Functional Diversity of the Rhodanese Homology Domain

Escherichia coli has eight genes predicted to encode sulfurtransferases having the active site consensus sequence Cys-Xaa-Xaa-Gly. One of these genes, ybbB, is frequently found within bacterial operons that contain selD, the selenophosphate synthetase gene, suggesting a role in selenium metabolism. We show that ybbB is required in vivo for the specific substitution of selenium for sulfur in 2-thiouridine residues in E. coli tRNA. This modified tRNA nucleoside, 5-methylaminomethyl-2-selenouridine (mnm5se2U), is located at the wobble position of the anticodons of tRNALys, tRNAGlu, and tRNA1Gln. Nucleoside analysis of tRNAs from wild-type and ybbB mutant strains revealed that production of mnm5se2U is lost in the ybbB mutant but that 5-methylaminomethyl-2-thiouridine, the mnm5se2U precursor, is unaffected by deletion of ybbB. Thus, ybbB is not required for the initial sulfurtransferase reaction but rather encodes a 2-selenouridine synthase that replaces a sulfur atom in 2-thiouridine in tRNA with selenium. Purified 2-selenouridine synthase containing a C-terminal His6 tag exhibited spectral properties consistent with tRNA bound to the enzyme. In vitro mnm5se2U synthesis is shown to be dependent on 2-selenouridine synthase, SePO3, and tRNA. Finally, we demonstrate that the conserved Cys97 (but not Cys96) in the rhodanese sequence motif Cys96-Cys97-Xaa-Xaa-Gly is required for 2-selenouridine synthase in vivo activity. These data are consistent with the ybbB gene encoding a tRNA 2-selenouridine synthase and identifies a new role for the rhodanese homology domain in enzymes.

• Publication year

  2004

• Venue

  Journal of Biological Chemistry

• Publication date

  2004-01-16

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1074/jbc.M310442200PMID 14594807
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2001cited by this paper
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  2001cited by this paper
• Evidence for the Transfer of Sulfane Sulfur from IscS to ThiI during the in Vitro Biosynthesis of 4-Thiouridine inEscherichia coli tRNA*

  2000cited by this paper
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  2000cited by this paper
• One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

  2000cited by this paper
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  2000cited by this paper
• Evidence that multiple proteins from Salmonella typhimurium are required for the biosynthesis of 5-methylaminomethyl-2-selenouridine in tRNAs.

  2000cited by this paper
• Characterization of a 12-Kilodalton Rhodanese Encoded byglpE of Escherichia coli and Its Interaction with Thioredoxin

  2000cited by this paper
• Effect of modified nucleotides on Escherichia coli tRNAGlu structure and on its aminoacylation by glutamyl-tRNA synthetase. Predominant and distinct roles of the mnm5 and s2 modifications of U34.

  1999cited by this paper
• Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin.

  1999cited by this paper
• Thiamin biosynthesis in prokaryotes

  1999cited by this paper
• Single atom modification (O-->S) of tRNA confers ribosome binding.

  1999cited by this paper
• Crystal structure of the catalytic domain of the human cell cycle control phosphatase, Cdc25A.

  1998cited by this paper
• Aminoacylation of hypomodified tRNAGlu in vivo.

  1998cited by this paper
• Sequence Analysis of Tn10 Insertion Sites in a Collection of Escherichia coli Strains Used for Genetic Mapping and Strain Construction

  1998cited by this paper
• The modification of the wobble base of tRNAGlu modulates the translation rate of glutamic acid codons in vivo.

  1998cited by this paper
• Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements.

  1997cited by this paper
• The complete genome sequence of Escherichia coli K-12.

  1997cited by this paper
• Selenocysteine.

  1996cited by this paper
• Use of engineered thrombin cleavage site for determination of translational reading frames.

  1996cited by this paper
• Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant.

  1995cited by this paper
• A purified selenophosphate-dependent enzyme from Salmonella typhimurium catalyzes the replacement of sulfur in 2-thiouridine residues in tRNAs with selenium.

