quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes implications for classification of enzyme function定量比较趋同进化酶的催化机理和总体反应影响酶的分类函数.pdfVIP

Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function 1,2,3 4 5 1,2,3 Daniel E. Almonacid , Emmanuel R. Yera , John B. O. Mitchell , Patricia C. Babbitt * 1 Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America, 2 Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America, 3 California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, United States of America, 4 Biological and Medical Informatics Graduate Program, University of California San Francisco, San Francisco, California, United States of America, 5 Centre for Biomolecular Sciences, University of St Andrews, St Andrews, United Kingdom Abstract Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets