MNME_ECOLI
ID MNME_ECOLI Reviewed; 454 AA.
AC P25522; Q2M819;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 15-JUL-1998, sequence version 3.
DT 03-AUG-2022, entry version 195.
DE RecName: Full=tRNA modification GTPase MnmE {ECO:0000255|HAMAP-Rule:MF_00379};
DE EC=3.6.-.- {ECO:0000255|HAMAP-Rule:MF_00379};
GN Name=mnmE {ECO:0000255|HAMAP-Rule:MF_00379};
GN Synonyms=thdF {ECO:0000255|HAMAP-Rule:MF_00379},
GN trmE {ECO:0000255|HAMAP-Rule:MF_00379}; OrderedLocusNames=b3706, JW3684;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP PRELIMINARY NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1917835; DOI=10.1128/jb.173.19.6018-6024.1991;
RA Alam K.Y., Clark D.P.;
RT "Molecular cloning and sequence of the thdF gene, which is involved in
RT thiophene and furan oxidation by Escherichia coli.";
RL J. Bacteriol. 173:6018-6024(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7686882; DOI=10.1006/geno.1993.1230;
RA Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
RT "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome:
RT organizational symmetry around the origin of replication.";
RL Genomics 16:551-561(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP CHARACTERIZATION, AND SUBCELLULAR LOCATION.
RX PubMed=10601028; DOI=10.1093/emboj/18.24.7063;
RA Cabedo H., Macian F., Villarroya M., Escudero J.C., Martinez-Vicente M.,
RA Knecht E., Armengod M.-E.;
RT "The Escherichia coli trmE (mnmE) gene, involved in tRNA modification,
RT codes for an evolutionarily conserved GTPase with unusual biochemical
RT properties.";
RL EMBO J. 18:7063-7076(1999).
RN [6]
RP GTPASE ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF GLY-228;
RP ASP-270; ASP-338 AND CYS-451.
RX PubMed=12730230; DOI=10.1074/jbc.m301381200;
RA Yim L., Martinez-Vicente M., Villarroya M., Aguado C., Knecht E.,
RA Armengod M.-E.;
RT "The GTPase activity and C-terminal cysteine of the Escherichia coli MnmE
RT protein are essential for its tRNA modifying function.";
RL J. Biol. Chem. 278:28378-28387(2003).
RN [7]
RP MUTAGENESIS OF ARG-224; GLY-249; THR-250; THR-251; ARG-252; ASP-253;
RP ARG-256; ARG-275 AND ARG-288.
RX PubMed=15983041; DOI=10.1074/jbc.m503223200;
RA Martinez-Vicente M., Yim L., Villarroya M., Mellado M., Perez-Paya E.,
RA Bjoerk G.R., Armengod M.-E.;
RT "Effects of mutagenesis in the switch I region and conserved arginines of
RT Escherichia coli MnmE protein, a GTPase involved in tRNA modification.";
RL J. Biol. Chem. 280:30660-30670(2005).
RN [8]
RP INTERACTION WITH MNMG.
RC STRAIN=K12;
RX PubMed=17062623; DOI=10.1093/nar/gkl752;
RA Yim L., Moukadiri I., Bjoerk G.R., Armengod M.-E.;
RT "Further insights into the tRNA modification process controlled by proteins
RT MnmE and GidA of Escherichia coli.";
RL Nucleic Acids Res. 34:5892-5905(2006).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 216-384 IN COMPLEXES WITH GDP;
RP TRANSITION STATE ANALOG; MAGNESIUM AND POTASSIUM IONS, SUBUNIT, AND
RP MUTAGENESIS OF ASN-226; LEU-255 AND GLU-282.
RX PubMed=16763562; DOI=10.1038/sj.emboj.7601171;
RA Scrima A., Wittinghofer A.;
RT "Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as
RT GTPase-activating element.";
RL EMBO J. 25:2940-2951(2006).
RN [10]
RP STRUCTURE BY NMR OF 210-377, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=17143896; DOI=10.1002/prot.21186;
RA Monleon D., Martinez-Vicente M., Esteve V., Yim L., Prado S.,
RA Armengod M.-E., Celda B.;
RT "Structural insights into the GTPase domain of Escherichia coli MnmE
RT protein.";
RL Proteins 66:726-739(2007).
CC -!- FUNCTION: Exhibits a very high intrinsic GTPase hydrolysis rate.
CC Involved in the addition of a carboxymethylaminomethyl (cmnm) group at
CC the wobble position (U34) of certain tRNAs, forming tRNA-
CC cmnm(5)s(2)U34.
