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Protein

tRNA modification GTPase MnmE

Gene

mnmE

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA-cmnm5s2U34.

Cofactori

K+Note: Binds 1 potassium ion per subunit.

Enzyme regulationi

GTPase activity is strongly activated by potassium ions.

Kineticsi

  1. KM=511 µM for GTP2 Publications
  2. KM=346 µM for XTP2 Publications
  1. Vmax=193 nmol/min/mg enzyme with GTP as substrate2 Publications
  2. Vmax=100 nmol/min/mg enzyme with XTP as substrate2 Publications

pH dependencei

Optimum pH is 7.5-9.5.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei23 – 231FormyltetrahydrofolateUniRule annotation
Binding sitei80 – 801FormyltetrahydrofolateUniRule annotation
Binding sitei120 – 1201FormyltetrahydrofolateUniRule annotation
Metal bindingi226 – 2261Potassium
Metal bindingi230 – 2301Magnesium
Metal bindingi245 – 2451Potassium; via carbonyl oxygen
Metal bindingi247 – 2471Potassium; via carbonyl oxygen
Metal bindingi250 – 2501Potassium
Metal bindingi251 – 2511Magnesium
Binding sitei454 – 4541FormyltetrahydrofolateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi226 – 2316GTP
Nucleotide bindingi245 – 2517GTP
Nucleotide bindingi270 – 2734GTP
Nucleotide bindingi335 – 3384GTP
Nucleotide bindingi358 – 3603GTP

GO - Molecular functioni

  • GDP binding Source: EcoCyc
  • GTPase activity Source: EcoCyc
  • GTP binding Source: EcoCyc
  • potassium ion binding Source: EcoCyc

GO - Biological processi

  • chaperone-mediated protein folding Source: EcoCyc
  • response to pH Source: EcoCyc
  • tRNA methylation Source: EcoCyc
  • tRNA wobble uridine modification Source: EcoCyc
  • xenobiotic metabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

GTP-binding, Magnesium, Metal-binding, Nucleotide-binding, Potassium

Enzyme and pathway databases

BioCyciEcoCyc:EG10997-MONOMER.
ECOL316407:JW3684-MONOMER.
MetaCyc:EG10997-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA modification GTPase MnmEUniRule annotation (EC:3.6.-.-UniRule annotation)
Gene namesi
Name:mnmEUniRule annotation
Synonyms:thdFUniRule annotation, trmEUniRule annotation
Ordered Locus Names:b3706, JW3684
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10997. mnmE.

Subcellular locationi

  • Cytoplasm UniRule annotation1 Publication

  • Note: Partially associated with the inner membrane.

GO - Cellular componenti

  • cytoplasm Source: EcoCyc
  • cytosol Source: EcoCyc
  • plasma membrane Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi224 – 2241R → A: 1.5-fold decrease in GTPase activity and almost no change in affinity. 1 Publication
Mutagenesisi226 – 2261N → A: 100-fold decrease in GTPase activity. 5-fold decrease of affinity for GTP. 1 Publication
Mutagenesisi226 – 2261N → K: 70-fold decrease in GTPase activity. 2-fold decrease of affinity for GTP. 1 Publication
Mutagenesisi228 – 2281G → A: Loss of GTP binding and hydrolase activity. Completely impairs tRNA modifying function. 1 Publication
Mutagenesisi249 – 2491G → A: 22-fold decrease in GTPase activity and 7-fold increase of affinity. 1 Publication
Mutagenesisi250 – 2501T → A: 4-fold decrease in GTPase activity and 1.5-fold increase of affinity. 1 Publication
Mutagenesisi250 – 2501T → S: 1.8-fold decrease in GTPase activity and 1.5-fold increase of affinity. 1 Publication
Mutagenesisi251 – 2511T → A: 92-fold decrease in GTPase activity and 59-fold increase of affinity. 1 Publication
Mutagenesisi251 – 2511T → S: 4-fold decrease in GTPase activity and 1.2-fold decrease of affinity. 1 Publication
Mutagenesisi252 – 2521R → A: 7-fold decrease in GTPase activity and 6-fold increase of affinity. 1 Publication
Mutagenesisi252 – 2521R → K: 2-fold decrease in GTPase activity and no change in affinity. 1 Publication
Mutagenesisi253 – 2531D → A: 9-fold decrease in GTPase activity and 13-fold increase of affinity. 1 Publication
Mutagenesisi255 – 2551L → D: 1.5-fold decrease in affinity for GTP. 1 Publication
Mutagenesisi256 – 2561R → A: 2-fold decrease in GTPase activity and almost no change in affinity. 1 Publication
Mutagenesisi270 – 2701D → A: Does not affect GTP binding, but impairs hydrolase activity. Completely impairs tRNA modifying function. 1 Publication
Mutagenesisi275 – 2751R → A: 6-fold decrease in GTPase activity and 1.9-fold increase of affinity. 1 Publication
Mutagenesisi282 – 2821E → A: 1900-fold decrease in GTPase activity. 1 Publication
Mutagenesisi282 – 2821E → Q: 370-fold decrease in GTPase activity. 1 Publication
Mutagenesisi288 – 2881R → A: 1.7-fold decrease in GTPase activity and 1.5-fold increase of affinity. 1 Publication
Mutagenesisi338 – 3381D → N: 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. 1 Publication
Mutagenesisi451 – 4511C → S: No change in GTP binding and hydrolase activity. Does not affect association to the cell inner membrane. Completely impairs tRNA modifying function. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 454454tRNA modification GTPase MnmEPRO_0000188874Add
BLAST

