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Literature summary for 2.1.1.229 extracted from

  • Byrne, R.T.; Whelan, F.; Aller, P.; Bird, L.E.; Dowle, A.; Lobley, C.M.; Reddivari, Y.; Nettleship, J.E.; Owens, R.J.; Antson, A.A.; Waterman, D.G.
    S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA (2013), Acta Crystallogr. Sect. D, 69, 1090-1098.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
gene cmoA, recombinant expression of N-terminally His-tagged enzyme in Escherichia coli strain Rosetta pLysS (DE3) Escherichia coli

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant detagged enzyme, sitting drop vapour diffusion method, mixing of 100 nl of 20 mg/ml protein in 200 mM NaCl, and 20 mM Tris, pH 7.5, with 100 nl of precipitation solution containing 0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol, 0.1 M MOPS/HEPES-Na, pH 7.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% w/v MPD, 5 h, X-ray diffraction structure determination and analysis at 1.73 A resolution, molecular replacement using the structure of Haemophilus influenzae YecO, PDB ID 1im8, chain B Escherichia coli

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
55600
-
2 x 52500, gel filtration, mass spectrometry, and crystal structure analysis, 2 * 55600, about, sequence calculation. There are two molecules of CmoA present in the asymmetric unit, both molecules of CmoA contain the novel derivative S-adenosyl-S-carboxymethyl-L-homocysteine, the two molecules adopt the same conformation Escherichia coli

Organism

Organism UniProt Comment Textmining
Escherichia coli P76290 strain MG1655, gene cmoA
-

Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged enzyme from Escherichia coli strain Rosetta pLysS (DE3) by nickel affinity chromatography and gel filtration, followed by cleavage of the N-terminal His6-tag with rhinovirus 3C protease and another step of nickel affinity chromatography to remove the tag Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
S-adenosyl-S-carboxymethyl-L-homocysteine + 5-methoxyuridine34 in tRNA proposed modification pathway of 5-oxyuridine derivatives, overview Escherichia coli S-adenosyl-L-methionine + uridine 5-oxyacetic acid in tRNA
-
?

Subunits

Subunits Comment Organism
dimer 2 x 52500, gel filtration, mass spectrometry, and crystal structure analysis, 2 * 55600, about, sequence calculation. There are two molecules of CmoA present in the asymmetric unit, both molecules of CmoA contain the novel derivative S-adenosyl-S-carboxymethyl-L-homocysteine, the two molecules adopt the same conformation Escherichia coli

Synonyms

Synonyms Comment Organism
CmoA
-
Escherichia coli

Cofactor

Cofactor Comment Organism Structure
S-adenosyl-S-carboxymethyl-L-homocysteine i.e. [(3S)-3-amino-3-carboxypropyl]{[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}(carboxymethyl)sulfanium, the enzyme contains a cofactor, S-adenosyl-S-carboxymethyl-L-homocysteine (SCM-SAH), in which the donor methyl group is substituted by a carboxymethyl group. The carboxyl moiety forms a salt-bridge interaction with Arg199 that is conserved in a large group of CmoA-related proteins but is not conserved in other S-adenosyl-L-methionine-containing enzymes. The active site contains one molecule cofactor S-adenosyl-S-carboxymethyl-L-homocysteine per monomer, and not S-adenosyl-L-methionine Escherichia coli

General Information

General Information Comment Organism
evolution conservation of Arg199, the key residue of CmoA that stabilizes the negative charge of the carboxyl group of the S-adenosyl-S-carboxymethyl-L-homocysteine cofactor, suggests that these proteins contain the S-adenosyl-S-carboxymethyl-L-homocysteine cofactor instead of S-adenosyl-L-methionine. The equivalent residue in known S-adenosyl-L-methionine-dependent methyltransferases is not conserved Escherichia coli
physiological function uridine at position 34 of bacterial transfer RNAs is commonly modified to uridine-5-oxyacetic acid (cmo5U) to increase the decoding capacity. The protein CmoA is involved in the formation of cmo5U Escherichia coli