CC -!- COFACTOR:
CC Name=K(+); Xref=ChEBI:CHEBI:29103;
CC Note=Binds 1 potassium ion per subunit.;
CC -!- ACTIVITY REGULATION: GTPase activity is strongly activated by potassium
CC ions.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=511 uM for GTP {ECO:0000269|PubMed:12730230,
CC ECO:0000269|PubMed:17143896};
CC KM=346 uM for XTP {ECO:0000269|PubMed:12730230,
CC ECO:0000269|PubMed:17143896};
CC Vmax=193 nmol/min/mg enzyme with GTP as substrate
CC {ECO:0000269|PubMed:12730230, ECO:0000269|PubMed:17143896};
CC Vmax=100 nmol/min/mg enzyme with XTP as substrate
CC {ECO:0000269|PubMed:12730230, ECO:0000269|PubMed:17143896};
CC pH dependence:
CC Optimum pH is 7.5-9.5. {ECO:0000269|PubMed:12730230,
CC ECO:0000269|PubMed:17143896};
CC -!- SUBUNIT: Homodimer. Heterotetramer of two MnmE and two MnmG subunits.
CC {ECO:0000255|HAMAP-Rule:MF_00379, ECO:0000269|PubMed:16763562}.
CC -!- INTERACTION:
CC P25522; P25522: mnmE; NbExp=3; IntAct=EBI-550986, EBI-550986;
CC P25522; P0A6U3: mnmG; NbExp=6; IntAct=EBI-550986, EBI-550977;
CC P25522; P69432: pgaD; NbExp=5; IntAct=EBI-550986, EBI-562069;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00379,
CC ECO:0000269|PubMed:10601028}. Note=Partially associated with the inner
CC membrane.
CC -!- SIMILARITY: Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like
CC GTPase superfamily. TrmE GTPase family. {ECO:0000255|HAMAP-
CC Rule:MF_00379}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB19981.1; Type=Miscellaneous discrepancy; Evidence={ECO:0000305};
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DR EMBL; S57109; AAB19981.1; ALT_SEQ; Genomic_DNA.
DR EMBL; L10328; AAA62057.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76729.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77587.1; -; Genomic_DNA.
DR PIR; A38160; A38160.
DR PIR; C65173; C65173.
DR RefSeq; NP_418162.1; NC_000913.3.
DR RefSeq; WP_001282346.1; NZ_SSZK01000035.1.
DR PDB; 1RFL; NMR; -; A=210-377.
DR PDB; 2GJ8; X-ray; 1.70 A; A/B/C/D=216-384.
DR PDB; 2GJ9; X-ray; 2.00 A; A/B/C/D=216-384.
DR PDB; 2GJA; X-ray; 1.85 A; A/B=216-384.
DR PDBsum; 1RFL; -.
DR PDBsum; 2GJ8; -.
DR PDBsum; 2GJ9; -.
DR PDBsum; 2GJA; -.
DR AlphaFoldDB; P25522; -.
DR SMR; P25522; -.
DR BioGRID; 4261522; 160.
DR BioGRID; 852524; 3.
DR ComplexPortal; CPX-5361; tRNA uridine 5-carboxymethylaminomethyl modification complex.
DR DIP; DIP-11033N; -.
DR IntAct; P25522; 24.
DR STRING; 511145.b3706; -.
DR jPOST; P25522; -.
DR PaxDb; P25522; -.
DR PRIDE; P25522; -.
DR EnsemblBacteria; AAC76729; AAC76729; b3706.
DR EnsemblBacteria; BAE77587; BAE77587; BAE77587.
DR GeneID; 948222; -.
DR KEGG; ecj:JW3684; -.
DR KEGG; eco:b3706; -.
DR PATRIC; fig|1411691.4.peg.2997; -.
DR EchoBASE; EB0990; -.
DR eggNOG; COG0486; Bacteria.
DR HOGENOM; CLU_019624_4_1_6; -.
DR InParanoid; P25522; -.
DR OMA; CEIQCHG; -.
DR PhylomeDB; P25522; -.
DR BioCyc; EcoCyc:EG10997-MON; -.
DR BioCyc; MetaCyc:EG10997-MON; -.
DR EvolutionaryTrace; P25522; -.
DR PRO; PR:P25522; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoCyc.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0002144; C:cytosolic tRNA wobble base thiouridylase complex; IPI:ComplexPortal.
DR GO; GO:0005886; C:plasma membrane; IDA:EcoCyc.
DR GO; GO:0019003; F:GDP binding; IDA:EcoCyc.
DR GO; GO:0005525; F:GTP binding; IDA:EcoCyc.
DR GO; GO:0003924; F:GTPase activity; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0030955; F:potassium ion binding; IDA:EcoCyc.
