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Literature summary extracted from

  • Wurm, J.; Meyer, B.; Bahr, U.; Held, M.; Frolow, O.; Koetter, P.; Engels, J.; Heckel, A.; Karas, M.; Entian, K.; Woehnert, J.
    The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase (2010), Nucleic Acids Res., 38, 2387-2398.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.1.1.260 gene NEP1, recombinaant expression of Nep1 Methanocaldococcus jannaschii
2.1.1.260 gene NEP1, recombinant expression of His-tagged Nep1 in Escherichia coli strain M15(pREP4) Homo sapiens

Protein Variants

EC Number Protein Variants Comment Organism
2.1.1.260 D86G the mutation causes the Bowen-Conradi syndrome Homo sapiens

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.1.1.260 S-adenosyl-L-methionine + pseudouridine1191 in yeast 18S rRNA Homo sapiens
-
S-adenosyl-L-homocysteine + N1-methylpseudouridine1191 in yeast 18S rRNA
-
?
2.1.1.260 S-adenosyl-L-methionine + pseudouridine1191 in yeast 18S rRNA Methanocaldococcus jannaschii
-
S-adenosyl-L-homocysteine + N1-methylpseudouridine1191 in yeast 18S rRNA
-
?

Organism

EC Number Organism UniProt Comment Textmining
2.1.1.257 Homo sapiens Q92979
-
-
2.1.1.257 Methanocaldococcus jannaschii Q57977
-
-
2.1.1.257 Methanocaldococcus jannaschii DSM 2661 Q57977
-
-
2.1.1.260 Homo sapiens
-
-
-
2.1.1.260 Methanocaldococcus jannaschii
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.1.1.260 recombinant His-tagged Nep1 from Escherichia coli strain M15(pREP4) by nickel affinity chromatography Homo sapiens
2.1.1.260 recombinant Nep1 by cation exchange chromatography and gel filtration Methanocaldococcus jannaschii

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.1.1.257 additional information substrate specificity analysis by NMR binding and affinity study for RNA, overview. The enzyme is highly specific for pseudouridine. Methanocaldococcus jannaschii Nep1 binds to the yeast Nep1 RNA consensus sequence Methanocaldococcus jannaschii ?
-
?
2.1.1.257 additional information substrate specificity analysis by NMR binding and affinity study for RNA, overview. The enzyme is highly specific for pseudouridine. Methanocaldococcus jannaschii Nep1 binds to the yeast Nep1 RNA consensus sequence Methanocaldococcus jannaschii DSM 2661 ?
-
?
2.1.1.257 S-adenosyl-L-methionine + pseudouridine in 5'-GAUPsiCAACGCC-3'
-
Methanocaldococcus jannaschii S-adenosyl-L-homocysteine + N1-methylpseudouridine in 5'-GAUmethylPsiCAACGCC-3'
-
?
2.1.1.257 S-adenosyl-L-methionine + pseudouridine in 5'-GAUPsiCAACGCC-3'
-
Methanocaldococcus jannaschii DSM 2661 S-adenosyl-L-homocysteine + N1-methylpseudouridine in 5'-GAUmethylPsiCAACGCC-3'
-
?
2.1.1.257 S-adenosyl-L-methionine + pseudouridine in 5'-PsiCAACGCC-3'
-
Methanocaldococcus jannaschii S-adenosyl-L-homocysteine + N1-methylpseudouridine in 5'-methylPsiCAACGCC-3'
-
?
2.1.1.257 S-adenosyl-L-methionine + pseudouridine in 5'-PsiCAACGCC-3'
-
Methanocaldococcus jannaschii DSM 2661 S-adenosyl-L-homocysteine + N1-methylpseudouridine in 5'-methylPsiCAACGCC-3'
-
?
2.1.1.257 S-adenosyl-L-methionine + pseudouridine in 5'-UPsiCAACGC--3'
-
Methanocaldococcus jannaschii S-adenosyl-L-homocysteine + N1-methylpseudouridine in 5'-UmethylPsiCAACGC--3'
-
?
2.1.1.257 S-adenosyl-L-methionine + pseudouridine in 5'-UPsiCAACGC--3'
-
Methanocaldococcus jannaschii DSM 2661 S-adenosyl-L-homocysteine + N1-methylpseudouridine in 5'-UmethylPsiCAACGC--3'
-
?
2.1.1.257 S-adenosyl-L-methionine + pseudouridine in 5'-UPsiCAACGCC-3'
-
Methanocaldococcus jannaschii S-adenosyl-L-homocysteine + N1-methylpseudouridine in 5'-UmethylPsiCAACGCC-3'
-
?
2.1.1.257 S-adenosyl-L-methionine + pseudouridine in 5'-UPsiCAACGCC-3'
-
Methanocaldococcus jannaschii DSM 2661 S-adenosyl-L-homocysteine + N1-methylpseudouridine in 5'-UmethylPsiCAACGCC-3'
-
?
2.1.1.260 additional information RNA-binding specificity by in vitro using fluorescence quenching assays and yeast three-hybrid screening. Identification of the binding site for methylation target RNAs by NMR-spectroscopy, overview Homo sapiens ?
-
?
2.1.1.260 additional information the Methanocaldococcus jannaschii Nep1 binds to the Saccharomyces cerevisiae Nep1 RNA consensus sequence 5'-UUCAAC-3' in the Methanocaldococcus jannaschii 16S rRNA. The region of Methanocaldococcus jannaschii 16S rRNA is equivalent to nt 1190-1195 in yeast 18S rRNA including the m1acp3-psi nucleotide at position 1191. And binding of MjNep1 to a 6mer RNA containing the consensus sequence 5'-UUCAAC-3'. Even a 5'-truncated RNA lacking the first uridine of the consensus sequence is bound with comparable affinity. RNA-binding specificity by in vitro using fluorescence quenching assays and yeast three-hybrid screening. Identification of the binding site for methylation target RNAs by NMR-spectroscopy, overview Methanocaldococcus jannaschii ?
-
?
2.1.1.260 S-adenosyl-L-methionine + pseudouridine1191 in yeast 18S rRNA
-
Homo sapiens S-adenosyl-L-homocysteine + N1-methylpseudouridine1191 in yeast 18S rRNA
-
?
2.1.1.260 S-adenosyl-L-methionine + pseudouridine1191 in yeast 18S rRNA
-
Methanocaldococcus jannaschii S-adenosyl-L-homocysteine + N1-methylpseudouridine1191 in yeast 18S rRNA
-
?
2.1.1.260 S-adenosyl-L-methionine + pseudouridine1191 in yeast 18S rRNA
-
Methanocaldococcus jannaschii S-adenosyl-L-homocysteine + N1-methylpseudouridine1191 in yeast 18S rRNA product identification by 1H-NMR-spectroscopy ?
2.1.1.260 S-adenosyl-L-methionine + pseudouridine1191 in yeast 18S rRNA RNA-oligonucleotides corresponding to nucleotides 1245-1255 of human 18S rRNA and containing pseudouridine (5'-GACWCAACACG-3') at position 1248. This position corresponds to nucleotide 914 of Methanocaldococcus jannaschii 16S rRNA and to nt 1191 of yeast 18S rRNA Homo sapiens S-adenosyl-L-homocysteine + N1-methylpseudouridine1191 in yeast 18S rRNA product identification by MALDI-mass spectrometrical analysis ?

