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Literature summary extracted from

  • Noma, A.; Yi, S.; Katoh, T.; Takai, Y.; Suzuki, T.; Suzuki, T.
    Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae (2011), RNA, 17, 1111-1119.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.1.1.B109 gene ABP140 or TRM140, DNA and amino acid sequence determination and analysis, expression of His6-tagged wild-type in Saccharomyces cerevisiae, expression of deletion mutant delD602-Q621 in the abp140DELTA null mutant strain Saccharomyces cerevisiae
2.1.1.268 expression of hexahistidine-tagged Abp140p in Saccharomces cerevisiae Saccharomyces cerevisiae

Protein Variants

EC Number Protein Variants Comment Organism
2.1.1.B109 D466A site-directed mutagenesis, inactive mutant Saccharomyces cerevisiae
2.1.1.B109 D547A site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type Saccharomyces cerevisiae
2.1.1.B109 F481A site-directed mutagenesis, the mutant shows unaltered activity compared to the wild-type Saccharomyces cerevisiae
2.1.1.B109 K559A site-directed mutagenesis, the mutant shows unaltered activity compared to the wild-type Saccharomyces cerevisiae
2.1.1.B109 additional information deletion of the conserved region near the C-terminus, i.e. delD602-Q621 and construction of the abp140DELTA knockout strain, expression of delD602-Q621 in the null mutant strain. Complementation of the yor239wD strain with plasmid-encoded ABP140 containing various mutations, in vitro reconstitution of m3C32 by recombinant Trm140p Saccharomyces cerevisiae
2.1.1.B109 additional information short-hairpin(sh)RNA knockdown of METTL2B mRNA in HeLa cells Homo sapiens
2.1.1.B109 Y569A site-directed mutagenesis, the mutant shows unaltered activity compared to the wild-type Saccharomyces cerevisiae
2.1.1.268 D466A no formation of N3-methylcytosine32 Saccharomyces cerevisiae
2.1.1.268 D547A decreased activity Saccharomyces cerevisiae
2.1.1.268 delD602-Q621 no formation of N3-methylcytosine32 Saccharomyces cerevisiae

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
2.1.1.B109 actin filament subcellular localization of Abp140p to actin filaments Saccharomyces cerevisiae 5884
-
2.1.1.268 actin filament subcellular localization of ABP140 to actin filaments is not involved in tRNA modification Saccharomyces cerevisiae 5884
-

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
2.1.1.B109 71500
-
 2 * 71500, about, sequence calculation Saccharomyces cerevisiae
2.1.1.B109 150000
-
 about, recombinant His6-tagged wild-type Abp140p, native PAGE Saccharomyces cerevisiae
2.1.1.268 71486
-
 2 * 71486, the homodimer is formed through covalent linkage(s) other than disulfide bond, calculated from sequence, SDS-PAGE Saccharomyces cerevisiae
2.1.1.268 71500
-
 2 * 71500, the homodimer is formed through covalent linkage(s) other than disulfide bond, SDS-PAGE Saccharomyces cerevisiae

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.1.1.B109 S-adenosyl-L-methionine + cytosine32 in tRNASer/Thr Saccharomyces cerevisiae
-
 S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNASer/Thr
-
 ?
2.1.1.B109 S-adenosyl-L-methionine + cytosine32 in tRNASer/Thr Homo sapiens
-
 S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNASer/Thr
-
 ?
2.1.1.B109 S-adenosyl-L-methionine + cytosine32 in tRNASer/Thr Saccharomyces cerevisiae BY4742
-
 S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNASer/Thr
-
 ?
2.1.1.268 S-adenosyl-L-methionine + cytosine32 in tRNA1Ser Saccharomyces cerevisiae tRNASer1 = tRNASer(UGA). Because position 32 of tRNA has an important role in accurate codon recognition, N3-methylcytosine32 formation in tRNAThr1 or tRNASer1 might play a role in modulating codon recognition and translational efficiency S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNA1Ser
-
 ?
2.1.1.268 S-adenosyl-L-methionine + cytosine32 in tRNA1Thr Saccharomyces cerevisiae tRNAThr1 = tRNAThr(IGU). Because position 32 of tRNA has an important role in accurate codon recognition, N3-methylcytosine32 formation in tRNAThr1 or tRNASer1 might play a role in modulating codon recognition and translational efficiency S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNA1Thr
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.1.1.B109 Homo sapiens Q6P1Q9 gene TRM140
-
2.1.1.B109 Saccharomyces cerevisiae
-
 gene ABP140 or TRM140
-
2.1.1.B109 Saccharomyces cerevisiae BY4742
-
 gene ABP140 or TRM140
-
2.1.1.268 Homo sapiens Q6P1Q9
-
-
2.1.1.268 Saccharomyces cerevisiae Q08641
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.1.1.B109 recombinant Abp140p from Saccharoymces cerevisiae by nickel affinity chromatography and dialysis Saccharomyces cerevisiae
2.1.1.268
-
 Saccharomyces cerevisiae

