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Escherichia coli K-12 substr. MG1655 Protein: GTPase, involved in modification of U34 in tRNA



Gene: mnmE Accession Numbers: EG10997 (EcoCyc), b3706, ECK3699

Synonyms: trmE, thdF

Regulation Summary Diagram: ?

Component of: 5-carboxymethylaminomethyluridine-tRNA synthase [multifunctional] (summary available)

Subunit composition of GTPase, involved in modification of U34 in tRNA = [MnmE]2
         GTPase, involved in modification of U34 in tRNA = MnmE

Summary:
MnmE is required for wild-type 5-methylaminomethyl-2-thiouridine modification of tRNA [Elseviers84]. The additional modification of m5U stabilizes the U·G pairing at the wobble position and thus plays a role in decoding NNG codons [Kurata08].

Together with MnmG, MnmE is involved in maintenance of the correct reading frame [Brierley97, Urbonavicius01, Bregeon01, Urbonavicius03]. MnmE also appeared to play a role in oxidation of thiophene and furan compounds [Alam91] and regulates glutamate-dependent acid resistance [Gong04, Sayed09].

MnmE is a GTP-binding protein that also exhibits GTPase activity, showing rapid GTP hydrolysis and low nucleotide affinity. The nucleotide binding and hydrolysis activities are localized within the central 17 kDa GTPase domain [Cabedo99]. The GTPase activity as well as the Cys451 residue in the C-terminal domain are required for the wild-type tRNA modification function [Yim03], but not sufficient [MartinezVicente05]. Dimerization of the GTPase domain is potassium ion-dependent; subsequent GTP hydrolysis activity is dependent on dimerization [Scrima06]. Low pH inhibits the GTP hydrolysis activity [Monleon07]. Unlike other GTPases, MnmE does not appear to use an "arginine finger" for catalysis [Scrima06, Monleon07].

While the GTPase domain is required for homodimerization, the helical domain of MnmE is responsible for the interaction with MnmG [Meyer08a]. Nucleotide binding leads to a conformational change in MnmE, and GTP-bound MnmE has a much higher affinity for MnmG [Meyer09]. Conversely, MnmG binding induces large conformational changes in MnmE [Bohme10]. MnmG stabilizes the MnmE homodimer and stimulates GTP hydrolysis [Meyer09, Bohme10].

Solution and crystal structures of the G-domain of MnmE have been solved [Monleon04, Scrima06, Monleon07]. MnmE can homomultimerize and localizes to the cytoplasm, showing some association with the cytoplasmic membrane [Cabedo99]. MnmE interacts specifically with MnmG [Yim06]. A fraction of MnmE protein appears to be associated with the plasma membrane [Cabedo99].

Viability of an mnmE mutation is dependent on the strain background [Cabedo99]. mnmE mutants are defective in the tRNA modification 5-methylaminomethyl-2-thiouridine; tRNA anticodons that are modified with 5-methylaminomethyl-2-thiouridine in the wild type show 2-thiouridine modification in the mutant, and mutants exhibit a defect in UAG readthrough [Elseviers84]. Unexpectedly, the hypomodified tRNALys of an mnmE mutant leads to decreased misreading of the anticodon [Hagervall98]. An mnmE deletion enhances the slow growth phenotype of a ΔyjeQ mutant [Campbell08] and partially supresses the cold-sensitive growth phenotype and MiaB activity defect of a ygfZ null mutant [Waller12].

Expression of mnmE is increased during stationary phase, but independent of the stationary phase sigma factor RpoS. Expression is also subject to catabolite repression and is decreased in the absence of oxygen [Zabel00].

ThdF: "thiophene degradation" [Alam91]

TrmE: "tRNA modification" [Elseviers84]

MnmE: "methylaminomethyl modification"

Reviews: [Mittenhuber01, Caldon01, Verstraeten11, Armengod12, El12]

Citations: [Scrima05, Gruian12, Ash12, Deng13]

Locations: inner membrane, cytosol

Map Position: [3,884,851 -> 3,886,215] (83.73 centisomes)
Length: 1365 bp / 454 aa

Molecular Weight of Polypeptide: 49.231 kD (from nucleotide sequence), 48 kD (experimental) [Alam91 ], 50 kD (experimental)

Unification Links: ASAP:ABE-0012123 , CGSC:17806 , DIP:DIP-11033N , EchoBASE:EB0990 , EcoGene:EG10997 , EcoliWiki:b3706 , ModBase:P25522 , OU-Microarray:b3706 , PortEco:mnmE , PR:PRO_000023256 , Pride:P25522 , Protein Model Portal:P25522 , RefSeq:NP_418162 , RegulonDB:EG10997 , SMR:P25522 , String:511145.b3706 , UniProt:P25522

Relationship Links: InterPro:IN-FAMILY:IPR004520 , InterPro:IN-FAMILY:IPR005225 , InterPro:IN-FAMILY:IPR006073 , InterPro:IN-FAMILY:IPR018948 , InterPro:IN-FAMILY:IPR025867 , InterPro:IN-FAMILY:IPR027266 , InterPro:IN-FAMILY:IPR027368 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:1RFL , PDB:Structure:2GJ8 , PDB:Structure:2GJ9 , PDB:Structure:2GJA , Pfam:IN-FAMILY:PF01926 , Pfam:IN-FAMILY:PF10396 , Pfam:IN-FAMILY:PF12631