Proteomic databases

PaxDbiP25522.
PRIDEiP25522.

Interactioni

Subunit structurei

Homodimer. Heterotetramer of two MnmE and two MnmG subunits.UniRule annotation1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
mnmGP0A6U34EBI-550986,EBI-550977
pgaDP694323EBI-550986,EBI-562069

Protein-protein interaction databases

BioGridi4261522. 119 interactions.
DIPiDIP-11033N.
IntActiP25522. 23 interactions.
STRINGi511145.b3706.

Structurei

Secondary structure

1
454
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi217 – 2248Combined sources
Helixi229 – 2379Combined sources
Beta strandi255 – 2617Combined sources
Beta strandi264 – 2707Combined sources
Helixi280 – 29415Combined sources
Beta strandi297 – 3048Combined sources
Turni305 – 3073Combined sources
Helixi313 – 3164Combined sources
Helixi318 – 3236Combined sources
Beta strandi330 – 3356Combined sources
Helixi337 – 3404Combined sources
Beta strandi345 – 3495Combined sources
Beta strandi352 – 3565Combined sources
Turni359 – 3613Combined sources
Helixi365 – 37511Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RFLNMR-A210-377[»]
2GJ8X-ray1.70A/B/C/D216-384[»]
2GJ9X-ray2.00A/B/C/D216-384[»]
2GJAX-ray1.85A/B216-384[»]
ProteinModelPortaliP25522.
SMRiP25522. Positions 5-454.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP25522.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini216 – 377162TrmE-type GAdd
BLAST

Sequence similaritiesi

Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. TrmE GTPase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C1H. Bacteria.
COG0486. LUCA.
HOGENOMiHOG000200714.
InParanoidiP25522.
KOiK03650.
OMAiFTPRYAY.
PhylomeDBiP25522.

Family and domain databases

Gene3Di1.20.120.430. 3 hits.
3.30.1360.120. 1 hit.
3.40.50.300. 2 hits.
HAMAPiMF_00379. GTPase_MnmE. 1 hit.
InterProiIPR031168. G_TrmE.
IPR018948. GTP-bd_TrmE_N.
IPR006073. GTP_binding_domain.
IPR004520. GTPase_MnmE.
IPR027368. MnmE_dom2.
IPR025867. MnmE_helical.
IPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR027266. TrmE/GcvT_dom1.
[Graphical view]
PfamiPF01926. MMR_HSR1. 1 hit.
PF12631. MnmE_helical. 1 hit.
PF10396. TrmE_N. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
TIGRFAMsiTIGR00450. mnmE_trmE_thdF. 1 hit.
TIGR00231. small_GTP. 1 hit.
PROSITEiPS51709. G_TRME. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P25522-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDNDTIVAQ ATPPGRGGVG ILRISGFKAR EVAETVLGKL PKPRYADYLP
60 70 80 90 100
FKDADGSVLD QGIALWFPGP NSFTGEDVLE LQGHGGPVIL DLLLKRILTI
110 120 130 140 150
PGLRIARPGE FSERAFLNDK LDLAQAEAIA DLIDASSEQA ARSALNSLQG
160 170 180 190 200
AFSARVNHLV EALTHLRIYV EAAIDFPDEE IDFLSDGKIE AQLNDVIADL
210 220 230 240 250
DAVRAEARQG SLLREGMKVV IAGRPNAGKS SLLNALAGRE AAIVTDIAGT
260 270 280 290 300
TRDVLREHIH IDGMPLHIID TAGLREASDE VERIGIERAW QEIEQADRVL
310 320 330 340 350
FMVDGTTTDA VDPAEIWPEF IARLPAKLPI TVVRNKADIT GETLGMSEVN
360 370 380 390 400
GHALIRLSAR TGEGVDVLRN HLKQSMGFDT NMEGGFLARR RHLQALEQAA
410 420 430 440 450
EHLQQGKAQL LGAWAGELLA EELRLAQQNL SEITGEFTSD DLLGRIFSSF

