Modomics - A Database of RNA Modifications

Full name:	tRNA uridine(34) 5-carboxymethylaminomethyl synthesis enzyme
Synonym:	GidA, TrmF
GI:	62288115
Orf:	b3741
COG:	COG0445
UniProt:	P0A6U3
Structures:	\| 3CP2 \| 3CES \|
Complex:	MnmG/MnmE
Enzyme type:	other
Position of modification - modification:	t:34 - cmnm5s2U t:34 - mnm5s2U t:34 - cmnm5Um t:34 - mnm5U

Comments:

Flavoprotein, using methyl-(or methylen)-tetrahydrofolate as a donor of one carbon. In a complex with GTPase MnmE they catalyze the formation of either cmnm5U or nm5U by reacting either with glycine or with ammonium. The choice between glycine and ammonium was shown to be influenced by growth phase and medium with glycine pathway being chosen in minimal medium and in exponential phase. However, in the case of tRNAGlncmnm5s2U the glycine pathway is always the dominant one and for tRNALeucmnm5Um the ammonium pathway was observed only in vitro. Mitochondrial homologue is Mto1. Not to be confused with bacterial Gid or small Gid (renamed TrmFO), also a flavoprotein displaying homology to N-terminus of MnmG (GidA) but catalysing a different reaction (m5U54 in tRNA).

Protein sequence:

MFYPDPFDVIIIGGGHAGTEAAMAAARMGQQTLLLTHNIDTLGQMSCNPAIGGIGKGHLVKEVDALGGLMAKAIDQAGIQFRILNASKGPAVRATRAQAD
RVLYRQAVRTALENQPNLMIFQQAVEDLIVENDRVVGAVTQMGLKFRAKAVVLTVGTFLDGKIHIGLDNYSGGRAGDPPSIPLSRRLRELPLRVGRLKTG
TPPRIDARTIDFSVLAQQHGDNPMPVFSFMGNASQHPQQVPCYITHTNEKTHDVIRSNLDRSPMYAGVIEGVGPRYCPSIEDKVMRFADRNQHQIFLEPE
GLTSNEIYPNGISTSLPFDVQMQIVRSMQGMENAKIVRPGYAIEYDFFDPRDLKPTLESKFIQGLFFAGQINGTTGYEEAAAQGLLAGLNAARLSADKEG
WAPARSQAYLGVLVDDLCTLGTKEPYRMFTSRAEYRLMLREDNADLRLTEIGRELGLVDDERWARFNEKLENIERERQRLKSTWVTPSAEAAAEVNAHLT
APLSREASGEDLLRRPEMTYEKLTTLTPFAPALTDEQAAEQVEIQVKYEGYIARQQDEIEKQLRNENTLLPATLDYRQVSGLSNEVIAKLNDHKPASIGQ
ASRISGVTPAAISILLVWLKKQGMLRRSA

Enzymatic activities:

Reaction	Substrate	Type	Position
U:cmnm5U	tRNA (t)	Lys/SUU/prokaryotic cytosol	34
U:nm5U	tRNA (t)	Lys/SUU/prokaryotic cytosol	34
s2U:nm5s2U	tRNA (t)	Lys/SUU/prokaryotic cytosol	34
se2U:nm5se2U	tRNA (t)		34
s2U:cmnm5s2U	tRNA (t)	Lys/SUU/prokaryotic cytosol	34
se2U:cmnm5se2U	tRNA (t)		34
Um:cmnm5Um	tRNA (t)	Leu/)AA/prokaryotic cytosol	34
s2U:nm5s2U	tRNA (t)	Glu/SUC/prokaryotic cytosol	34
s2U:cmnm5s2U	tRNA (t)	Glu/SUC/prokaryotic cytosol	34
U:nm5U	tRNA (t)	Glu/SUC/prokaryotic cytosol	34
U:cmnm5U	tRNA (t)	Glu/SUC/prokaryotic cytosol	34
s2U:nm5s2U	tRNA (t)	Gln/$UG/prokaryotic cytosol	34
s2U:cmnm5s2U	tRNA (t)	Gln/$UG/prokaryotic cytosol	34
U:nm5U	tRNA (t)	Gln/$UG/prokaryotic cytosol	34
U:cmnm5U	tRNA (t)	Gln/$UG/prokaryotic cytosol	34
U:cmnm5U	tRNA (t)	Leu/)AA/prokaryotic cytosol	34
U:nm5U	tRNA (t)	Leu/)AA/prokaryotic cytosol	34
U:nm5U	tRNA (t)	Arg/{CU/prokaryotic cytosol	34
U:cmnm5U	tRNA (t)	Arg/{CU/prokaryotic cytosol	34
U:cmnm5U	tRNA (t)	Gly/{CC/prokaryotic cytosol	34
U:nm5U	tRNA (t)	Gly/{CC/prokaryotic cytosol	34

Publications:

Title	Authors	Journal	Details	PubMed Id	DOI
Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli.	Yim L, Moukadiri I, Bjork GR, Armengod ME	Nucleic Acids Res	[details]	17062623	-
Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate.	Meyer S, Scrima A, Versées W, Wittinghofer A	J Mol Biol	[details]	18565343	-
Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift.	Brégeon D, Colot V, Radman M, Taddei F	Genes Dev	[details]	11544186	-
Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions.	Moukadiri I, Prado S, Piera J, Velázquez-Campoy A, Björk GR, Armengod ME	Nucleic Acids Res	[details]	19767610	-
Enzymology of tRNA modification in the bacterial MnmEG pathway.	Armengod ME, Moukadiri I, Prado S, Ruiz-Partida R, Benitez-Paez A, Villarroya M, Lomas R, Garzon MJ, Martinez-Zamora A, Meseguer S, Navarro-Gonzalez C	Biochimie	[details]	22386868	-
The output of the tRNA modification pathways controlled by the Escherichia coli MnmEG and MnmC enzymes depends on the growth conditions and the tRNA species.	Moukadiri I, Garzon MJ, Bjork GR, Armengod ME...	Nucleic Acids Res	[details]	24293650	-
SAXS analysis of the tRNA-modifying enzyme complex MnmE/MnmG reveals a novel interaction mode and GTP-induced oligomerization.	Fislage M, Brosens E, Deyaert E, Spilotros A, Pardon E, Loris R, Steyaert J, Garcia-Pino A, Versees W...	Nucleic Acids Res	[details]	24634441	-

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