Mechanism of the Reaction Catalyzed by Acetoacetate Decarboxylase. Importance of Lysine 116 in Determining the pKaof Active-Site Lysine 115†

Biochemistry ◽  
1996 ◽  
Vol 35 (1) ◽  
pp. 41-46 ◽  
Author(s):  
Lane A. Highbarger ◽  
John A. Gerlt ◽  
George L. Kenyon
Keyword(s):  
Active Site ◽  
Acetoacetate Decarboxylase ◽  
Mechanism Of The Reaction

pK of the lysine amino group at the active site of acetoacetate decarboxylase

Biochemistry ◽  
1971 ◽  
Vol 10 (7) ◽  
pp. 1249-1253 ◽  
Author(s):  
Frank H. Westheimer ◽  
Donald E. Schmidt
Keyword(s):  
Active Site ◽  
Amino Group ◽  
Acetoacetate Decarboxylase

scholarly journals Swit_4259, an acetoacetate decarboxylase-like enzyme from Sphingomonas wittichii RW1

2017 ◽  
Vol 73 (12) ◽  
pp. 672-681 ◽  
Author(s):  
Lisa S. Mydy ◽  
Zahra Mashhadi ◽  
T. William Knight ◽  
Tyler Fenske ◽  
Trevor Hagemann ◽  
...  
Keyword(s):  
Active Site ◽  
Tertiary Structure ◽  
Gene Clusters ◽  
Decarboxylase Activity ◽  
Negative Bacterium ◽  
Genomic Context ◽  
The Family ◽  
Acetoacetate Decarboxylase ◽  
Sphingomonas Wittichii ◽  
Dehydratase Activity

The Gram-negative bacterium Sphingomonas wittichii RW1 is notable for its ability to metabolize a variety of aromatic hydrocarbons. Not surprisingly, the S. wittichii genome contains a number of putative aromatic hydrocarbon-degrading gene clusters. One of these includes an enzyme of unknown function, Swit_4259, which belongs to the acetoacetate decarboxylase-like superfamily (ADCSF). Here, it is reported that Swit_4259 is a small (28.8 kDa) tetrameric ADCSF enzyme that, unlike the prototypical members of the superfamily, does not have acetoacetate decarboxylase activity. Structural characterization shows that the tertiary structure of Swit_4259 is nearly identical to that of the true decarboxylases, but there are important differences in the fine structure of the Swit_4259 active site that lead to a divergence in function. In addition, it is shown that while it is a poor substrate, Swit_4259 can catalyze the hydration of 2-oxo-hex-3-enedioate to yield 2-oxo-4-hydroxyhexanedioate. It is also demonstrated that Swit_4259 has pyruvate aldolase-dehydratase activity, a feature that is common to all of the family V ADCSF enzymes studied to date. The enzymatic activity, together with the genomic context, suggests that Swit_4259 may be a hydratase with a role in the metabolism of an as-yet-unknown hydrocarbon. These data have implications for engineering bioremediation pathways to degrade specific pollutants, as well as structure–function relationships within the ADCSF in general.

Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-.ANG. resolution: identification of the active site and possible catalytic residues

Biochemistry ◽  
1991 ◽  
Vol 30 (38) ◽  
pp. 9264-9273 ◽  
Author(s):  
David J. Neidhart ◽  
P. Lynne Howell ◽  
Gregory A. Petsko ◽  
Vincent M. Powers ◽  
Rongshi Li ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Catalytic Residues ◽  
Mandelate Racemase ◽  
Mechanism Of The Reaction

Acetoacetate Decarboxylase. Identification of Lysine at the Active Site*

Biochemistry ◽  
1966 ◽  
Vol 5 (3) ◽  
pp. 817-823 ◽  
Author(s):  
Stuart Warren ◽  
Burt Zerner ◽  
F. H. Westheimer
Keyword(s):  
Active Site ◽  
Acetoacetate Decarboxylase

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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