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0002098 - tRNA wobble uridine modification Inferred from experiment [Elseviers84, Moukadiri09]
GO:0006805 - xenobiotic metabolic process Inferred from experiment [Alam91]
GO:0009268 - response to pH Inferred from experiment [Gong04]
GO:0030488 - tRNA methylation Inferred from experiment [Elseviers84]
GO:0061077 - chaperone-mediated protein folding Inferred from experiment [Wang12a]
GO:0006184 - GTP catabolic process Inferred by computational analysis [GOA01]
GO:0006400 - tRNA modification Inferred by computational analysis [GOA06, GOA01]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003924 - GTPase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Yim03]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0005525 - GTP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Cabedo99]
GO:0019003 - GDP binding Inferred from experiment [Scrima05]
GO:0030955 - potassium ion binding Inferred from experiment [Scrima06]
GO:0042803 - protein homodimerization activity Inferred from experiment [Meyer09]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, Cabedo99]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Zhang07, Cabedo99, Watt07]
GO:0005886 - plasma membrane Inferred from experiment [Cabedo99]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]

MultiFun Terms: information transfer RNA related RNA modification
information transfer RNA related tRNA

Essentiality data for mnmE knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Credits:
Created 15-Jun-2007 by Keseler I , SRI International
Last-Curated ? 22-Jul-2013 by Keseler I , SRI International


Subunit of: 5-carboxymethylaminomethyluridine-tRNA synthase [multifunctional]

Subunit composition of 5-carboxymethylaminomethyluridine-tRNA synthase [multifunctional] = [(MnmE)2][(MnmG)2]
         GTPase, involved in modification of U34 in tRNA = (MnmE)2
                 GTPase, involved in modification of U34 in tRNA = MnmE
         protein involved in modification of U34 in tRNA = (MnmG)2
                 protein involved in modification of U34 in tRNA = MnmG

Summary:
The heterotetrameric MnmEG complex is required for 5-carboxymethylaminomethyl modification of the wobble base of certain tRNAs. Both complex formation and GTP hydrolysis are required for tRNA modification activity [Meyer09, Moukadiri09].

Utilizing either ammonium or glycine as a substrate, the MnmEG complex catalyzes formation of the 5-aminomethyl- or 5-carboxymethylaminomethyl modification of tRNA at the U34 wobble base [Moukadiri09]. All its tRNA substrates can be modified via the ammonium pathway; growth conditions influence which modification pathway is utilized [Moukadiri14].

Thiolation of the C2 position (catalyzed by MnmA) and modification of the C5 position of U34 are independent of each other.

Citations: [Meyer08a, Yim06]

Credits:
Created 15-Jun-2007 by Keseler I , SRI International
Last-Curated ? 16-Dec-2013 by Keseler I , SRI International


Enzymatic reaction of: 5-carboxymethylaminomethyluridine-tRNA synthase

a tRNA uridine34 + GTP + a 5,10-methylene-tetrahydrofolate + glycine + H2O <=> a tRNA containing 5-carboxymethylaminomethyluridine + GDP + a 7,8-dihydrofolate + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

Reversibility of this reaction is unspecified.

a tRNA 2-thiouridine34 + GTP + glycine + a 5,10-methylene-tetrahydrofolate + H2O <=> a tRNA containing 5-carboxymethylaminomethyl-2-thiouridine + GDP + a 7,8-dihydrofolate + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

Reversibility of this reaction is unspecified.

Cofactors or Prosthetic Groups: FAD [Moukadiri09]


Enzymatic reaction of: 5-aminomethyluridine-tRNA synthase

a tRNA 2-thiouridine34 + a 5,10-methylene-tetrahydrofolate + ammonium + GTP + H2O <=> a tRNA containing 5-aminomethyl-2-thiouridine + a 7,8-dihydrofolate + GDP + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: FAD [Moukadiri09]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
a tRNA 2-thiouridine34
0.6
0.012
[Moukadiri14]


