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Uridine at position 34 of bacterial transfer RNAs is commonly modified to uridine-5-oxyacetic acid (cmo(5)U) to increase the decoding capacity. The protein CmoA is involved in the formation of cmo(5)U and was annotated as an S-adenosyl-L-methionine-dependent (SAM-dependent) methyltransferase on the basis of its sequence homology to other SAM-containing enzymes. However, both the crystal structure of Escherichia coli CmoA at 1.73 Å resolution and mass spectrometry demonstrate that it contains a novel 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 SAM-containing enzymes. This raises the possibility that a number of enzymes that have previously been annotated as SAM-dependent are in fact SCM-SAH-dependent. Indeed, inspection of electron density for one such enzyme with known X-ray structure, PDB entry 1im8, suggests that the active site contains SCM-SAH and not SAM.

Original publication

DOI

10.1107/S0907444913004939

Type

Journal article

Journal

Acta Crystallogr D Biol Crystallogr

Publication Date

06/2013

Volume

69

Pages

1090 - 1098

Keywords

Escherichia coli, SCM-SAH, cmo5U biosynthesis, putative tRNA-modification enzyme, Crystallography, X-Ray, Escherichia coli, Escherichia coli Proteins, One-Carbon Group Transferases, RNA, Transfer, S-Adenosylhomocysteine, Tandem Mass Spectrometry