Evolution of biocatalysis 1. Possible pre-genetic-code RNA catalysts which are their own replicase.
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Biomedical subjects
Publications and source records attributed to C M Visser.
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Analysis of the partially refined X-ray crystallographic structure of the active site of p-hydroxybenzoate hydroxylase shows clearly that the enzyme is complementary to a flavin C4,C4a-dioxetane derivative. A mechanism is proposed based on such an intermediate as the oxenoid transferring agent. A non-enzymatic analogue of this reaction is not known in organic chemistry. A possible evolutionary pathway for such a non-imitable enzyme is discussed.
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The evolutionary information obtained from sequencing proteins and RNA's fades out completely for early periods in evolution. Information for tracing evolution even further could stem from the analysis of coenzyme mechanisms. Likewise, placing cofactors in their proper evolutionary context gives new hints concerning their actual mechanisms of catalysis.
Analysis of the possible evolution of flavin catalysis in succinate dehydrogenase suggests as the ultimate state an active site that bears one or more acid functions and uses the enediol form of the substrate rather than the carbanion as a nucleophile. In the case of flavoenzyme catalyzed oxidation of fatty acylCoA, alpha-amino acids and alpha-hydroxy acids evolution to a similar mechanism seems to be blocked.
A challenging theme in bioorganic chemistry is the unification of established theories of biochemistry and organic chemistry to provide new patterns for interpretation and experimentation. Especially relevant examples of such interactions can be drawn from the field of enzyme catalysis and, in particular, the role of cofactors therein. Knowledge of the chemical mechanisms by which some of the cofactors function has progressed rapidly with the aid of studies of the cofactors themselves (or compounds of related structure, "models") stripped of the accompanying apoenzyme. The striking successes in this field likely arise from a fundamental resemblance between bioorganic chemistry (especially coenzyme models) and chemical evolution before the appearance of coded polypeptide enzymes.
In the previous article we try to give an explanation for the success of models of enzymatic reactions in which coenzymes play a role. However, one vital cofactor that has thus far not yielded appreciably to this approach is biotin. We attempt to show that biotin presents a fundamentally new sort of problem to bioorganic chemistry; this problem requires consideration both of the origin of life and subsequent evolution in any attempt to understand the anomalies offered by this cofactor.