Structural Insights into Radical Generation by the Radical SAM Superfamily

Abstract

Table of Contents Table of Contents 1. Introduction 2. Unresolved Questions in the Radical SAM Enzyme Field 3. Highlighted Radical SAM Enzymes 3.1. Pyruvate Formate-Lyase Activating Enzyme (PFL-AE) 3.2. Oxygen-Independent Coproporphyrinogen III Oxidase (HemN) 3.3. Biotin Synthase (BioB) 3.4. Molybdenum Cofactor Biosynthesis Protein MoaA 3.5. Lysine Aminomutase (LAM) 3.6. Wye-Base Biosynthetic Protein TYW1 3.7. [Fe−Fe] Hydrogenase Maturase Protein HydE 4. Overall Fold 4.1. Radical SAM Core 4.2. Protein Elements Outside of the Radical SAM Core 5. FeS cluster 5.1. Location of the 4Fe−4S Cluster Binding Site 5.2. Environment Surrounding the Cluster 5.3. Interactions between the 4Fe−4S Cluster and AdoMet 6. AdoMet Binding 6.1. AdoMet Conformation 6.2. General Properties of the AdoMet Binding Site 6.3. Overall Description of the AdoMet Binding Site 6.3.1. AdoMet Methionyl Moiety 6.3.2. AdoMet Ribose 6.3.3. AdoMet Adenine Moiety 6.4. AdoMet Binding Motifs in the Radical SAM Superfamily 6.5. Deviations and Variations in AdoMet Binding between the Subfamilies 7. Implications of AdoMet Binding Site Architecture on Function and Reactivity 7.1. Tailoring the Reaction to Specific Substrates 7.2. AdoMet Usage as Cofactor or Cosubstrate 7.3. AdoMet Reaction Stoichiometry 7.4. HemN’s Second AdoMet (SAM2) 8. Substrate Binding to Radical SAM Enzymes 8.1. Positioning of the Substrate 8.2. Additional Cofactors in Some Radical SAM Substrate Binding Sites 8.3. Conformational Changes Associated with Substrate Binding in Radical SAM Enzymes 9. Reductant Binding in Radical SAM Enzymes 10. Other Known AdoMet-Binding Protein Folds 11. Conclusions