DR GO; GO:0061077; P:chaperone-mediated protein folding; IDA:EcoCyc.
DR GO; GO:0140018; P:regulation of cytoplasmic translational fidelity; IC:ComplexPortal.
DR GO; GO:0009268; P:response to pH; IMP:EcoCyc.
DR GO; GO:0030488; P:tRNA methylation; IMP:EcoCyc.
DR GO; GO:0002926; P:tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation; IDA:ComplexPortal.
DR GO; GO:0002098; P:tRNA wobble uridine modification; IDA:EcoCyc.
DR CDD; cd04164; trmE; 1.
DR Gene3D; 1.20.120.430; -; 1.
DR Gene3D; 3.30.1360.120; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_00379; GTPase_MnmE; 1.
DR InterPro; IPR031168; G_TrmE.
DR InterPro; IPR006073; GTP-bd.
DR InterPro; IPR018948; GTP-bd_TrmE_N.
DR InterPro; IPR004520; GTPase_MnmE.
DR InterPro; IPR027368; MnmE_dom2.
DR InterPro; IPR025867; MnmE_helical.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR005225; Small_GTP-bd_dom.
DR InterPro; IPR027266; TrmE/GcvT_dom1.
DR Pfam; PF01926; MMR_HSR1; 1.
DR Pfam; PF12631; MnmE_helical; 1.
DR Pfam; PF10396; TrmE_N; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00450; mnmE_trmE_thdF; 1.
DR TIGRFAMs; TIGR00231; small_GTP; 1.
DR PROSITE; PS51709; G_TRME; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; GTP-binding; Hydrolase; Magnesium; Metal-binding;
KW Nucleotide-binding; Potassium; Reference proteome; tRNA processing.
FT CHAIN 1..454
FT /note="tRNA modification GTPase MnmE"
FT /id="PRO_0000188874"
FT DOMAIN 216..377
FT /note="TrmE-type G"
FT BINDING 23
FT /ligand="(6S)-5-formyl-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57457"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00379"
FT BINDING 80
FT /ligand="(6S)-5-formyl-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57457"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00379"
FT BINDING 120
FT /ligand="(6S)-5-formyl-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57457"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00379"
FT BINDING 226..231
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT BINDING 226
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT BINDING 230
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 245..251
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT BINDING 245
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT BINDING 247
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT BINDING 250
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT BINDING 251
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 270..273
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT BINDING 335..338
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT BINDING 358..360
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT BINDING 454
FT /ligand="(6S)-5-formyl-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57457"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00379"
FT MUTAGEN 224
FT /note="R->A: 1.5-fold decrease in GTPase activity and
FT almost no change in affinity."
FT /evidence="ECO:0000269|PubMed:15983041"
FT MUTAGEN 226
FT /note="N->A: 100-fold decrease in GTPase activity. 5-fold
FT decrease of affinity for GTP."
FT /evidence="ECO:0000269|PubMed:16763562"
FT MUTAGEN 226
FT /note="N->K: 70-fold decrease in GTPase activity. 2-fold
FT decrease of affinity for GTP."
FT /evidence="ECO:0000269|PubMed:16763562"
FT MUTAGEN 228
FT /note="G->A: Loss of GTP binding and hydrolase activity.
FT Completely impairs tRNA modifying function."
FT /evidence="ECO:0000269|PubMed:12730230"
FT MUTAGEN 249
FT /note="G->A: 22-fold decrease in GTPase activity and 7-fold
FT increase of affinity."
FT /evidence="ECO:0000269|PubMed:15983041"
FT MUTAGEN 250
FT /note="T->A: 4-fold decrease in GTPase activity and 1.5-
FT fold increase of affinity."
FT /evidence="ECO:0000269|PubMed:15983041"
FT MUTAGEN 250
FT /note="T->S: 1.8-fold decrease in GTPase activity and 1.5-
FT fold increase of affinity."
FT /evidence="ECO:0000269|PubMed:15983041"
FT MUTAGEN 251
FT /note="T->A: 92-fold decrease in GTPase activity and 59-
FT fold increase of affinity."
FT /evidence="ECO:0000269|PubMed:15983041"
FT MUTAGEN 251
FT /note="T->S: 4-fold decrease in GTPase activity and 1.2-
FT fold decrease of affinity."
FT /evidence="ECO:0000269|PubMed:15983041"
FT MUTAGEN 252
FT /note="R->A: 7-fold decrease in GTPase activity and 6-fold
FT increase of affinity."
FT /evidence="ECO:0000269|PubMed:15983041"
FT MUTAGEN 252
FT /note="R->K: 2-fold decrease in GTPase activity and no
FT change in affinity."
