Complex Biotransformations Catalyzed by Radical S-Adenosylmethionine Enzymes

Zhang, Qi; Li, Wen

doi:10.1074/jbc.r111.272690

Cited by 26 publications

(25 citation statements)

References 79 publications

(80 reference statements)

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“…11) shows relatively weak sequence conservation compared to other families of Radical-SAM enzymes, consistent with the trend observed in the superfamily. The weak inter-family conservation has been interpreted to indicate that direct interaction of the SAM cofactor with the [4Fe-4S] cluster is the dominant factor controlling generation of the reactive radical-SAM species and that the active-site structure has evolved primarily to control substrate-binding geometry and affinity 17,18 . Only residue F154 in RimO, which makes an edge-to-face interaction with the adenine moiety of SAM in existing ligand-bound stuctures, is broadly conserved in the Radical-SAM superfamily.…”

Section: Resultsmentioning

confidence: 99%

Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases

et al. 2013

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How living organisms create carbon-sulfur bonds during biosynthesis of critical sulphur-containing compounds is still poorly understood. The methylthiotransferases MiaB and RimO catalyze sulfur insertion into tRNAs and ribosomal protein S12, respectively. Both belong to a sub-group of Radical-SAM enzymes that bear two [4Fe-4S] clusters. One cluster binds S-Adenosylmethionine and generates an Ado• radical via a well- established mechanism. However, the precise role of the second cluster is unclear. For some sulfur-inserting Radical-SAM enzymes, this cluster has been proposed to act as a sacrificial source of sulfur for the reaction. In this paper, we report parallel enzymological, spectroscopic and crystallographic investigations of RimO and MiaB, which provide the first evidence that these enzymes are true catalysts and support a new sulfation mechanism involving activation of an exogenous sulfur co-substrate at an exchangeable coordination site on the second cluster, which remains intact during the reaction.

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Section: Resultsmentioning

confidence: 99%

Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases

et al. 2013

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“…Many radical SAM enzymes are known to catalyze complex rearrangement reactions 23,28 . MoaA has also been considered to catalyze the majority, if not all, of the complex rearrangement of GTP to form the pyranopterin ring of cPMP 5,6,29,30 .…”

Section: Introductionmentioning

confidence: 99%

Identification of a Cyclic Nucleotide as a Cryptic Intermediate in Molybdenum Cofactor Biosynthesis

et al. 2013

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The molybdenum cofactor (Moco) is a redox cofactor found in all kingdoms of life and its biosynthesis is essential for survival of many organisms including humans. The first step of Moco biosynthesis is a unique transformation of GTP into cyclic pyranopterin monophosphate (cPMP). In bacteria, MoaA and MoaC catalyze this transformation, although the specific functions of these enzymes were not fully understood. Here, we report the first isolation and structural characterization of a product of MoaA. This molecule was isolated under anaerobic conditions from a solution of MoaA incubated with GTP, SAM and sodium dithionite in the absence of MoaC. Structural characterization by chemical derivatization, MS, and NMR spectroscopy, suggested the structure of this molecule to be (8S)-3′,8-cyclo-7,8-dihydroguanosine 5′-triphosphate (3′,8-cH2GTP). The isolated 3′,8-cH2GTP was converted to cPMP by MoaC or its human homolog, MOCS1B, with high specificities (Km < 0.060 μM and 0.79 ±0.24 μM for MoaC and MOCS1B, respectively), suggesting the physiological relevance of 3′,8-cH2GTP. These observations, in combination with some mechanistic studies of MoaA, unambiguously demonstrates that MoaA catalyzes a unique radical C-C bond formation reaction, and that, in contrast to previous proposals, MoaC plays a major role in the complex rearrangement to generate the pyranopterin ring.

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“…This radical (5′-dA • ) can abstract a hydrogen atom from either the substrate molecule or other residue of the protein to initiate a variety of enzymatic reactions, including DNA repair, enzyme activation, protein and nucleic acid modification, primary metabolism, and cofactor synthesis. 27,28 Although QueE belongs to the SAM superfamily, it exhibits a clear structural difference compared to the common SAM enzyme. Most of the SAM radical enzymes obtained so far display the adoption of either a partial or full (β/α) 8 triose− phosphate isomerase (TIM) barrel fold, [18][19][20][21][22]29 which is called the SAM radical core.…”

Section: Introductionmentioning

confidence: 99%

Ring Contraction Catalyzed by the Metal-Dependent Radical SAM Enzyme: 7-Carboxy-7-deazaguanine Synthase from B. multivorans. Theoretical Insights into the Reaction Mechanism and the Influence of Metal Ions

Zhu

Liu

2015

ACS Catal.

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7-Carboxy-7-deazaguanine synthase (QueE) is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the conversion of 6-carboxy-5,6,7,8-tetrahydropterin (CPH 4 ) to 7-carboxy-7-deazaguanine (CDG). QueE also shows a clear dependence on Mg 2+ ion and is considered a new feature for a radical SAM enzyme. The catalytic mechanism of QueE from B. multivorans has been studied using a combined quantum mechanics and molecular mechanics (QM/MM) method. The results of our calculations reveal that the key ring-contraction step involves a bridged intermediate rather than a ring-opening one. For the QueE−Mg 2+ system, the elimination of ammonia is calculated to be rate limiting with a free energy barrier of 18.8 kcal/mol, which is basically in accordance with the estimated value (20.9 kcal/mol) from the experiment. For QueE−Na + complex, the rate-limiting step switches to the formation of the bridged intermediate with an energy barrier of 29.3 kcal/mol. Natural population analysis indicates that the metal ions do not act as Lewis acids; therefore, they mainly play a role in fixing the substrate in its reactive conformation. The different coordination of Mg 2+ and Na + with the substrate is suggested to be the main reason for leading to the different activities of QueE−Mg 2+ and QueE−Na + complexes.

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Complex Biotransformations Catalyzed by Radical S-Adenosylmethionine Enzymes

Cited by 26 publications

References 79 publications

Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases

Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases

Identification of a Cyclic Nucleotide as a Cryptic Intermediate in Molybdenum Cofactor Biosynthesis

Ring Contraction Catalyzed by the Metal-Dependent Radical SAM Enzyme: 7-Carboxy-7-deazaguanine Synthase from B. multivorans. Theoretical Insights into the Reaction Mechanism and the Influence of Metal Ions

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