Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes Implications for Classification of Enzyme Function 英文参考文献.docVIP

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Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes Implications for Classification of Enzyme Function 英文参考文献.doc

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Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes Implications for Classification of Enzyme Function 英文参考文献

QuantitativeComparisonofCatalyticMechanismsand OverallReactionsinConvergentlyEvolvedEnzymes: ImplicationsforClassificationofEnzymeFunction DanielE.Almonacid1,2,3,EmmanuelR.Yera4,JohnB.O.Mitchell5,PatriciaC.Babbitt1,2,3* 1Department ofBioengineeringandTherapeuticSciences,UniversityofCaliforniaSanFrancisco,SanFrancisco,California,UnitedStatesofAmerica,2Department of Pharmaceutical Chemistry,UniversityofCaliforniaSanFrancisco,San Francisco, California, United States ofAmerica, 3California Institute for Quantitative Biosciences, UniversityofCaliforniaSanFrancisco,SanFrancisco,California,UnitedStatesofAmerica,4BiologicalandMedicalInformaticsGraduateProgram,UniversityofCalifornia SanFrancisco,SanFrancisco,California,UnitedStatesofAmerica,5CentreforBiomolecularSciences,UniversityofStAndrews,StAndrews,UnitedKingdom Abstract Functionallyanalogousenzymesarethosethatcatalyzesimilarreactionsonsimilarsubstratesbutdonotsharecommon ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identificationanduseofthisinformationtoimprovereactionclassificationandcomputationalannotationofenzymesnewly discoveredinthegenomeprojectswouldbenefitfromsystematicdeterminationofreactionsimilarities.Here,wequantified similarityinbondchangesforoverallreactionsandcatalyticmechanismsfor95pairsoffunctionallyanalogousenzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overallreactionswascomputedbycomparingthesetsofbondchangesinthetransformationsfromsubstratestoproducts. Forsimilarityofmechanisms,setsofbondchangesoccurringineachmechanisticstepwerecompared;thesesimilarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionallyanalogousenzymesinthedatasethadsignificantlysimilaroverallreactions.Fortheseenzymes,convergenceto thesamemechanismoccurredin33%ofcases,withmostpairshavingatleastoneiden