FT /evidence="ECO:0000269|PubMed:15983041"
FT MUTAGEN 253
FT /note="D->A: 9-fold decrease in GTPase activity and 13-fold
FT increase of affinity."
FT /evidence="ECO:0000269|PubMed:15983041"
FT MUTAGEN 255
FT /note="L->D: 1.5-fold decrease in affinity for GTP."
FT /evidence="ECO:0000269|PubMed:16763562"
FT MUTAGEN 256
FT /note="R->A: 2-fold decrease in GTPase activity and almost
FT no change in affinity."
FT /evidence="ECO:0000269|PubMed:15983041"
FT MUTAGEN 270
FT /note="D->A: Does not affect GTP binding, but impairs
FT hydrolase activity. Completely impairs tRNA modifying
FT function."
FT /evidence="ECO:0000269|PubMed:12730230"
FT MUTAGEN 275
FT /note="R->A: 6-fold decrease in GTPase activity and 1.9-
FT fold increase of affinity."
FT /evidence="ECO:0000269|PubMed:15983041"
FT MUTAGEN 282
FT /note="E->A: 1900-fold decrease in GTPase activity."
FT /evidence="ECO:0000269|PubMed:16763562"
FT MUTAGEN 282
FT /note="E->Q: 370-fold decrease in GTPase activity."
FT /evidence="ECO:0000269|PubMed:16763562"
FT MUTAGEN 288
FT /note="R->A: 1.7-fold decrease in GTPase activity and 1.5-
FT fold increase of affinity."
FT /evidence="ECO:0000269|PubMed:15983041"
FT MUTAGEN 338
FT /note="D->N: Strong decrease in GTP binding. Does not
FT affect hydrolase activity, but has 10-fold higher affinity
FT for XTP than for GTP. Partially impairs tRNA modifying
FT function."
FT /evidence="ECO:0000269|PubMed:12730230"
FT MUTAGEN 451
FT /note="C->S: No change in GTP binding and hydrolase
FT activity. Does not affect association to the cell inner
FT membrane. Completely impairs tRNA modifying function."
FT /evidence="ECO:0000269|PubMed:12730230"
FT STRAND 217..224
FT /evidence="ECO:0007829|PDB:2GJ8"
FT HELIX 229..237
FT /evidence="ECO:0007829|PDB:2GJ8"
FT STRAND 255..261
FT /evidence="ECO:0007829|PDB:2GJ8"
FT STRAND 264..270
FT /evidence="ECO:0007829|PDB:2GJ8"
FT HELIX 280..294
FT /evidence="ECO:0007829|PDB:2GJ8"
FT STRAND 297..304
FT /evidence="ECO:0007829|PDB:2GJ8"
FT TURN 305..307
FT /evidence="ECO:0007829|PDB:2GJ8"
FT HELIX 313..316
FT /evidence="ECO:0007829|PDB:2GJ8"
FT HELIX 318..323
FT /evidence="ECO:0007829|PDB:2GJ8"
FT STRAND 330..335
FT /evidence="ECO:0007829|PDB:2GJ8"
FT HELIX 337..340
FT /evidence="ECO:0007829|PDB:2GJ8"
FT STRAND 345..349
FT /evidence="ECO:0007829|PDB:2GJ8"
FT STRAND 352..356
FT /evidence="ECO:0007829|PDB:2GJ8"
FT TURN 359..361
FT /evidence="ECO:0007829|PDB:2GJ8"
FT HELIX 365..375
FT /evidence="ECO:0007829|PDB:2GJ8"
SQ SEQUENCE 454 AA; 49231 MW; 032211797805D2FE CRC64;
MSDNDTIVAQ ATPPGRGGVG ILRISGFKAR EVAETVLGKL PKPRYADYLP FKDADGSVLD
QGIALWFPGP NSFTGEDVLE LQGHGGPVIL DLLLKRILTI PGLRIARPGE FSERAFLNDK
LDLAQAEAIA DLIDASSEQA ARSALNSLQG AFSARVNHLV EALTHLRIYV EAAIDFPDEE
IDFLSDGKIE AQLNDVIADL DAVRAEARQG SLLREGMKVV IAGRPNAGKS SLLNALAGRE
AAIVTDIAGT TRDVLREHIH IDGMPLHIID TAGLREASDE VERIGIERAW QEIEQADRVL
FMVDGTTTDA VDPAEIWPEF IARLPAKLPI TVVRNKADIT GETLGMSEVN GHALIRLSAR
TGEGVDVLRN HLKQSMGFDT NMEGGFLARR RHLQALEQAA EHLQQGKAQL LGAWAGELLA
EELRLAQQNL SEITGEFTSD DLLGRIFSSF CIGK