Subunits

EC Number Subunits Comment Organism
2.1.1.257 dimer Nep1 structure reveals a dimer with a fold similar to the SPOUT-class of RNA-methyltransferases Homo sapiens
2.1.1.257 dimer Nep1 structure reveals a dimer with a fold similar to the SPOUT-class of RNA-methyltransferases Methanocaldococcus jannaschii
2.1.1.260 dimer three-dimensional structure of the Nep1 dimer, overview Homo sapiens
2.1.1.260 dimer three-dimensional structure of the Nep1 dimer, overview Methanocaldococcus jannaschii

Synonyms

EC Number Synonyms Comment Organism
2.1.1.257 Emg1
-
Homo sapiens
2.1.1.257 MjNep1
-
Methanocaldococcus jannaschii
2.1.1.257 Nep1
-
Homo sapiens
2.1.1.257 Nep1
-
Methanocaldococcus jannaschii
2.1.1.257 pseudouridine-N1-specific methyltransferase
-
Homo sapiens
2.1.1.257 pseudouridine-N1-specific methyltransferase
-
Methanocaldococcus jannaschii
2.1.1.257 ribosome assembly factor Nep1
-
Homo sapiens
2.1.1.257 ribosome assembly factor Nep1
-
Methanocaldococcus jannaschii
2.1.1.260 Emg1
-
Homo sapiens
2.1.1.260 Emg1
-
Methanocaldococcus jannaschii
2.1.1.260 Nep1
-
Homo sapiens
2.1.1.260 Nep1
-
Methanocaldococcus jannaschii
2.1.1.260 Nep1 methyltransferase
-
Homo sapiens
2.1.1.260 Nep1 methyltransferase
-
Methanocaldococcus jannaschii
2.1.1.260 pseudouridine-N1-specific methyltransferase
-
Homo sapiens
2.1.1.260 pseudouridine-N1-specific methyltransferase
-
Methanocaldococcus jannaschii

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.1.1.260 37
-
assay at Homo sapiens
2.1.1.260 65
-
assay at Methanocaldococcus jannaschii

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.1.1.260 7.5
-
assay at Homo sapiens
2.1.1.260 7.5
-
assay at Methanocaldococcus jannaschii

Cofactor

EC Number Cofactor Comment Organism Structure
2.1.1.260 S-adenosyl-L-methionine
-
Homo sapiens
2.1.1.260 S-adenosyl-L-methionine
-
Methanocaldococcus jannaschii

General Information

EC Number General Information Comment Organism
2.1.1.257 evolution Nep1 structure reveals a dimer with a fold similar to the SPOUT-class of RNA-methyltransferases Homo sapiens
2.1.1.257 evolution Nep1 structure reveals a dimer with a fold similar to the SPOUT-class of RNA-methyltransferases Methanocaldococcus jannaschii
2.1.1.257 malfunction a mutation in the human Nep1 homolog causes Bowen-Conradi syndrome, a severe developmental disorder Homo sapiens
2.1.1.257 physiological function Nep1 acts as a methyltransferase in ribosome biogenesis Homo sapiens
2.1.1.257 physiological function Nep1 acts as a methyltransferase in ribosome biogenesis Methanocaldococcus jannaschii
2.1.1.260 evolution Nep1 belongs to the SPOUT-class RNA methyltransferases, Nep1 subfamily Homo sapiens
2.1.1.260 evolution Nep1 belongs to the SPOUT-class RNA methyltransferases, Nep1 subfamily Methanocaldococcus jannaschii
2.1.1.260 physiological function MjNep1 binds its RNA target along an extended basic surface cleft at the dimer interface that involves both insertions to the SPOUT-class core fold in an orientation consistent with the proposed methylation of nt 914 in Methanocaldococcus jannaschii 16S rRNA Methanocaldococcus jannaschii