Literature summary 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.
Cloned(Commentary)
EC Number |
Cloned (Comment) |
Organism |
---|
2.1.1.229 |
gene cmoA, recombinant expression of N-terminally His-tagged enzyme in Escherichia coli strain Rosetta pLysS (DE3) |
Escherichia coli |
Crystallization (Commentary)
EC Number |
Crystallization (Comment) |
Organism |
---|
2.1.1.229 |
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]
EC Number |
Molecular Weight [Da] |
Molecular Weight Maximum [Da] |
Comment |
Organism |
---|
2.1.1.229 |
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
EC Number |
Organism |
UniProt |
Comment |
Textmining |
---|
2.1.1.229 |
Escherichia coli |
P76290 |
strain MG1655, gene cmoA |
- |
Purification (Commentary)
EC Number |
Purification (Comment) |
Organism |
---|
2.1.1.229 |
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)
EC Number |
Substrates |
Comment Substrates |
Organism |
Products |
Comment (Products) |
Rev. |
Reac. |
---|
2.1.1.229 |
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
EC Number |
Subunits |
Comment |
Organism |
---|
2.1.1.229 |
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
EC Number |
Synonyms |
Comment |
Organism |
---|
2.1.1.229 |
CmoA |
- |
Escherichia coli |
Cofactor
EC Number |
Cofactor |
Comment |
Organism |
Structure |
---|
2.1.1.229 |
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
EC Number |
General Information |
Comment |
Organism |
---|
2.1.1.229 |
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 |
2.1.1.229 |
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 |