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
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
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