Reaction

EC Number Reaction Comment Organism Reaction ID
2.1.1.B109 S-adenosyl-L-methionine + cytosine32 in tRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytosine32 in tRNA the actin-binding protein ABP140 is responsible for m3C formation in both tRNAThr1 Homo sapiens
a
2.1.1.B109 S-adenosyl-L-methionine + cytosine32 in tRNA = S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNA the actin-binding protein ABP140 is responsible for m3C formation in both tRNAThr1, and is also active with tRNASer1. In Saccharomyces cerevisiae, 3-methylcytidine is found at position 32 of the tRNAs for Thr and Ser Saccharomyces cerevisiae
a
2.1.1.268 S-adenosyl-L-methionine + cytosine32 in tRNASer = S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNASer (2) Saccharomyces cerevisiae
a
2.1.1.268 S-adenosyl-L-methionine + cytosine32 in tRNAThr = S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNAThr (1) Saccharomyces cerevisiae
a

Source Tissue

EC Number Source Tissue Comment Organism Textmining
2.1.1.268 HeLa cell
-
 Homo sapiens
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.1.1.B109 additional information secondary structures of Saccharomyces cerevisiae tRNAThr1 and tRNASer1 with modified nucleosides, including 3-methylcytidine, overview Saccharomyces cerevisiae ?
-
 ?
2.1.1.B109 additional information secondary structures of Saccharomyces cerevisiae tRNAThr1 and tRNASer1 with modified nucleosides, including 3-methylcytidine, overview Saccharomyces cerevisiae BY4742 ?
-
 ?
2.1.1.B109 S-adenosyl-L-methionine + cytosine32 in tRNASer/Thr
-
 Saccharomyces cerevisiae S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNASer/Thr
-
 ?
2.1.1.B109 S-adenosyl-L-methionine + cytosine32 in tRNASer/Thr
-
 Homo sapiens S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNASer/Thr
-
 ?
2.1.1.B109 S-adenosyl-L-methionine + cytosine32 in tRNASer/Thr tRNASer1 is not methylated by Abp140p under the same condition as the methylation of tRNAThr1 in vitro, overview. Some essential factor(s) is required for m3C formation in tRNASer1 Saccharomyces cerevisiae S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNASer/Thr mass spectrometric analysis of tRNA products ?
2.1.1.B109 S-adenosyl-L-methionine + cytosine32 in tRNASer/Thr
-
 Saccharomyces cerevisiae BY4742 S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNASer/Thr
-
 ?
2.1.1.B109 S-adenosyl-L-methionine + cytosine32 in tRNASer/Thr tRNASer1 is not methylated by Abp140p under the same condition as the methylation of tRNAThr1 in vitro, overview. Some essential factor(s) is required for m3C formation in tRNASer1 Saccharomyces cerevisiae BY4742 S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNASer/Thr mass spectrometric analysis of tRNA products ?
2.1.1.268 S-adenosyl-L-methionine + cytosine32 in tRNA1Ser tRNASer1 = tRNASer(UGA). Because position 32 of tRNA has an important role in accurate codon recognition, N3-methylcytosine32 formation in tRNAThr1 or tRNASer1 might play a role in modulating codon recognition and translational efficiency Saccharomyces cerevisiae S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNA1Ser
-
 ?
2.1.1.268 S-adenosyl-L-methionine + cytosine32 in tRNA1Ser tRNAThr1 = tRNAThr(IGU). ABP140 is identified as the protein responsible for N3-methylcytosine32 formation in both tRNAThr1 and tRNASer1 by systematic reverse genetic approach combined with mass spectrometry (ribonucleome analysis). N3-Methylcytosine32 formation in tRNAThr1 can be reconstituted using recombinant Abp140p in the presence of S-adenosyl-L-methionine, whereas N3-methylcytosine32 does not form in tRNASer1 in vitro, indicating the absence of a factor(s) required for tRNASer1 N3-methylcytosine32 formation Saccharomyces cerevisiae S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNA1Ser
-
 ?
2.1.1.268 S-adenosyl-L-methionine + cytosine32 in tRNA1Thr tRNAThr1 = tRNAThr(IGU). Because position 32 of tRNA has an important role in accurate codon recognition, N3-methylcytosine32 formation in tRNAThr1 or tRNASer1 might play a role in modulating codon recognition and translational efficiency Saccharomyces cerevisiae S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNA1Thr
-
 ?
2.1.1.268 S-adenosyl-L-methionine + cytosine32 in tRNA1Thr tRNAThr1 = tRNAThr(IGU). ABP140 is identified as the protein responsible for N3-methylcytosine32 formation in both tRNAThr1 and tRNASer1 by systematic reverse genetic approach combined with mass spectrometry (ribonucleome analysis). N3-Methylcytosine32 formation in tRNAThr1 can be reconstituted using recombinant Abp140p in the presence of S-adenosyl-L-methionine, whereas N3-methylcytosine32 does not form in tRNASer1 in vitro, indicating the absence of a factor(s) required for tRNASer1 N3-methylcytosine32 formation Saccharomyces cerevisiae S-adenosyl-L-homocysteine + N3-methylcytosine32 in tRNA1Thr
-
 ?