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 23
[UniProt10]
UniProt: Formyltetrahydrofolate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 80
[UniProt10]
UniProt: Formyltetrahydrofolate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 120
[UniProt10]
UniProt: Formyltetrahydrofolate; Non-Experimental Qualifier: by similarity;
Conserved-Region 218 -> 336
[UniProt13]
UniProt: G.
Mutagenesis-Variant 224
[MartinezVicente05, UniProt11]
Alternate sequence: R → A; UniProt: 1.5-fold decrease in GTPase activity and almost no change in affinity.
Mutagenesis-Variant 226
[Scrima06, UniProt11]
Alternate sequence: N → K; UniProt: 70-fold decrease in GTPase activity. 2-fold decrease of affinity for GTP.
Alternate sequence: N → A; UniProt: 100-fold decrease in GTPase activity. 5-fold decrease of affinity for GTP.
Metal-Binding-Site 226
[UniProt10a]
UniProt: Potassium;
Nucleotide-Phosphate-Binding-Region 226 -> 231
[UniProt10a]
UniProt: GTP;
Mutagenesis-Variant 228
[Yim03, UniProt11]
Alternate sequence: G → A; UniProt: Loss of GTP binding and hydrolase activity. Completely impairs tRNA modifying function.
Metal-Binding-Site 230
[UniProt10a]
UniProt: Magnesium;
Metal-Binding-Site 245
[UniProt10a]
UniProt: Potassium; via carbonyl oxygen;
Nucleotide-Phosphate-Binding-Region 245 -> 251
[UniProt10a]
UniProt: GTP;
Metal-Binding-Site 247
[UniProt10a]
UniProt: Potassium; via carbonyl oxygen;
Mutagenesis-Variant 249
[MartinezVicente05, UniProt11]
Alternate sequence: G → A; UniProt: 22-fold decrease in GTPase activity and 7-fold increase of affinity.
Mutagenesis-Variant 250
[MartinezVicente05, UniProt11]
Alternate sequence: T → S; UniProt: 1.8-fold decrease in GTPase activity and 1.5-fold increase of affinity.
Alternate sequence: T → A; UniProt: 4-fold decrease in GTPase activity and 1.5-fold increase of affinity.
Metal-Binding-Site 250
[UniProt10a]
UniProt: Potassium;
Mutagenesis-Variant 251
[MartinezVicente05, UniProt11]
Alternate sequence: T → S; UniProt: 4-fold decrease in GTPase activity and 1.2-fold decrease of affinity.
Alternate sequence: T → A; UniProt: 92-fold decrease in GTPase activity and 59-fold increase of affinity.
Metal-Binding-Site 251
[UniProt10a]
UniProt: Magnesium;
Mutagenesis-Variant 252
[MartinezVicente05, UniProt11]
Alternate sequence: R → K; UniProt: 2-fold decrease in GTPase activity and no change in affinity.
Alternate sequence: R → A; UniProt: 7-fold decrease in GTPase activity and 6-fold increase of affinity.
Mutagenesis-Variant 253
[MartinezVicente05, UniProt11]
Alternate sequence: D → A; UniProt: 9-fold decrease in GTPase activity and 13-fold increase of affinity.
Mutagenesis-Variant 255
[Scrima06, UniProt11]
Alternate sequence: L → D; UniProt: 1.5-fold decrease in affinity for GTP.
Mutagenesis-Variant 256
[MartinezVicente05, UniProt11]
Alternate sequence: R → A; UniProt: 2-fold decrease in GTPase activity and almost no change in affinity.
Mutagenesis-Variant 270
[Yim03, UniProt11]
Alternate sequence: D → A; UniProt: Does not affect GTP binding, but impairs hydrolase activity. Completely impairs tRNA modifying function.
Nucleotide-Phosphate-Binding-Region 270 -> 273
[UniProt10a]
UniProt: GTP;
Mutagenesis-Variant 275
[MartinezVicente05, UniProt11]
Alternate sequence: R → A; UniProt: 6-fold decrease in GTPase activity and 1.9-fold increase of affinity.
Mutagenesis-Variant 282
[Scrima06, UniProt11]
Alternate sequence: E → Q; UniProt: 370-fold decrease in GTPase activity.
Alternate sequence: E → A; UniProt: 1900-fold decrease in GTPase activity.
Mutagenesis-Variant 288
[MartinezVicente05, UniProt11]
Alternate sequence: R → A; UniProt: 1.7-fold decrease in GTPase activity and 1.5-fold increase of affinity.
Nucleotide-Phosphate-Binding-Region 335 -> 338
[UniProt10a]
UniProt: GTP;
Mutagenesis-Variant 338
[Yim03, UniProt11]
Alternate sequence: D → N; UniProt: Strong decrease in GTP binding. Does not affect hydrolase activity, but has 10-fold higher affinity for XTP than for GTP. Partially impairs tRNA modifying function.
Nucleotide-Phosphate-Binding-Region 358 -> 360
[UniProt10a]
UniProt: GTP;
Mutagenesis-Variant 451
[Yim03, UniProt11]
Alternate sequence: C → S; UniProt: No change in GTP binding and hydrolase activity. Does not affect association to the cell inner membrane. Completely impairs tRNA modifying function.
Amino-Acid-Sites-That-Bind 454
[UniProt10]
UniProt: Formyltetrahydrofolate; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3706 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10997; confirmed by SwissProt match.


References

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Ash12: Ash MR, Maher MJ, Mitchell Guss J, Jormakka M (2012). "The cation-dependent G-proteins: In a class of their own." FEBS Lett 586(16);2218-24. PMID: 22750478

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Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

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Meyer08a: Meyer S, Scrima A, Versees W, Wittinghofer A (2008). "Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate." J Mol Biol 380(3);532-47. PMID: 18565343

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Monleon04: Monleon D, Yim L, Martinez-Vicente M, Armengod ME, Celda B (2004). "Backbone 1H, 13C and 15N resonance assignments for the 18.7 kDa GTPase domain of Escherichia coli MnmE protein." J Biomol NMR 28(3);307-8. PMID: 14752268

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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