[4Fe-4S]-dependent radical S-adenosylmethionine(SAM)proteins are a superfamily of oxidoreductases that can catalyze a series of challenging transformations using the common 5-d Ado radical intermediate.Although the st...[4Fe-4S]-dependent radical S-adenosylmethionine(SAM)proteins are a superfamily of oxidoreductases that can catalyze a series of challenging transformations using the common 5-d Ado radical intermediate.Although the structures and functions of radical SAM enzymes have been extensively studied,the electronic state-dependent reactions of the[4Fe-4S]clusters in these enzymes are still elusive.Herein we performed QM/MM calculations to elucidate the electronic state-dependent reactivity of the[4Fe-4S]cluster in pyruvate-formate lyase activating enzyme.Our calculations show that the electronic statedependent SAM activation by the[4Fe-4S]clusters in radical SAM enzyme is determined by both the super-exchange and exchange-enhanced reactivities.The super-exchange coupling in the[4Fe-4S]cluster favors the antiferromagnetic coupling between two neighbouring pairs,which results in theα-electron rather than theβ-electron donation from the[4Fe-4S]^(1+)cluster toward the SAM activation.Meanwhile,in the most favorable electronic state for the reductive cleavage of S-C5′,Fe4 would donate itsα-electron to gain the maximum exchange interactions in the Fe4-block.Such super-exchange and exchange-enhanced reactivity could be the general principles for reactivities of[4Fe-4S]cluster in RS enzymes.展开更多
Three-residue cyclophane-forming enzymes(3-Cy FEs) are a group of radical S-adenosylmethionine(SAM)enzymes involved in the biosynthesis of ribosomally synthesized and posttranslationally modified peptides(Ri PPs). 3-C...Three-residue cyclophane-forming enzymes(3-Cy FEs) are a group of radical S-adenosylmethionine(SAM)enzymes involved in the biosynthesis of ribosomally synthesized and posttranslationally modified peptides(Ri PPs). 3-Cy FE catalyzes the crosslinking between an aromatic residue(Ω1) and a non-aromatic residue(X3) in a Ω1-X2-X3 motif to produce a cyclophane ring, a key step in the biosynthesis of the Ri PP natural product triceptide. In this study, we perform a genome-wide search for the Xye-type triceptides, showing these Ri PPs are likely class-specific and only present in gamma-proteobacteria. The 3-Cy FE Pau B from Photorhabdus australis exhibits a relaxed substrate specificity on the X3 position, but glycine in this position is not suitable for cyclophane formation. We also reconstituted the activity of Pau B in vitro,showing it produces the N-terminal cyclophane firstly, and then the C-terminal ring, whereas the middle cyclophane is produced in the last step.展开更多
基金supported by the National Natural Science Foundation of China (No.22073077, No.21933009,and No.21907082)
文摘[4Fe-4S]-dependent radical S-adenosylmethionine(SAM)proteins are a superfamily of oxidoreductases that can catalyze a series of challenging transformations using the common 5-d Ado radical intermediate.Although the structures and functions of radical SAM enzymes have been extensively studied,the electronic state-dependent reactions of the[4Fe-4S]clusters in these enzymes are still elusive.Herein we performed QM/MM calculations to elucidate the electronic state-dependent reactivity of the[4Fe-4S]cluster in pyruvate-formate lyase activating enzyme.Our calculations show that the electronic statedependent SAM activation by the[4Fe-4S]clusters in radical SAM enzyme is determined by both the super-exchange and exchange-enhanced reactivities.The super-exchange coupling in the[4Fe-4S]cluster favors the antiferromagnetic coupling between two neighbouring pairs,which results in theα-electron rather than theβ-electron donation from the[4Fe-4S]^(1+)cluster toward the SAM activation.Meanwhile,in the most favorable electronic state for the reductive cleavage of S-C5′,Fe4 would donate itsα-electron to gain the maximum exchange interactions in the Fe4-block.Such super-exchange and exchange-enhanced reactivity could be the general principles for reactivities of[4Fe-4S]cluster in RS enzymes.
基金supported by grants from the National Key Research and Development Program (Nos. 2018YFA0900402 and 2021YFA0910501)the National Natural Science Foundation of China (Nos. 21822703, 21921003, and 32070050)+2 种基金the funding of Innovative research team of high-level local universities in Shanghaia key laboratory program of the Education Commission of Shanghai Municipality (No. ZDSYS14005)West Light Foundation of the Chinese Academy of Sciences (No. xbzgzdsys-202105)。
文摘Three-residue cyclophane-forming enzymes(3-Cy FEs) are a group of radical S-adenosylmethionine(SAM)enzymes involved in the biosynthesis of ribosomally synthesized and posttranslationally modified peptides(Ri PPs). 3-Cy FE catalyzes the crosslinking between an aromatic residue(Ω1) and a non-aromatic residue(X3) in a Ω1-X2-X3 motif to produce a cyclophane ring, a key step in the biosynthesis of the Ri PP natural product triceptide. In this study, we perform a genome-wide search for the Xye-type triceptides, showing these Ri PPs are likely class-specific and only present in gamma-proteobacteria. The 3-Cy FE Pau B from Photorhabdus australis exhibits a relaxed substrate specificity on the X3 position, but glycine in this position is not suitable for cyclophane formation. We also reconstituted the activity of Pau B in vitro,showing it produces the N-terminal cyclophane firstly, and then the C-terminal ring, whereas the middle cyclophane is produced in the last step.