  1994cited by this paper
• Selenophosphate synthetase: Enzyme properties and catalytic reaction

  1994cited by this paper
• Selenium biochemistry--selected topics.

  1994cited by this paper
• A 2-thiouridine derivative in tRNAGlu is a positive determinant for aminoacylation by Escherichia coli glutamyl-tRNA synthetase.

  1993cited by this paper
• A superfamily of ATPases with diverse functions containing either classical or deviant ATP-binding motif.

  1993cited by this paper
• Selenium-containing tRNA(Glu) and tRNA(Lys) from Escherichia coli: purification, codon specificity and translational activity.

  1989cited by this paper
• Selenium-containing tRNA(Glu) and tRNA(Lys) from Escherichia coli: purification, codon specificity and translational activity.

  1989cited by this paper
• Biochemical and genetic analysis of Salmonella typhimurium and Escherichia coli mutants defective in specific incorporation of selenium into formate dehydrogenase and tRNAs.

  1989cited by this paper
• Isolation and characterization of a selenium metabolism mutant of Salmonella typhimurium

  1988cited by this paper
• Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes.

  1986cited by this paper
• Biosynthesis of 5-methylaminomethyl-2-selenouridine, a naturally occurring nucleoside in Escherichia coli tRNA.

  1986cited by this paper
• A selenium-containing nucleoside at the first position of the anticodon in seleno-tRNAGlu from Clostridium sticklandii.

  1985cited by this paper
• Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon.

  1985cited by this paper
• Selenium-containing transfer RNAs.

  1985cited by this paper
• Antisuppressor mutation in Escherichia coli defective in biosynthesis of 5-methylaminomethyl-2-thiouridine

  1985cited by this paper
• Specific incorporation of selenium into lysine- and glutamate- accepting tRNAs from Escherichia coli.

  1983cited by this paper
• Distantly related sequences in the alpha‐ and beta‐subunits of ATP synthase, myosin, kinases and other ATP‐requiring enzymes and a common nucleotide binding fold.

  1982cited by this paper
• Quantitative enzymatic hydrolysis of tRNAs: reversed-phase high-performance liquid chromatography of tRNA nucleosides.

  1982cited by this paper
• Cerenkov photon absorption detector for liquid chromatography : I. Preliminary experiments

  1982cited by this paper
• Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes.

  1981cited by this paper
• Reaction of selenium with sodium borohydride in protic solvents. A Facile Method for the introduction of selenium into organic molecules

  1973cited by this paper

• A Geranylated Natural Product Simamycin Disrupts the Allosteric Catalysis of tRNA-2-selenouridine Synthase SelU

  2025cites this paper
• Decoding TBCK: from bioinformatic insights of domain architecture to disease implications

  2025cites this paper
• Crystallographic analysis of the Escherichia coli tRNA seleno-modification enzyme in complex with tRNA.

  2025cites this paper
• Enzymatic strategies for selenium incorporation into biological molecules.

  2024cites this paper
• Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery

  2024cites this paper
• Proteomic and transcriptomic analysis of selenium utilization in Methanococcus maripaludis

  2024cites this paper
• Selenium metabolism and selenoproteins function in brain and encephalopathy

  2024cites this paper
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  2024cites this paper
• New biochemistry in the Rhodanese-phosphatase superfamily: emerging roles in diverse metabolic processes, nucleic acid modifications, and biological conflicts.

  2023cites this paper
• The Rhodanese PspE Converts Thiosulfate to Cellular Sulfane Sulfur in Escherichia coli

  2023cites this paper
• Organoselenium compounds. Chemistry and applications in organic synthesis.

  2023cites this paper
• 2-Selenouridine, a Modified Nucleoside of Bacterial tRNAs, Its Reactivity in the Presence of Oxidizing and Reducing Reagents

  2022cites this paper
• Escherichia coli tRNA 2-selenouridine synthase SelU selects its prenyl substrate to accomplish its enzymatic function.

