Conformational changes during catalysis

Escherichia coli thioredoxin reductase refined at 2 A resolution. Implication of a large conformational change during catalysis. Journal of Molecular Biology, 236, 800-16. 

A key structural and mechanistic feature of lactate and malate dehydrogenases is the active site loop, residues 98-110 of the lactate enzyme, which was seen in the crystal structure to close over the reagents in the ternary complex.49,50 The loop has two functions it carries Arg-109, which helps to stabilize the transition state during hydride transfer and contacts around 101-103 are the main determinants of specificity. Tryptophan residues were placed in various parts of lactate dehydrogenase to monitor conformational changes during catalysis.54,59,60 Loop closure is the slowest of the motions. 

Crepin, T., Schmitt, E., Mechulam, Y., et al. (2003) Use of analogues of methionine and methio-nyl adenylate to sample conformational changes during catalysis in Escherichia coli methionyl-tRNA synthetase. J. Mol. Biol., 332(1), 59-72. 

Some enzymes are known to nndergo large conformation changes during catalysis. It is likely that the flexibility allows the active site to adapt to each species along the reaction coordinate. 

In both schemes, the specificities of the pump for catalysis change in the two enzyme states. Jencks points out that coupling is determined (a) by the chemical specificity achieved in catalyzing phosphoryl transfer to and from the enzyme (wherein E-Ca2 reversibly binds ATP, and E reacts reversibly with orthophosphate), and (b) by the vectorial specificity for ion binding and dissociation (wherein E reversibly binds/dissociates cytoplasmic calcium ion, and E—P reversibly binds/dissociates luminal calcium). There must be a single conformation change during the reaction cycle between Ei and E2 in the free enzyme and from Ei P-Ca2 to E2-P-Ca2 after enzyme phosphorylation. 

The supposition that protonic equilibria are usually faster than binding, conformation changes or catalysis can be used to draw useful conclusions from the following argument. One can think in terms of the enzyme being in the protonated form for a fraction of the time, rather than that a fraction of the enzyme is in that form. The proton will go on and off many times during the lifetime of a particular enzyme intermediate. This enables one to draw the conclusion that a pH independent and a pH dependent maximum velocity point to the fact that only steps prior to the rate limiting one contribute to Km... 

No large conformational changes occur in the enzyme during catalysis, but many small movements take place. The structural basis for the catalytic power of ribonuclease thus resides in several different features tight, specihc binding of a strained conformation of the substrate, general acid-base catalysis by His-12 and His-119, and preferential stabilization of the transition state by ionic interactions with Lys-41. 

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