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Saccharomyces cerevisiae Eukaryotic Elongation Factor 1A (eEF1A) Is Methylated at Lys-390 by a METTL21-Like Methyltransferase.

Jakobsson ME, Davydova E, Małecki J, Moen A, Falnes PØ - PLoS ONE (2015)

Bottom Line: Despite being most similar to METTL21A, the Ynl024c protein does not methylate yeast Hsp70 proteins, which were found to be unmethylated on the relevant lysine residue.Eukaryotic translation elongation factor eEF1A in yeast has been reported to contain four methylated lysine residues (Lys30, Lys79, Lys318 and Lys390), and we here show that the YNL024C gene is required for methylation of eEF1A at Lys390, the only of these methylations for which the responsible MTase has not yet been identified.Our results demonstrate that Ynl024c is the enzyme responsible for methylation of eEF1A at Lys390, and in accordance with prior naming of similar enzymes, we suggest that Ynl024c is renamed to Efm6 (Elongation factor MTase 6).

View Article: PubMed Central - PubMed

Affiliation: Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0316, Norway.

ABSTRACT
The human methyltransferases (MTases) METTL21A and VCP-KMT (METTL21D) were recently shown to methylate single lysine residues in Hsp70 proteins and in VCP, respectively. The yet uncharacterized MTase encoded by the YNL024C gene in Saccharomyces cerevisiae shows high sequence similarity to METTL21A and VCP-KMT, as well as to their uncharacterized paralogues METTL21B and METTL21C. Despite being most similar to METTL21A, the Ynl024c protein does not methylate yeast Hsp70 proteins, which were found to be unmethylated on the relevant lysine residue. Eukaryotic translation elongation factor eEF1A in yeast has been reported to contain four methylated lysine residues (Lys30, Lys79, Lys318 and Lys390), and we here show that the YNL024C gene is required for methylation of eEF1A at Lys390, the only of these methylations for which the responsible MTase has not yet been identified. Lys390 was found in a partially monomethylated state in wild-type yeast cells but was exclusively unmethylated in a ynl024cΔ strain, and over-expression of Ynl024c caused a dramatic increase in Lys390 methylation, with trimethylation becoming the predominant state. Our results demonstrate that Ynl024c is the enzyme responsible for methylation of eEF1A at Lys390, and in accordance with prior naming of similar enzymes, we suggest that Ynl024c is renamed to Efm6 (Elongation factor MTase 6).

No MeSH data available.


Related in: MedlinePlus

Sequence analysis and structural modelling of Ynl024c.(A) Topology diagram of the canonical 7BS MTase fold. Arrows and rectangles indicate β-strands and α-helices, respectively. The seven β-strands are designated “1–7”, the α-helices connecting them “A-F”, and the secondary structure elements preceding the 7BS-fold denoted “Z”. B, Protein sequence alignment of Ynl024c and human METTL21 proteins. Motifs “I”, “Post I” and “II”, which are shared by all 7BS MTases, as well as the DXXY motif, a hallmark of MTF16, are indicated by boxes. Above the alignment are indicated the secondary structure elements from the solved crystal structures of VCP-KMT (red; pdb 4LG1), METTL21A (green; pdb 4LEC), METTL21B (blue; pdb 4QPN) and METTL21C (orange; pdb 4MTL), a predicted Ynl024c structure (black; see also (C)), as well as a secondary structure prediction for Ynl024c, performed with Jpred 3 (dashed, black). β-strands and α-helices are indicated by arrows and thick lines, respectively, and the numbering/lettering of these are as outlined in A). Asterisks indicate conserved active site residues represented in (D). (C) Predicted structural model of Ynl024c. The model was generated by one-to-one threading with Phyre2, using METTL21A as a template. (D) localization of putatively important catalytic residues (green) in the active site of the Ynl024c structural model. AdoMet is shown in purple. The shown residues are indicated by asterisk in the sequence alignment in (B). (E) Structural alignment of human VCP-KMT, METTL21A, METTL21B and METTL21C (Color code as in (B)).
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pone.0131426.g001: Sequence analysis and structural modelling of Ynl024c.(A) Topology diagram of the canonical 7BS MTase fold. Arrows and rectangles indicate β-strands and α-helices, respectively. The seven β-strands are designated “1–7”, the α-helices connecting them “A-F”, and the secondary structure elements preceding the 7BS-fold denoted “Z”. B, Protein sequence alignment of Ynl024c and human METTL21 proteins. Motifs “I”, “Post I” and “II”, which are shared by all 7BS MTases, as well as the DXXY motif, a hallmark of MTF16, are indicated by boxes. Above the alignment are indicated the secondary structure elements from the solved crystal structures of VCP-KMT (red; pdb 4LG1), METTL21A (green; pdb 4LEC), METTL21B (blue; pdb 4QPN) and METTL21C (orange; pdb 4MTL), a predicted Ynl024c structure (black; see also (C)), as well as a secondary structure prediction for Ynl024c, performed with Jpred 3 (dashed, black). β-strands and α-helices are indicated by arrows and thick lines, respectively, and the numbering/lettering of these are as outlined in A). Asterisks indicate conserved active site residues represented in (D). (C) Predicted structural model of Ynl024c. The model was generated by one-to-one threading with Phyre2, using METTL21A as a template. (D) localization of putatively important catalytic residues (green) in the active site of the Ynl024c structural model. AdoMet is shown in purple. The shown residues are indicated by asterisk in the sequence alignment in (B). (E) Structural alignment of human VCP-KMT, METTL21A, METTL21B and METTL21C (Color code as in (B)).