  2022cites this paper
• A Novel and Prevalent Pathway in Microbial Selenium Metabolism

  2022cites this paper
• Escherichia coli tRNA 2-Selenouridine Synthase (SelU): Elucidation of Substrate Specificity to Understand the Role of S-Geranyl-tRNA in the Conversion of 2-Thio- into 2-Selenouridines in Bacterial tRNA

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  2022cites this paper
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  2021cites this paper
• Sulfur modification in natural RNA and therapeutic oligonucleotides

  2021cites this paper
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  2021cites this paper
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  2020cites this paper
• Microbial selenium metabolism: A brief history, biogeochemistry and ecophysiology.

  2020cites this paper
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  2020cites this paper
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  2020cites this paper
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  2020cites this paper
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  2020cites this paper
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  2020cites this paper
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  2019cites this paper
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  2019cites this paper
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  2019cites this paper
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  2019cites this paper
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  2019cites this paper
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• Selenoprotein synthesis and regulation in Archaea.

  2018cites this paper
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  2018cites this paper
• Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions

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  2017cites this paper
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  2017cites this paper
• Synthesis of Geranyl‐2‐Thiouridine‐Modified RNA

  2017influential citation
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  2015cites this paper
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  2015cites this paper
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• Transcriptional Response of Selenopolypeptide Genes and Selenocysteine Biosynthesis Machinery Genes in Escherichia coli during Selenite Reduction

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  2013cites this paper
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  2013cites this paper
• Discovery and biological characterization of geranylated RNA in bacteria

  2012cites this paper
• Selenomodification of tRNA in archaea requires a bipartite rhodanese enzyme

  2012influential citation
• Photoperiodic mediation of differential gene expression in Scytosiphon lomentaria (Phaeophyceae)

  2012cites this paper
• Enzymology of tRNA modification in the bacterial MnmEG pathway.

  2012cites this paper
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  2012cites this paper
• Adventures with Frameshift Supressor tRNAs

  2011cites this paper
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  2011cites this paper
• Characterization of an NADH-dependent persulfide reductase from Shewanella loihica PV-4: implications for the mechanism of sulfur respiration via FAD-dependent enzymes.

  2011cites this paper
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  2011cites this paper
• RNA Modifying Enzymes

  2010cites this paper
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  2010cites this paper
• Synthesis, Structure, Function and Biomedical Studies of Nucleic Acid Derivatized with Selenium

  2010cites this paper
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  2010cites this paper
• Genes and proteins involved in RNA modification: evolutionary genomic context and characterization of YibK and GidB Methyltransferases

  2010cites this paper
• YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors.

  2010cites this paper
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  2010cites this paper
• Characterization of a new periplasmic single-domain rhodanese encoded by a sulfur-regulated gene in a hyperthermophilic bacterium Aquifex aeolicus.

  2010cites this paper
• Comparative genomics of trace elements: emerging dynamic view of trace element utilization and function.

  2009cites this paper
• A Gripping Tale of Ribosomal Frameshifting: Extragenic Suppressors of Frameshift Mutations Spotlight P-Site Realignment

  2009cites this paper
• Selenoproteins in Archaea and Gram-positive bacteria.

  2009cites this paper
• Crystal structure of YnjE from Escherichia coli, a sulfurtransferase with three rhodanese domains

  2009cites this paper
• Synthesis, Structure and Function Studies of Selenium and Tellurium Derivatized Nucleic Acids

  2009cites this paper
• Sequence–structure–function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA

  2008cites this paper
• In silico identification of genes involved in selenium metabolism: evidence for a third selenium utilization trait

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• Biochemistry of Selenium‐Derivatized Naturally Occurring and Unnatural Nucleic Acids

  2008cites this paper
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  2008cites this paper
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  2007cites this paper
• A new sulfurtransferase from the hyperthermophilic bacterium Aquifex aeolicus

  2007cites this paper
• [The system of selenoprotein biosynthesis].

  2007cites this paper
• Identification of genes encoding tRNA modification enzymes by comparative genomics.

  2007cites this paper
• Wobble modifications and other features in transfer RNA important for decoding and reading frame maintenance

  2007cites this paper
• Common themes and variations in the rhodanese superfamily

  2007cites this paper
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  2007cites this paper
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  2007cites this paper
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  2006cites this paper