Active Site Loop Motion in Triosephosphate Isomerase:  T-Jump Relaxation Spectroscopy of Thermal Activation†

Biochemistry ◽  
2003 ◽  
Vol 42 (10) ◽  
pp. 2941-2951 ◽  
Author(s):  
Ruel Desamero ◽  
Sharon Rozovsky ◽  
Nick Zhadin ◽  
Ann McDermott ◽  
Robert Callender
Keyword(s):  
Active Site ◽  
Thermal Activation ◽  
Triosephosphate Isomerase ◽  
Loop Motion

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.

The adaptability of the active site of trypanosomal triosephosphate isomerase as observed in the crystal structures of three different complexes

1991 ◽  
Vol 10 (1) ◽  
pp. 50-69 ◽  
Author(s):  
Martin E. M. Noble ◽  
Rik K. Wierenga ◽  
Anne-Marie Lambeir ◽  
Fred R. Opperdoes ◽  
Andy-Mark W. H. Thunnissen ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Active Site ◽  
Triosephosphate Isomerase

scholarly journals Uncovering the Role of Key Active Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalysed by Wild-Type and Variants of Triosephosphate Isomerase

2019 ◽  
Author(s):  
Yashraj S. Kulkarni ◽  
Tina L. Amyes ◽  
John Richard ◽  
Shina Caroline Lynn Kamerlin
Keyword(s):  
Active Site ◽  
Triosephosphate Isomerase ◽  
Valence Bond ◽  
Side Chains ◽  
Wild Type ◽  
Empirical Valence Bond

Manuscript and supporting information outlining an analysis of an extended Brønsted relationship obtained from empirical valence bond simulations of substrate deprotonation catalyzed by wild-type and mutant variants of triosephosphate isomerase.

A competent catalytic active site is necessary for substrate induced dimer assembly in triosephosphate isomerase

2017 ◽  
Vol 1865 (11) ◽  
pp. 1423-1432 ◽  
Author(s):  
Pedro Jimenez-Sandoval ◽  
Jose Luis Vique-Sanchez ◽  
Marisol López Hidalgo ◽  
Gilberto Velazquez-Juarez ◽  
Corina Diaz-Quezada ◽  
...  
Keyword(s):  
Active Site ◽  
Triosephosphate Isomerase ◽  
Catalytic Active Site
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