Literature summary for 2.1.1.176 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.

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Crystallization (Commentary)

Crystallization (Comment)	Organism
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

Crystallization (Comment)

Organism

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)

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

Organism

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

Substrates and Products (Substrate)

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

Subunits

Subunits	Comment	Organism
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
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
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

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

Cofactor

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

General Information

General Information	Comment	Organism
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
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
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