CIGK
Length:454
Mass (Da):49,231
Last modified:July 15, 1998 - v3
Checksum:i032211797805D2FE
GO

Sequence cautioni

The sequence AAB19981 differs from that shown.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S57109 Genomic DNA. Translation: AAB19981.1. Sequence problems.
L10328 Genomic DNA. Translation: AAA62057.1.
U00096 Genomic DNA. Translation: AAC76729.1.
AP009048 Genomic DNA. Translation: BAE77587.1.
PIRiA38160.
C65173.
RefSeqiNP_418162.1. NC_000913.3.
WP_001282346.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76729; AAC76729; b3706.
BAE77587; BAE77587; BAE77587.
GeneIDi948222.
KEGGiecj:JW3684.
eco:b3706.
PATRICi32122909. VBIEscCol129921_3830.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S57109 Genomic DNA. Translation: AAB19981.1. Sequence problems.
L10328 Genomic DNA. Translation: AAA62057.1.
U00096 Genomic DNA. Translation: AAC76729.1.
AP009048 Genomic DNA. Translation: BAE77587.1.
PIRiA38160.
C65173.
RefSeqiNP_418162.1. NC_000913.3.
WP_001282346.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RFLNMR-A210-377[»]
2GJ8X-ray1.70A/B/C/D216-384[»]
2GJ9X-ray2.00A/B/C/D216-384[»]
2GJAX-ray1.85A/B216-384[»]
ProteinModelPortaliP25522.
SMRiP25522. Positions 5-454.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261522. 119 interactions.
DIPiDIP-11033N.
IntActiP25522. 23 interactions.
STRINGi511145.b3706.

Proteomic databases

PaxDbiP25522.
PRIDEiP25522.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76729; AAC76729; b3706.
BAE77587; BAE77587; BAE77587.
GeneIDi948222.
KEGGiecj:JW3684.
eco:b3706.
PATRICi32122909. VBIEscCol129921_3830.

Organism-specific databases

EchoBASEiEB0990.
EcoGeneiEG10997. mnmE.

Phylogenomic databases

eggNOGiENOG4105C1H. Bacteria.
COG0486. LUCA.
HOGENOMiHOG000200714.
InParanoidiP25522.
KOiK03650.
OMAiFTPRYAY.
PhylomeDBiP25522.

Enzyme and pathway databases

BioCyciEcoCyc:EG10997-MONOMER.
ECOL316407:JW3684-MONOMER.
MetaCyc:EG10997-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP25522.
PROiP25522.

Family and domain databases

Gene3Di1.20.120.430. 3 hits.
3.30.1360.120. 1 hit.
3.40.50.300. 2 hits.
HAMAPiMF_00379. GTPase_MnmE. 1 hit.
InterProiIPR031168. G_TrmE.
IPR018948. GTP-bd_TrmE_N.
IPR006073. GTP_binding_domain.
IPR004520. GTPase_MnmE.
IPR027368. MnmE_dom2.
IPR025867. MnmE_helical.
IPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR027266. TrmE/GcvT_dom1.
[Graphical view]
PfamiPF01926. MMR_HSR1. 1 hit.
PF12631. MnmE_helical. 1 hit.
PF10396. TrmE_N. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 2 hits.
TIGRFAMsiTIGR00450. mnmE_trmE_thdF. 1 hit.
TIGR00231. small_GTP. 1 hit.
PROSITEiPS51709. G_TRME. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiMNME_ECOLI
AccessioniPrimary (citable) accession number: P25522
Secondary accession number(s): Q2M819
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: July 15, 1998
Last modified: September 7, 2016
This is version 159 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.