Enzyme-bound transition state

In a strict sense, the term transition state becomes misused in the previous discussion. An enzyme-bound transition state (E TS ) occupies a minimum along the reaction... 

Analysis by Kelly et al. (27) of subsites B-D in the enzyme complex with MurNAc-GlcNAc-MurNAc clearly shows an alternative arrangement at subsite D in which the pyranose chair conformation is accommodated with slight repositioning of amino acids relative to the bound transition-state analog, albeit with the chair conformation less imbedded than the half-chair. The ability of the catalytic site to accommodate both forms might depict the protein structure of a Michaelis complex in one case and the transition-state structure in the other case (27). 

The origin of the dependencies of AAg on rion can be rationalized in the following way. When the smaller metals are bound to the enzyme, the free energy of ij/2 will be lowered considerably more than that of the transition state (as well as i//3) since in the former the OH " ion is free to interact with or ligate the metal, while it is becoming partially bound to the 5 -P atom at the transition state with accompanying charge delocalization. On the other... 

Strictly speaking, the conformations and relative geometries of the reactants must be known over the entire reaction coordinate moreover, there are indications that the transition states in enzyme reactions, which often have very different preferred conformations from those of the bound substrates, may be more tightly bound to the enzyme than either the starting materials or the products (1). 

Zn -PDF, 37 pM versus E. coli Fe -PDF), it was successfully used to provide co-crystals bound in the active site of both Co - and Zn -E. coli PDF [58], These structures reveal that the H-phosphonate binds to the metal in a monodentate fashion, adopting a tetrahedral coordination state similar to that of the native resting state of the enzyme. This is in contrast to later co-crystal structures obtained with more potent hydroxamic acid or reverse hydroxamate inhibitors, which bind to the metal in a bidentate fashion vide infra). Presumably these bidentate inhibitors mimic the true transition state of the enzyme, in which the metal centre slips to a penta-coordinate geometry in order to activate the Wformyl carbonyl of the substrate [56, 67]. 

Before our work [39], only one catalytic mechanism for zinc dependent HDACs has been proposed in the literature, which was originated from the crystallographic study of HDLP [47], a histone-deacetylase-like protein that is widely used as a model for class-I HDACs. In the enzyme active site, the catalytic metal zinc is penta-coordinated by two asp residues, one histidine residues as well as the inhibitor [47], Based on their crystal structures, Finnin et al. [47] postulated a catalytic mechanism for HDACs in which the first reaction step is analogous to the hydroxide mechanism for zinc proteases zinc-bound water is a nucleophile and Zn2+ is five-fold coordinated during the reaction process. However, recent experimental studies by Kapustin et al. suggested that the transition state of HDACs may not be analogous to zinc-proteases [48], which cast some doubts on this mechanism. 

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