Segmental motion in catalysis: investigation of a hydrogen bond critical for loop closure in the reaction of triosephosphate isomerase

Biochemistry ◽  
1992 ◽  
Vol 31 (36) ◽  
pp. 8488-8494 ◽  
Author(s):  
Nicole S. Sampson ◽  
Jeremy R. Knowles
Keyword(s):  
Hydrogen Bond ◽  
Triosephosphate Isomerase ◽  
Segmental Motion ◽  
Loop Closure

scholarly journals Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps

IUCrJ ◽  
2021 ◽  
Vol 8 (4) ◽  
Author(s):  
Vinardas Kelpšas ◽  
Octav Caldararu ◽  
Matthew P. Blakeley ◽  
Nicolas Coquelle ◽  
Rikkert K. Wierenga ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Density Functional ◽  
Triosephosphate Isomerase ◽  
Density Functional Theory Calculations ◽  
Dihydroxyacetone Phosphate ◽  
Leishmania Mexicana ◽  
Functional Theory ◽  
Full Picture ◽  
Key Enzyme ◽  
Proton Shuttling

Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. This simple reaction involves the shuttling of protons mediated by protolysable side chains. The catalytic power of TIM is thought to stem from its ability to facilitate the deprotonation of a carbon next to a carbonyl group to generate an enediolate intermediate. The enediolate intermediate is believed to be mimicked by the inhibitor 2-phosphoglycolate (PGA) and the subsequent enediol intermediate by phosphoglycolohydroxamate (PGH). Here, neutron structures of Leishmania mexicana TIM have been determined with both inhibitors, and joint neutron/X-ray refinement followed by quantum refinement has been performed. The structures show that in the PGA complex the postulated general base Glu167 is protonated, while in the PGH complex it remains deprotonated. The deuteron is clearly localized on Glu167 in the PGA–TIM structure, suggesting an asymmetric hydrogen bond instead of a low-barrier hydrogen bond. The full picture of the active-site protonation states allowed an investigation of the reaction mechanism using density-functional theory calculations.

scholarly journals Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

2010 ◽  
Vol 6 (1) ◽  
pp. e1000645 ◽  
Author(s):  
Isabella Daidone ◽  
Hannes Neuweiler ◽  
Sören Doose ◽  
Markus Sauer ◽  
Jeremy C. Smith
Keyword(s):  
Hydrogen Bond ◽  
Loop Closure ◽  
Polypeptide Chains

Value of a Hydrogen Bond in Triosephosphate Isomerase Loop Motion†

Biochemistry ◽  
2007 ◽  
Vol 46 (20) ◽  
pp. 6001-6010 ◽  
Author(s):  
Rebecca B. Berlow ◽  
Tatyana I. Igumenova ◽  
J. Patrick Loria
Keyword(s):  
Hydrogen Bond ◽  
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.

Segmental motion of alkyl chains grafted on silica gel, studied by neutron scattering

1983 ◽  
Vol 44 (4) ◽  
pp. 497-503 ◽  
Author(s):  
J.P. Beaufils ◽  
M. C. Hennion ◽  
R. Rosset
Keyword(s):  
Neutron Scattering ◽  
Silica Gel ◽  
Segmental Motion ◽  
Alkyl Chains
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