Mentions: The 7BS MTases show an archetypical topology (Fig 1A) and several characteristic sequence motifs. An alignment of Ynl024c with the human METTL21 proteins clearly demonstrates that Ynl024c harbours hallmark conserved motifs found in 7BS MTases, i. e. Motif I, Motif post I and Motif II (Fig 1B). Similar to other MTF16 members, Ynl024c possesses the characteristic DXXY [(D/E)-X-X-(Y/F)] motif located downstream of Motif II (Fig 1B).


Saccharomyces cerevisiae Eukaryotic Elongation Factor 1A (eEF1A) Is Methylated at Lys-390 by a METTL21-Like Methyltransferase.

Jakobsson ME, Davydova E, Małecki J, Moen A, Falnes PØ - PLoS ONE (2015)

Sequence analysis and structural modelling of Ynl024c.(A) Topology diagram of the canonical 7BS MTase fold. Arrows and rectangles indicate β-strands and α-helices, respectively. The seven β-strands are designated “1–7”, the α-helices connecting them “A-F”, and the secondary structure elements preceding the 7BS-fold denoted “Z”. B, Protein sequence alignment of Ynl024c and human METTL21 proteins. Motifs “I”, “Post I” and “II”, which are shared by all 7BS MTases, as well as the DXXY motif, a hallmark of MTF16, are indicated by boxes. Above the alignment are indicated the secondary structure elements from the solved crystal structures of VCP-KMT (red; pdb 4LG1), METTL21A (green; pdb 4LEC), METTL21B (blue; pdb 4QPN) and METTL21C (orange; pdb 4MTL), a predicted Ynl024c structure (black; see also (C)), as well as a secondary structure prediction for Ynl024c, performed with Jpred 3 (dashed, black). β-strands and α-helices are indicated by arrows and thick lines, respectively, and the numbering/lettering of these are as outlined in A). Asterisks indicate conserved active site residues represented in (D). (C) Predicted structural model of Ynl024c. The model was generated by one-to-one threading with Phyre2, using METTL21A as a template. (D) localization of putatively important catalytic residues (green) in the active site of the Ynl024c structural model. AdoMet is shown in purple. The shown residues are indicated by asterisk in the sequence alignment in (B). (E) Structural alignment of human VCP-KMT, METTL21A, METTL21B and METTL21C (Color code as in (B)).
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4482628&req=5

