Two Fe-S Clusters Catalyze Sulfur Insertion by Radical-SAM Methylthiotransferases

Overview

Journal Nat Chem Biol

Specialties Biochemistry
Biology
Chemistry

Date 2013 Apr 2

PMID 23542644

Citations 56

Authors

Farhad Forouhar

Simon Arragain

Mohamed Atta

Serge Gambarelli

Jean-Marie Mouesca

Munif Hussain

Rong Xiao

Sylvie Kieffer-Jaquinod

Jayaraman Seetharaman

Thomas B Acton

Gaetano T Montelione

Etienne Mulliez

John F Hunt

Marc Fontecave

Affiliations

Soon will be listed here.

Abstract

How living organisms create carbon-sulfur bonds during the biosynthesis of critical sulfur-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 subgroup of radical-S-adenosylmethionine (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 what is to our knowledge the first evidence that these enzymes are true catalysts and support a new sulfation mechanism involving activation of an exogenous sulfur cosubstrate at an exchangeable coordination site on the second cluster, which remains intact during the reaction.

Citing Articles

Radical -Adenosylmethionine Sulfurtransferase MybB Catalyzed Formation of the 4-Thiazolidinone Core in Mycobacidin Represents an Intersection between Primary and Secondary Metabolism.

Zhao H, Bu J, Liu H J Am Chem Soc. 2025; 147(5):4180-4187.

PMID: 39853311 PMC: 11826332. DOI: 10.1021/jacs.4c13760.

Alternate routes to mnmsU synthesis in Gram-positive bacteria.

Jaroch M, Sun G, Tsui H, Reed C, Sun J, Jorg M J Bacteriol. 2024; 206(4):e0045223.

PMID: 38551342 PMC: 11025329. DOI: 10.1128/jb.00452-23.

Discovery of a Biotin Synthase That Utilizes an Auxiliary 4Fe-5S Cluster for Sulfur Insertion.

Lachowicz J, Lennox-Hvenekilde D, Myling-Petersen N, Salomonsen B, Verkleij G, Acevedo-Rocha C J Am Chem Soc. 2024; 146(3):1860-1873.

PMID: 38215281 PMC: 10813225. DOI: 10.1021/jacs.3c05481.

Structure-based insights into the mechanism of [4Fe-4S]-dependent sulfur insertase LarE.

Zecchin P, Pecqueur L, Oltmanns J, Velours C, Schunemann V, Fontecave M Protein Sci. 2023; 33(2):e4874.

PMID: 38100250 PMC: 10806937. DOI: 10.1002/pro.4874.

Biochemical and genetic studies define the functions of methylthiotransferases in methanogenic and methanotrophic archaea.

Boswinkle K, Dinh T, Allen K Front Microbiol. 2023; 14:1304671.

PMID: 38075885 PMC: 10702137. DOI: 10.3389/fmicb.2023.1304671.

References

Frey P, Hegeman A, Ruzicka F . The Radical SAM Superfamily. Crit Rev Biochem Mol Biol. 2008; 43(1):63-88. DOI: 10.1080/10409230701829169. View

Sofia H, Chen G, Hetzler B, MILLER N . Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic Acids Res. 2001; 29(5):1097-106. PMC: 29726. DOI: 10.1093/nar/29.5.1097. View

Otwinowski Z, Minor W . Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997; 276:307-26. DOI: 10.1016/S0076-6879(97)76066-X. View

Duschene K, Veneziano S, Silver S, Broderick J . Control of radical chemistry in the AdoMet radical enzymes. Curr Opin Chem Biol. 2009; 13(1):74-83. PMC: 2703739. DOI: 10.1016/j.cbpa.2009.01.022. View

Porter S, Wadhams G, Armitage J . Signal processing in complex chemotaxis pathways. Nat Rev Microbiol. 2011; 9(3):153-65. DOI: 10.1038/nrmicro2505. View

