title: S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA.
abstract: 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.
authors.affiliation: York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington YO10 5DD, England.
authors.forename: Robert T
authors.initials: RT
authors.lastname: Byrne
authors.forename: Fiona
authors.initials: F
authors.lastname: Whelan
authors.forename: Pierre
authors.initials: P
authors.lastname: Aller
authors.forename: Louise E
authors.initials: LE
authors.lastname: Bird
authors.forename: Adam
authors.initials: A
authors.lastname: Dowle
authors.forename: Carina M C
authors.initials: CM
authors.lastname: Lobley
authors.forename: Yamini
authors.initials: Y
authors.lastname: Reddivari
authors.forename: Joanne E
authors.initials: JE
authors.lastname: Nettleship
authors.forename: Raymond J
authors.initials: RJ
authors.lastname: Owens
authors.forename: Alfred A
authors.initials: AA
authors.lastname: Antson
authors.forename: David G
authors.initials: DG
authors.lastname: Waterman
mesh_terms: D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D019875:One-Carbon Group Transferases / Q000737:chemistry* / Q000378:metabolism; D012343:RNA, Transfer / Q000378:metabolism*; D012435:S-Adenosylhomocysteine / Q000378:metabolism*; D053719:Tandem Mass Spectrometry
chemical_list: D029968:Escherichia coli Proteins; D012343:RNA, Transfer; D012435:S-Adenosylhomocysteine; C581858:CmoA protein, E coli; D019875:One-Carbon Group Transferases
keywords: Escherichia coli; SCM-SAH; cmo5U biosynthesis; putative tRNA-modification enzyme