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Literature summary for 3.1.26.4 extracted from

  • Rosta, E.; Woodcock, H.L.; Brooks, B.R.; Hummer, G.
    Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H (2009), J. Comput. Chem., 30, 1634-1641.
    View publication on PubMedView publication on EuropePMC

Organism

Organism UniProt Comment Textmining
Halalkalibacterium halodurans
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Reaction

Reaction Comment Organism Reaction ID
Endonucleolytic cleavage to a 5'-phosphomonoester in the initial attack of the phosphate diester by water, the oxygen-phosphorus distances alone are not sufficient as reaction coordinates, resulting in substantial hysteresis in the proton degrees of freedom and a barrier that is too low. If the proton degrees of freedom are included in an extended reaction coordinate, we obtain a barrier of 21.6 kcal/mol consistent with the experimental rates. As the barrier is approached, the attacking water molecule transfers one of its protons to the O1P oxygen of the phosphate group. At the barrier top, the resulting hydroxide ion forms a penta-coordinated phosphate intermediate Halalkalibacterium halodurans