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Literature summary extracted from

  • Hikida, Y.; Kuratani, M.; Bessho, Y.; Sekine, S.I.; Yokoyama, S.
    Structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase (2010), Acta Crystallogr. Sect. D, 66, 1301-1307.
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.1.1.176 purified wild-type and SeMet-labeled PH0851 complexed with S-adenosyl-L-methionine-analogue sinefungin, hanging drop vapour diffusion method, mixing of protein solution, containing 1.7 mg/ml protein in 20 mM Tris-HCl buffer, pH 8.0, 400 mM NaCl, and 1 mM sinefungin, with reservoir solution, containing 80 mM HEPES-Na buffer, pH 7.0, 1.15 M sodium citrate, and 7-15% w/v 1,6-hexanediol, in a 4:1 ratio, 20°C, 1 week, X-ray diffraction structure determination and analysis at 2.55-3.0 A resolution, molecular replacement Pyrococcus horikoshii

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.1.1.176 S-adenosyl-L-methionine + cytosine967 in 16S rRNA Escherichia coli
-
 S-adenosyl-L-homocysteine + 5-methylcytosine967 in 16S rRNA
-
 ?
2.1.1.176 S-adenosyl-L-methionine + cytosine967 in 16S rRNA Pyrococcus horikoshii
-
 S-adenosyl-L-homocysteine + 5-methylcytosine967 in 16S rRNA
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.1.1.176 Escherichia coli
-
 gene rsmB or rrmB, formerly fmu
-
2.1.1.176 Pyrococcus horikoshii O58581
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.1.1.176 S-adenosyl-L-methionine + cytosine967 in 16S rRNA
-
 Escherichia coli S-adenosyl-L-homocysteine + 5-methylcytosine967 in 16S rRNA
-
 ?
2.1.1.176 S-adenosyl-L-methionine + cytosine967 in 16S rRNA
-
 Pyrococcus horikoshii S-adenosyl-L-homocysteine + 5-methylcytosine967 in 16S rRNA
-
 ?

Subunits

EC Number Subunits Comment Organism
2.1.1.176 monomer two domains and one linker: an N-terminal domain formed by residues 1-145, a C-terminal domain formed by residues 185-448, and an alpha-helical linker formed by residues 146-184 Pyrococcus horikoshii
2.1.1.176 More next to the S-adenosyl-L-methionine-binding site is a positively charged cleft, formed between the N- and C-terminal domains, that seems to be suitable for binding the RNA substrate. The N-terminal domains of Pyrococcus horikoshii PH0851 and Escherichia coli Fmu/RsmB/RrmB are both alpha-helical and adopt a similar topology, sequence and structure comparison, overview Escherichia coli
2.1.1.176 More next to the S-adenosyl-L-methionine-binding site is a positively charged cleft, formed between the N- and C-terminal domains, which is conserved in the archaeal PH0851 homologues and seems to be suitable for binding the RNA substrate. The N-terminal domains of Pyrococcus horikoshii PH0851 and Escherichia coli Fmu/RsmB/RrmB are both alpha-helical and adopt a similar topology, sequence and structure comparison, overview Pyrococcus horikoshii

Synonyms

EC Number Synonyms Comment Organism
2.1.1.176 Fmu/RsmB/RrmB
-
 Escherichia coli
2.1.1.176 Fmu/RsmB/RrmB
-
 Pyrococcus horikoshii
2.1.1.176 Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase
-
 Escherichia coli
2.1.1.176 Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase
-
 Pyrococcus horikoshii
2.1.1.176 PH0851
-
 Pyrococcus horikoshii
2.1.1.176 RNA:m5C MTase
-
 Escherichia coli
2.1.1.176 RNA:m5C MTase
-
 Pyrococcus horikoshii

Cofactor

EC Number Cofactor Comment Organism Structure
2.1.1.176 S-adenosyl-L-methionine dependent on Escherichia coli
2.1.1.176 S-adenosyl-L-methionine dependent on Pyrococcus horikoshii

General Information

EC Number General Information Comment Organism
2.1.1.176 evolution Fmu/RsmB/RrmB homologues exist not only in bacteria but also in archaea and eukarya and constitute a large orthologous group in the RNA:m5C methyltransferase family. The sequence of the N-terminal domain is negligibly conserved between the bacterial and archaeal subfamilies Escherichia coli
2.1.1.176 evolution Fmu/RsmB/RrmB homologues exist not only in bacteria but also in archaea and eukarya and constitute a large orthologous group in the RNA:m5C methyltransferase family. The sequence of the N-terminal domain is negligibly conserved between the bacterial and archaeal subfamilies Pyrococcus horikoshii
2.1.1.176 additional information next to the S-adenosyl-L-methionine-binding site is a positively charged cleft, formed between the N- and C-terminal domains, which is conserved in the archaeal PH0851 homologues and seems to be suitable for binding the RNA substrate Pyrococcus horikoshii