Literature summary for 2.1.1.260 extracted from

Taylor, A.B.; Meyer, B.; Leal, B.Z.; Koetter, P.; Schirf, V.; Demeler, B.; Hart, P.J.; Entian, K.D.; Woehnert, J.
The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site (2008), Nucleic Acids Res., 36, 1542-1554.

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Cloned(Commentary)

Cloned (Comment)	Organism
gene NEP1, DNA and amino acid sequence determination and analysis, expression in Escherichia coli strain BL21(DE3)	Methanocaldococcus jannaschii

Crystallization (Commentary)

Crystallization (Comment)	Organism
Nep1 in its free form and bound to S-adenosylhomocysteine or the antibiotic and general methyltransferase inhibitor sinefungin, hanging drop vapour diffusion method, 10-15 mg/ml protein in 100 mM BisTris-propane buffer, pH 9.5, 6-10% PEG 400, 30-48% glycerol, and 0-400 mM trimethylamine-N-oxide, at 4°C, crystals of the selenomethionine containing protein in the presence or absence of a 3fold excess of S-adenosyl-L-homocysteine are grown under similar conditions at 16°C, X-ray diffraction structure determination and analysis at 2.2 A, 2.15 A, and 2.25 A resolution, respectively	Methanocaldococcus jannaschii

Crystallization (Comment)

Organism

Nep1 in its free form and bound to S-adenosylhomocysteine or the antibiotic and general methyltransferase inhibitor sinefungin, hanging drop vapour diffusion method, 10-15 mg/ml protein in 100 mM BisTris-propane buffer, pH 9.5, 6-10% PEG 400, 30-48% glycerol, and 0-400 mM trimethylamine-N-oxide, at 4°C, crystals of the selenomethionine containing protein in the presence or absence of a 3fold excess of S-adenosyl-L-homocysteine are grown under similar conditions at 16°C, X-ray diffraction structure determination and analysis at 2.2 A, 2.15 A, and 2.25 A resolution, respectively

Methanocaldococcus jannaschii

Inhibitors

Inhibitors	Comment	Organism	Structure
sinefungin	sinefungin binds to Nep1 at a preformed binding site that is topologically equivalent to the cofactor binding site in other SPOUT-class methyltransferases	Methanocaldococcus jannaschii

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
S-adenosyl-L-methionine + pseudouridine1191 in yeast 18S rRNA	Methanocaldococcus jannaschii	-	S-adenosyl-L-homocysteine + N1-methylpseudouridine1191 in yeast 18S rRNA	-	?
S-adenosyl-L-methionine + pseudouridine1191 in yeast 18S rRNA	Methanocaldococcus jannaschii DSM 2661	-	S-adenosyl-L-homocysteine + N1-methylpseudouridine1191 in yeast 18S rRNA	-	?

Organism

Organism	UniProt	Comment	Textmining
Methanocaldococcus jannaschii	Q57977	-	-
Methanocaldococcus jannaschii DSM 2661	Q57977	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant Nep1p from Escherichia coli strain BL21(DE3) by ion exchange chromatography and gel filtration	Methanocaldococcus jannaschii

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
S-adenosyl-L-methionine + pseudouridine1191 in yeast 18S rRNA	-	Methanocaldococcus jannaschii	S-adenosyl-L-homocysteine + N1-methylpseudouridine1191 in yeast 18S rRNA	-	?
S-adenosyl-L-methionine + pseudouridine1191 in yeast 18S rRNA	S-adenosyl-L-methionine binding site structure, overview	Methanocaldococcus jannaschii	S-adenosyl-L-homocysteine + N1-methylpseudouridine1191 in yeast 18S rRNA	S-adenosyl-L-homocysteine binds to Nep1 at a preformed binding site that is topologically equivalent to the cofactor binding site in other SPOUT-class methyltransferases, intermolecular interactions, overview	?
S-adenosyl-L-methionine + pseudouridine1191 in yeast 18S rRNA	-	Methanocaldococcus jannaschii DSM 2661	S-adenosyl-L-homocysteine + N1-methylpseudouridine1191 in yeast 18S rRNA	-	?
S-adenosyl-L-methionine + pseudouridine1191 in yeast 18S rRNA	S-adenosyl-L-methionine binding site structure, overview	Methanocaldococcus jannaschii DSM 2661	S-adenosyl-L-homocysteine + N1-methylpseudouridine1191 in yeast 18S rRNA	S-adenosyl-L-homocysteine binds to Nep1 at a preformed binding site that is topologically equivalent to the cofactor binding site in other SPOUT-class methyltransferases, intermolecular interactions, overview	?

Subunits

Subunits	Comment	Organism
More	Nep1 monomer and dimer structures, detailed overview	Methanocaldococcus jannaschii

Synonyms

Synonyms	Comment	Organism
Nep1	-	Methanocaldococcus jannaschii

Cofactor

Cofactor	Comment	Organism	Structure
S-adenosyl-L-methionine	-	Methanocaldococcus jannaschii

General Information

General Information	Comment	Organism
malfunction	addition of SAM to the medium restores growth at elevated temperatures in yeast with temperature sensitive mutants of the yeast Nep1 protein	Methanocaldococcus jannaschii
additional information	active site structure and ligand binding, overview	Methanocaldococcus jannaschii
physiological function	Nep1 is a genuine rRNA methyltransferase and is essential for ribosome biogenesis	Methanocaldococcus jannaschii