Zhai X, Amyes TL, Richard JP. Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase.
J Am Chem Soc 2015;
137:15185-97. [PMID:
26570983 PMCID:
PMC4694050 DOI:
10.1021/jacs.5b09328]
[Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The side chains of
Y208 and S211 from loop 7 of triosephosphate
isomerase (TIM) form hydrogen bonds to backbone amides and carbonyls
from loop 6 to stabilize the caged enzyme–substrate complex.
The effect of seven mutations [Y208T, Y208S, Y208A, Y208F, S211G,
S211A, Y208T/S211G] on the kinetic parameters for TIM catalyzed reactions
of the whole substrates dihydroxyacetone phosphate and d-glyceraldehyde
3-phosphate [(kcat/Km)GAP and (kcat/Km)DHAP] and of the substrate pieces
glycolaldehyde and phosphite dianion (kcat/KHPiKGA)
are reported. The linear logarithmic correlation between these kinetic
parameters, with slope of 1.04 ± 0.03, shows that most mutations
of TIM result in an identical change in the activation barriers for
the catalyzed reactions of whole substrate and substrate pieces, so
that the transition states for these reactions are stabilized by similar
interactions with the protein catalyst. The second linear logarithmic
correlation [slope = 0.53 ± 0.16] between kcat for isomerization of GAP and Kd⧧ for phosphite dianion binding to the transition
state for wildtype and many mutant TIM-catalyzed reactions of substrate
pieces shows that ca. 50% of the wildtype TIM dianion binding energy,
eliminated by these mutations, is expressed at the wildtype Michaelis
complex, and ca. 50% is only expressed at the wildtype transition
state. Negative deviations from this correlation are observed when
the mutation results in a decrease in enzyme reactivity at the catalytic
site. The main effect of Y208T, Y208S, and Y208A mutations is to cause
a reduction in the total intrinsic dianion binding energy, but the
effect of Y208F extends to the catalytic site.
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