scholarly journals Corrigendum: Mutations Closer to the Active Site Improve the Promiscuous Aldolase Activity of 4-Oxalocrotonate Tautomerase More Effectively than Distant Mutations

ChemBioChem ◽  
2016 ◽  
Vol 17 (13) ◽  
pp. 1290-1290 ◽  
Author(s):  
Mehran Rahimi ◽  
Jan-Ytzen van der Meer ◽  
Edzard M. Geertsema ◽  
Harshwardhan Poddar ◽  
Bert-Jan Baas ◽  
...  
Keyword(s):  
Active Site ◽  
Aldolase Activity

Mutations Closer to the Active Site Improve the Promiscuous Aldolase Activity of 4-Oxalocrotonate Tautomerase More Effectively than Distant Mutations

ChemBioChem ◽  
2016 ◽  
Vol 17 (13) ◽  
pp. 1225-1228 ◽  
Author(s):  
Mehran Rahimi ◽  
Jan-Ytzen van der Meer ◽  
Edzard M. Geertsema ◽  
Harshwardhan Poddar ◽  
Bert-Jan Baas ◽  
...  
Keyword(s):  
Active Site ◽  
Aldolase Activity

scholarly journals 6-Pyruvoyltetrahydropterin Synthase Paralogs Replace the Folate Synthesis Enzyme Dihydroneopterin Aldolase in Diverse Bacteria

2009 ◽  
Vol 191 (13) ◽  
pp. 4158-4165 ◽  
Author(s):  
Anne Pribat ◽  
Linda Jeanguenin ◽  
Aurora Lara-Núñez ◽  
Michael J. Ziemak ◽  
John E. Hyde ◽  
...  
Keyword(s):  
Active Site ◽  
Genes Encoding ◽  
Folate Biosynthesis ◽  
Catalytic Cysteine ◽  
Aldolase Activity ◽  
Bacterial Genes ◽  
Almost All ◽  
Dihydroneopterin Aldolase

ABSTRACT Dihydroneopterin aldolase (FolB) catalyzes conversion of dihydroneopterin to 6-hydroxymethyldihydropterin (HMDHP) in the classical folate biosynthesis pathway. However, folB genes are missing from the genomes of certain bacteria from the phyla Chloroflexi, Acidobacteria, Firmicutes, Planctomycetes, and Spirochaetes. Almost all of these folB-deficient genomes contain an unusual paralog of the tetrahydrobiopterin synthesis enzyme 6-pyruvoyltetrahydropterin synthase (PTPS) in which a glutamate residue replaces or accompanies the catalytic cysteine. A similar PTPS paralog from the malaria parasite Plasmodium falciparum is known to form HMDHP from dihydroneopterin triphosphate in vitro and has been proposed to provide a bypass to the FolB step in vivo. Bacterial genes encoding PTPS-like proteins with active-site glutamate, cysteine, or both residues were accordingly tested together with the P. falciparum gene for complementation of the Escherichia coli folB mutation. The P. falciparum sequence and bacterial sequences with glutamate or glutamate plus cysteine were active; those with cysteine alone were not. These results demonstrate that PTPS paralogs with an active-site glutamate (designated PTPS-III proteins) can functionally replace FolB in vivo. Recombinant bacterial PTPS-III proteins, like the P. falciparum enzyme, mediated conversion of dihydroneopterin triphosphate to HMDHP, but other PTPS proteins did not. Neither PTPS-III nor other PTPS proteins exhibited significant dihydroneopterin aldolase activity. Phylogenetic analysis indicated that PTPS-III proteins may have arisen independently in various PTPS lineages. Consistent with this possibility, merely introducing a glutamate residue into the active site of a PTPS protein conferred incipient activity in the growth complementation assay, and replacing glutamate with alanine in a PTPS-III protein abolished complementation.

scholarly journals Aldolase A Ins(1,4,5)P3-binding domains as determined by site-directed mutagenesis

1999 ◽  
Vol 341 (3) ◽  
pp. 805-812 ◽  
Author(s):  
Carl B. BARON ◽  
Dean R. TOLAN ◽  
Kyung H. CHOI ◽  
Ronald F. COBURN
Keyword(s):  
Catalytic Activity ◽  
Active Site ◽  
Electrostatic Interactions ◽  
Bond Cleavage ◽  
Site Directed Mutagenesis ◽  
Binding Domains ◽  
Carbon Carbon Bond ◽  
Catalytically Active ◽  
Aldolase Activity ◽  
Aldolase A

