Keyword(s):  
Electron Spin ◽  
Active Site ◽  
Active State ◽  
Spin Distribution ◽  
Endor Spectroscopy ◽  
State Determination

Trapping H-Bound to the Nitrogenase FeMo-Cofactor Active Site during H2Evolution:  Characterization by ENDOR Spectroscopy

2005 ◽  
Vol 127 (17) ◽  
pp. 6231-6241 ◽  
Author(s):  
Robert Y. Igarashi ◽  
Mikhail Laryukhin ◽  
Patricia C. Dos Santos ◽  
Hong-In Lee ◽  
Dennis R. Dean ◽  
...  
Keyword(s):  
Active Site ◽  
Endor Spectroscopy ◽  
Femo Cofactor

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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