Deep Knot Structure for Construction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme

Nureki, Osamu; Watanabe, Kazunori; Fukai, Shuya; Ishii, Ryohei; Endo, Yaeta; Hori, Hiroyuki; Yokoyama, Shigeyuki

doi:10.1016/j.str.2004.03.003

Cited by 115 publications

(188 citation statements)

References 30 publications

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“…Dimerization is consistent with other SPOUT methyltransferase crystal structures, although in some cases (e.g., RrmA and RsmE) the monomers are nearly perpendicular instead of being antiparallel. Dimerization is thought to be important for methyltransferase function as the knotted topology alone is not sufficient for maintaining the active conformation of the cofactor and substrate binding site (Nureki et al 2004;Mallam and Jackson 2007a,b).…”

Section: Discussionmentioning

confidence: 99%

Identification of pseudouridine methyltransferase in Escherichia coli

Ero¹,

Peil²,

Liiv³

et al. 2008

RNA

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In ribosomal RNA, modified nucleosides are found in functionally important regions, but their function is obscure. Stem-loop 69 of Escherichia coli 23S rRNA contains three modified nucleosides: pseudouridines at positions 1911 and 1917, and N3 methylpseudouridine (m 3 C) at position 1915. The gene for pseudouridine methyltransferase was previously not known. We identified E. coli protein YbeA as the methyltransferase methylating C1915 in 23S rRNA. The E. coli ybeA gene deletion strain lacks the N3 methylation at position 1915 of 23S rRNA as revealed by primer extension and nucleoside analysis by HPLC. Methylation at position 1915 is restored in the ybeA deletion strain when recombinant YbeA protein is expressed from a plasmid. In addition, we show that purified YbeA protein is able to methylate pseudouridine in vitro using 70S ribosomes but not 50S subunits from the ybeA deletion strain as substrate. Pseudouridine is the preferred substrate as revealed by the inability of YbeA to methylate uridine at position 1915. This shows that YbeA is acting at the final stage during ribosome assembly, probably during translation initiation. Hereby, we propose to rename the YbeA protein to RlmH according to uniform nomenclature of RNA methyltransferases. RlmH belongs to the SPOUT superfamily of methyltransferases. RlmH was found to be well conserved in bacteria, and the gene is present in plant and in several archaeal genomes. RlmH is the first pseudouridine specific methyltransferase identified so far and is likely to be the only one existing in bacteria, as m 3 C1915 is the only methylated pseudouridine in bacteria described to date.

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Section: Discussionmentioning

confidence: 99%

Identification of pseudouridine methyltransferase in Escherichia coli

Ero¹,

Peil²,

Liiv³

et al. 2008

RNA

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“…Several crystal structures of SPOUT MTases have been determined (Ahn et al 2003;Elkins et al 2003;Lim et al 2003;Nureki et al 2004;Liu et al 2013;Shao et al 2013). The SPOUT class MTases are characterized by an N-terminal Rossmanoidal α/β fold fused to a C-terminal topological knot.…”

Section: Introductionmentioning

confidence: 99%

Characterization of two homologous 2′-O-methyltransferases showing different specificities for their tRNA substrates

Somme

Laer

Roovers³

et al. 2014

RNA

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The 2 ′ -O-methylation of the nucleoside at position 32 of tRNA is found in organisms belonging to the three domains of life. Unrelated enzymes catalyzing this modification in Bacteria (TrmJ) and Eukarya (Trm7) have already been identified, but until now, no information is available for the archaeal enzyme. In this work we have identified the methyltransferase of the archaeon Sulfolobus acidocaldarius responsible for the 2 ′ -O-methylation at position 32. This enzyme is a homolog of the bacterial TrmJ. Remarkably, both enzymes have different specificities for the nature of the nucleoside at position 32. While the four canonical nucleosides are substrates of the Escherichia coli enzyme, the archaeal TrmJ can only methylate the ribose of a cytidine. Moreover, the two enzymes recognize their tRNA substrates in a different way. We have solved the crystal structure of the catalytic domain of both enzymes to gain better understanding of these differences at a molecular level.

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“…Also, by focusing on the m 1 G37 reaction, kinetic analysis can identify AdoMet analogs that specifically inhibit the reaction, rather than those that inhibit other AdoMet-dependent reactions. For example, analogs that target TrmD can be separated by cross-reactivity analysis from those that target TrmH (Nureki et al 2004) and TrmL (Benítez-Páez et al 2010), which adopt the same trefoil-knot structure as in TrmD but synthesize Gm18 and Um34 on tRNA, respectively.…”

Section: Introductionmentioning

confidence: 99%

Differentiating analogous tRNA methyltransferases by fragments of the methyl donor

Lahoud¹,

Goto-Ito²,

Yoshida³

et al. 2011

RNA

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Bacterial TrmD and eukaryotic-archaeal Trm5 form a pair of analogous tRNA methyltransferase that catalyze methyl transfer from S-adenosyl methionine (AdoMet) to N 1 of G37, using catalytic motifs that share no sequence or structural homology. Here we show that natural and synthetic analogs of AdoMet are unable to distinguish TrmD from Trm5. Instead, fragments of AdoMet, adenosine and methionine, are selectively inhibitory of TrmD rather than Trm5. Detailed structural information of the two enzymes in complex with adenosine reveals how Trm5 escapes targeting by adopting an altered structure, whereas TrmD is trapped by targeting due to its rigid structure that stably accommodates the fragment. Free energy analysis exposes energetic disparities between the two enzymes in how they approach the binding of AdoMet versus fragments and provides insights into the design of inhibitors selective for TrmD.

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Deep Knot Structure for Construction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme

Cited by 115 publications

References 30 publications

Identification of pseudouridine methyltransferase in Escherichia coli

Identification of pseudouridine methyltransferase in Escherichia coli

Characterization of two homologous 2′-O-methyltransferases showing different specificities for their tRNA substrates

Differentiating analogous tRNA methyltransferases by fragments of the methyl donor

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