Subunits

EC Number Subunits Comment Organism
2.1.1.B109 homodimer 2 * 71500, about, sequence calculation Saccharomyces cerevisiae
2.1.1.B109 More ABP140 consists of an N-terminal actin-binding motif, a +1 frameshift site, and the C-terminal Ado-Met binding motif. The homodimer is formed through covalent linkage(s) other than disulfide bond Saccharomyces cerevisiae
2.1.1.B109 More ABP140 consists of an N-terminal actin-binding sequence and a C-terminal S-adenosylmethionine binding motif Homo sapiens
2.1.1.268 dimer 2 * 71486, the homodimer is formed through covalent linkage(s) other than disulfide bond, calculated from sequence, SDS-PAGE Saccharomyces cerevisiae
2.1.1.268 dimer 2 * 71500, the homodimer is formed through covalent linkage(s) other than disulfide bond, SDS-PAGE Saccharomyces cerevisiae

Synonyms

EC Number Synonyms Comment Organism
2.1.1.B109 Abp140p
-
 Saccharomyces cerevisiae
2.1.1.B109 Abp140p
-
 Homo sapiens
2.1.1.B109 methyltransferase-like protein 2B
-
 Homo sapiens
2.1.1.B109 METTL2B
-
 Homo sapiens
2.1.1.B109 Trm140p
-
 Saccharomyces cerevisiae
2.1.1.B109 Trm140p
-
 Homo sapiens
2.1.1.268 ABP140
-
 Saccharomyces cerevisiae
2.1.1.268 METTL2B
-
 Homo sapiens

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.1.1.B109 30
-
 assay at Saccharomyces cerevisiae
2.1.1.268 30
-
 assay at Saccharomyces cerevisiae

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.1.1.B109 8
-
 assay at Saccharomyces cerevisiae
2.1.1.268 8
-
 assay at Saccharomyces cerevisiae

Cofactor

EC Number Cofactor Comment Organism Structure
2.1.1.B109 S-adenosyl-L-methionine
-
 Homo sapiens
2.1.1.B109 S-adenosyl-L-methionine the conserved S-adenosyl-L-methionine binding motif in ABP140 is required for m3C formation Saccharomyces cerevisiae

General Information

EC Number General Information Comment Organism
2.1.1.B109 malfunction deletion of the actin-binding sequence in ABP140 does not affect m3C formation. The yor240wDELTA strain, lacking the half of gene ABP140, hatbors tRNAs Ser and Thr that are not m3C methylated, mass spectrometric aanalysis Saccharomyces cerevisiae
2.1.1.B109 malfunction specific reduction of m3C formation in HeLa cells by siRNA-mediated knockdown of the human orthologue of TRM14 Homo sapiens
2.1.1.B109 additional information some partner proteins of METTL2B might be required to reconstitute m3C formation in tRNAs Homo sapiens
2.1.1.B109 additional information subcellular localization of ABP140 to actin filaments is not involved in tRNA modification Saccharomyces cerevisiae
2.1.1.B109 physiological function methyl modification of m3C32 might modulate accurate codon recognition at the A-site and the proper ribosomal positioning at the P-site. Abp140p interacts with filamentous actin and has an activity to cross-link F-actin into a bundle in vitro. In the cell, Abp140p colocalizes with cortical actin patches and cytoplasmic actin filaments, but it is not required for cell growth or organization of F-actin Saccharomyces cerevisiae
2.1.1.268 malfunction N3-methylcytosine32 modification is absent in strains that lack the entire ABP140 gene Saccharomyces cerevisiae
2.1.1.268 malfunction specific reduction of N3-methylcytosine formation in HeLa cells by siRNA-mediated knock down of METTL2B Homo sapiens
2.1.1.268 physiological function N3-methylcytosine32 formation in tRNAThr1 or tRNASer1 might play a role in modulating codon recognition and translational efficiency Saccharomyces cerevisiae