We substituted neutral amino acids for some positively charged residues (R42, K107, K146, R148 and K229) that line the active site of aldolase A in an effort to determine binding sites for inositol 1,4,5-trisphosphate. In addition, D33 (involved in carbon-carbon bond cleavage) was mutated. K229A and D33S aldolases showed almost no catalytic activity, but Ins(1,4,5)P3 binding was similar to that determined with the use of wild-type aldolase A. R42A, K107A, K146R and R148A had markedly decreased affinities for Ins(1,4,5)P3 binding, increased EC50 values for Fru(1,6)P2-evoked release of bound Ins(1,4,5)P3 and increased Ki values for Ins(1,4,5)P3-evoked inhibition of aldolase activity. K146Q (positive charge removal) had essentially no catalytic activity and could not bind Ins(1,4,5)P3. Computer-simulated docking of Ins(1,4,5)P3 in the aldolase A structure was consistent with electrostatic binding of Ins(1,4,5)P3 to K107, K146, R148, R42, R303 and backbone nitrogens, as has been reported for Fru(1,6)P2 binding. Results indicate that Ins(1,4,5)P3 binding occurs at the active site and is not dependent on having a catalytically active enzyme; they also suggest that there is competition between Ins(1,4,5)P3 and Fru(1,6)P2 for binding. Although Ins(1,4,5)P3 binding to aldolase involved electrostatic interactions, the aldolase A Ins(1,4,5)P3-binding domain did not show other similarities to pleckstrin homology domains or phosphotyrosine-binding domains known to bind Ins(1,4,5)P3 in other proteins.

scholarly journals Replacement of a Phenylalanine by a Tyrosine in the Active Site Confers Fructose-6-phosphate Aldolase Activity to the Transaldolase ofEscherichia coliand Human Origin

2008 ◽  
Vol 283 (44) ◽  
pp. 30064-30072 ◽  
Author(s):  
Sarah Schneider ◽  
Tatyana Sandalova ◽  
Gunter Schneider ◽  
Georg A. Sprenger ◽  
Anne K. Samland
Keyword(s):  
Active Site ◽  
Human Origin ◽  
Aldolase Activity

Novel mode of inhibition byD-tagatose 6-phosphate through a Heyns rearrangement in the active site of transaldolase B variants

2016 ◽  
Vol 72 (4) ◽  
pp. 467-476
Author(s):  
Lena Stellmacher ◽  
Tatyana Sandalova ◽  
Sarah Schneider ◽  
Gunter Schneider ◽  
Georg A. Sprenger ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Ring Structure ◽  
Open Chain ◽  
E Coli ◽  
Bond Forming ◽  
Closed Ring ◽  
Kinetic Inhibition ◽  
Aldolase Activity ◽  
Inhibition Studies

Transaldolase B (TalB) and D-fructose-6-phosphate aldolase A (FSAA) fromEscherichia coliare C—C bond-forming enzymes. Using kinetic inhibition studies and mass spectrometry, it is shown that enzyme variants of FSAA and TalB that exhibit D-fructose-6-phosphate aldolase activity are inhibited covalently and irreversibly by D-tagatose 6-phosphate (D-T6P), whereas no inhibition was observed for wild-type transaldolase B fromE. coli. The crystal structure of the variant TalBF178Ywith bound sugar phosphate was solved to a resolution of 1.46 Å and revealed a novel mode of covalent inhibition. The sugar is bound covalentlyviaits C2 atom to the ∊-NH2group of the active-site residue Lys132. It is neither bound in the open-chain form nor as the closed-ring form of D-T6P, but has been converted to β-D-galactofuranose 6-phosphate (D-G6P), a five-membered ring structure. The furanose ring of the covalent adduct is formedviaa Heyns rearrangement and subsequent hemiacetal formation. This reaction is facilitated by Tyr178, which is proposed to act as acid–base catalyst. The crystal structure of the inhibitor complex is compared with the structure of the Schiff-base intermediate of TalBE96Qformed with the substrate D-fructose 6-phosphate determined to a resolution of 2.20 Å. This comparison highlights the differences in stereochemistry at the C4 atom of the ligand as an essential determinant for the formation of the inhibitor adduct in the active site of the enzyme.

scholarly journals Improving upon Nature: Active Site Remodeling Produces Highly Efficient Aldolase Activity toward Hydrophobic Electrophilic Substrates

Biochemistry ◽  
2012 ◽  
Vol 51 (8) ◽  
pp. 1658-1668 ◽  
Author(s):  
Manoj Cheriyan ◽  
Eric J. Toone ◽  
Carol A. Fierke
Keyword(s):  
Active Site ◽  
Highly Efficient ◽  
Aldolase Activity

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.

Contributions of the substrate-binding arginine residues to maleate-induced closure of the active site of Escherichia coli aspartate aminotransferase

2001 ◽  
Vol 268 (6) ◽  
pp. 1640-1645
Author(s):  
Annelise Matharu ◽  
Hideyuki Hayashi ◽  
Hiroyuki Kagamiyama ◽  
Bruno Maras ◽  
Robert A. John
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
Aspartate Aminotransferase ◽  
Substrate Binding ◽  
Arginine Residues

Alkane upgrading effected by silica-supported pincer-iridium catalysts: Evidence of a shared active site with solution-phase species

2020 ◽  
Author(s):  
Alan Goldman ◽  
Boris Sheludko ◽  
Fuat Celik ◽  
Cristina Castro
Keyword(s):  
Active Site ◽  
Solution Phase ◽  
Iridium Catalysts
Sign in / Sign up

Export Citation Format

Share Document