pone.0131426.g001: Sequence analysis and structural modelling of Ynl024c.(A) Topology diagram of the canonical 7BS MTase fold. Arrows and rectangles indicate β-strands and α-helices, respectively. The seven β-strands are designated “1–7”, the α-helices connecting them “A-F”, and the secondary structure elements preceding the 7BS-fold denoted “Z”. B, Protein sequence alignment of Ynl024c and human METTL21 proteins. Motifs “I”, “Post I” and “II”, which are shared by all 7BS MTases, as well as the DXXY motif, a hallmark of MTF16, are indicated by boxes. Above the alignment are indicated the secondary structure elements from the solved crystal structures of VCP-KMT (red; pdb 4LG1), METTL21A (green; pdb 4LEC), METTL21B (blue; pdb 4QPN) and METTL21C (orange; pdb 4MTL), a predicted Ynl024c structure (black; see also (C)), as well as a secondary structure prediction for Ynl024c, performed with Jpred 3 (dashed, black). β-strands and α-helices are indicated by arrows and thick lines, respectively, and the numbering/lettering of these are as outlined in A). Asterisks indicate conserved active site residues represented in (D). (C) Predicted structural model of Ynl024c. The model was generated by one-to-one threading with Phyre2, using METTL21A as a template. (D) localization of putatively important catalytic residues (green) in the active site of the Ynl024c structural model. AdoMet is shown in purple. The shown residues are indicated by asterisk in the sequence alignment in (B). (E) Structural alignment of human VCP-KMT, METTL21A, METTL21B and METTL21C (Color code as in (B)).
Mentions: The 7BS MTases show an archetypical topology (Fig 1A) and several characteristic sequence motifs. An alignment of Ynl024c with the human METTL21 proteins clearly demonstrates that Ynl024c harbours hallmark conserved motifs found in 7BS MTases, i. e. Motif I, Motif post I and Motif II (Fig 1B). Similar to other MTF16 members, Ynl024c possesses the characteristic DXXY [(D/E)-X-X-(Y/F)] motif located downstream of Motif II (Fig 1B).

Bottom Line: Despite being most similar to METTL21A, the Ynl024c protein does not methylate yeast Hsp70 proteins, which were found to be unmethylated on the relevant lysine residue.Eukaryotic translation elongation factor eEF1A in yeast has been reported to contain four methylated lysine residues (Lys30, Lys79, Lys318 and Lys390), and we here show that the YNL024C gene is required for methylation of eEF1A at Lys390, the only of these methylations for which the responsible MTase has not yet been identified.Our results demonstrate that Ynl024c is the enzyme responsible for methylation of eEF1A at Lys390, and in accordance with prior naming of similar enzymes, we suggest that Ynl024c is renamed to Efm6 (Elongation factor MTase 6).

View Article: PubMed Central - PubMed

Affiliation: Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0316, Norway.

ABSTRACT
The human methyltransferases (MTases) METTL21A and VCP-KMT (METTL21D) were recently shown to methylate single lysine residues in Hsp70 proteins and in VCP, respectively. The yet uncharacterized MTase encoded by the YNL024C gene in Saccharomyces cerevisiae shows high sequence similarity to METTL21A and VCP-KMT, as well as to their uncharacterized paralogues METTL21B and METTL21C. Despite being most similar to METTL21A, the Ynl024c protein does not methylate yeast Hsp70 proteins, which were found to be unmethylated on the relevant lysine residue. Eukaryotic translation elongation factor eEF1A in yeast has been reported to contain four methylated lysine residues (Lys30, Lys79, Lys318 and Lys390), and we here show that the YNL024C gene is required for methylation of eEF1A at Lys390, the only of these methylations for which the responsible MTase has not yet been identified. Lys390 was found in a partially monomethylated state in wild-type yeast cells but was exclusively unmethylated in a ynl024cΔ strain, and over-expression of Ynl024c caused a dramatic increase in Lys390 methylation, with trimethylation becoming the predominant state. Our results demonstrate that Ynl024c is the enzyme responsible for methylation of eEF1A at Lys390, and in accordance with prior naming of similar enzymes, we suggest that Ynl024c is renamed to Efm6 (Elongation factor MTase 6).

No MeSH data available.


Related in: MedlinePlus