Tse Sum Bui B, Mattioli T, Florentin D, Bolbach G, Marquet A . Escherichia coli biotin synthase produces selenobiotin. Further evidence of the involvement of the [2Fe-2S]2+ cluster in the sulfur insertion step. Biochemistry. 2006; 45(11):3824-34. DOI: 10.1021/bi052388m. View

Atta M, Mulliez E, Arragain S, Forouhar F, Hunt J, Fontecave M . S-Adenosylmethionine-dependent radical-based modification of biological macromolecules. Curr Opin Struct Biol. 2010; 20(6):684-92. DOI: 10.1016/j.sbi.2010.09.009. View

Zhang Q, Liu W . Complex biotransformations catalyzed by radical S-adenosylmethionine enzymes. J Biol Chem. 2011; 286(35):30245-30252. PMC: 3162382. DOI: 10.1074/jbc.R111.272690. View

Lees N, Hanzelmann P, Hernandez H, Subramanian S, Schindelin H, Johnson M . ENDOR spectroscopy shows that guanine N1 binds to [4Fe-4S] cluster II of the S-adenosylmethionine-dependent enzyme MoaA: mechanistic implications. J Am Chem Soc. 2009; 131(26):9184-5. PMC: 2757093. DOI: 10.1021/ja903978u. View

10.

Arragain S, Garcia-Serres R, Blondin G, Douki T, Clemancey M, Latour J . Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase. J Biol Chem. 2009; 285(8):5792-801. PMC: 2820805. DOI: 10.1074/jbc.M109.065516. View

11.

Booker S, Cicchillo R, Grove T . Self-sacrifice in radical S-adenosylmethionine proteins. Curr Opin Chem Biol. 2007; 11(5):543-52. PMC: 2637762. DOI: 10.1016/j.cbpa.2007.08.028. View

12.

Holm L, Rosenstrom P . Dali server: conservation mapping in 3D. Nucleic Acids Res. 2010; 38(Web Server issue):W545-9. PMC: 2896194. DOI: 10.1093/nar/gkq366. View

13.

BEINERT H . Semi-micro methods for analysis of labile sulfide and of labile sulfide plus sulfane sulfur in unusually stable iron-sulfur proteins. Anal Biochem. 1983; 131(2):373-8. DOI: 10.1016/0003-2697(83)90186-0. View

14.

McRee D . XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density. J Struct Biol. 1999; 125(2-3):156-65. DOI: 10.1006/jsbi.1999.4094. View

15.

Pierrel F, Douki T, Fontecave M, Atta M . MiaB protein is a bifunctional radical-S-adenosylmethionine enzyme involved in thiolation and methylation of tRNA. J Biol Chem. 2004; 279(46):47555-63. DOI: 10.1074/jbc.M408562200. View

16.

Petrey D, Honig B . GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol. 2003; 374:492-509. DOI: 10.1016/S0076-6879(03)74021-X. View

17.

Lee K, Saleh L, Anton B, Madinger C, Benner J, Iwig D . Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily. Biochemistry. 2009; 48(42):10162-74. PMC: 2952840. DOI: 10.1021/bi900939w. View

18.

Doublie S, Kapp U, Aberg A, Brown K, Strub K, Cusack S . Crystallization and preliminary X-ray analysis of the 9 kDa protein of the mouse signal recognition particle and the selenomethionyl-SRP9. FEBS Lett. 1996; 384(3):219-21. DOI: 10.1016/0014-5793(96)00316-x. View

19.

Fontecave M, Ollagnier-de-Choudens S, Mulliez E . Biological radical sulfur insertion reactions. Chem Rev. 2003; 103(6):2149-66. DOI: 10.1021/cr020427j. View

20.

Vey J, Drennan C . Structural insights into radical generation by the radical SAM superfamily. Chem Rev. 2011; 111(4):2487-506. PMC: 5930932. DOI: 10.1021/cr9002616. View