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Protein

tRNA/tmRNA (uracil-C(5))-methyltransferase

Gene

trmA

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

Functioni

Dual-specificity methyltransferase that catalyzes the formation of 5-methyluridine at position 54 (m5U54) in all tRNAs, and that of position 341 (m5U341) in tmRNA (transfer-mRNA).UniRule annotation3 Publications

Catalytic activityi

S-adenosyl-L-methionine + uracil(54) in tRNA = S-adenosyl-L-homocysteine + 5-methyluracil(54) in tRNA.UniRule annotation1 Publication
S-adenosyl-L-methionine + uracil(341) in tmRNA = S-adenosyl-L-homocysteine + 5-methyluracil(341) in tmRNA.UniRule annotation1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei190S-adenosyl-L-methionineUniRule annotation1
Binding sitei218S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation1
Binding sitei223S-adenosyl-L-methionineUniRule annotation1
Binding sitei239S-adenosyl-L-methionineUniRule annotation1
Binding sitei299S-adenosyl-L-methionineUniRule annotation1
Active sitei324NucleophileUniRule annotation1 Publication1
Active sitei358Proton acceptorUniRule annotation1 Publication1

GO - Molecular functioni

  • rRNA binding Source: EcoCyc
  • S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity Source: EcoCyc
  • tRNA binding Source: EcoCyc

GO - Biological processi

  • tRNA methylation Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciEcoCyc:EG11022-MONOMER.
ECOL316407:JW3937-MONOMER.
MetaCyc:EG11022-MONOMER.
BRENDAi2.1.1.35. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA/tmRNA (uracil-C(5))-methyltransferaseUniRule annotation (EC:2.1.1.-UniRule annotation, EC:2.1.1.35UniRule annotation)
Alternative name(s):
tRNA (uracil(54)-C(5))-methyltransferaseUniRule annotation
tRNA(m5U54)-methyltransferaseUniRule annotation
Short name:
RUMTUniRule annotation
tmRNA (uracil(341)-C(5))-methyltransferaseUniRule annotation
Gene namesi
Name:trmAUniRule annotation
Ordered Locus Names:b3965, JW3937
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11022. trmA.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene exhibit a lack of m5U modification in tmRNA.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi358E → Q: Loss of catalytic activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001618591 – 366tRNA/tmRNA (uracil-C(5))-methyltransferaseAdd BLAST366

Proteomic databases

PaxDbiP23003.
PRIDEiP23003.

Expressioni

Inductioni

Growth rate-dependent regulation of transcription. Is a novel example of a mRNA regulated through a mechanism similar to that of a stable RNA (rRNA).

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei190Interaction with RNA1
Sitei299Interaction with RNA1
Sitei302Interaction with RNA1

Protein-protein interaction databases

DIPiDIP-11031N.
IntActiP23003. 5 interactors.
MINTiMINT-1223595.
STRINGi511145.b3965.

Structurei

Secondary structure

1366
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi8 – 10Combined sources3
Helixi11 – 26Combined sources16
Turni27 – 29Combined sources3
Beta strandi35 – 37Combined sources3
Beta strandi41 – 43Combined sources3
Beta strandi45 – 55Combined sources11
Beta strandi58 – 64Combined sources7
Turni66 – 68Combined sources3
Beta strandi71 – 73Combined sources3
Helixi82 – 95Combined sources14
Helixi99 – 102Combined sources4
Beta strandi105 – 112Combined sources8
Beta strandi117 – 126Combined sources10
Helixi130 – 144Combined sources15
Turni145 – 147Combined sources3
Beta strandi149 – 156Combined sources8
Beta strandi159 – 164Combined sources6
Beta strandi166 – 171Combined sources6
Beta strandi180 – 184Combined sources5
Helixi193 – 206Combined sources14
Turni207 – 209Combined sources3
Beta strandi212 – 218Combined sources7
Helixi223 – 228Combined sources6
Helixi229 – 231Combined sources3
Beta strandi232 – 238Combined sources7
Helixi242 – 254Combined sources13
Beta strandi259 – 263Combined sources5
Helixi268 – 274Combined sources7
Helixi283 – 285Combined sources3
Helixi288 – 290Combined sources3
Beta strandi293 – 298Combined sources6
Helixi307 – 313Combined sources7
Beta strandi316 – 324Combined sources9
Helixi326 – 339Combined sources14
Beta strandi340 – 348Combined sources9
Beta strandi358 – 365Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BT7X-ray2.43A/B1-366[»]
ProteinModelPortaliP23003.
SMRiP23003.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP23003.

Family & Domainsi

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family. TrmA subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107R9T. Bacteria.
COG2265. LUCA.
HOGENOMiHOG000218626.
InParanoidiP23003.
KOiK00557.
OMAiESAQYNI.
PhylomeDBiP23003.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01011. RNA_methyltr_TrmA. 1 hit.
InterProiIPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR029063. SAM-dependent_MTases.
IPR011869. TrmA_MeTrfase.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR02143. trmA_only. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P23003-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTPEHLPTEQ YEAQLAEKVV RLQSMMAPFS DLVPEVFRSP VSHYRMRAEF
60 70 80 90 100
RIWHDGDDLY HIIFDQQTKS RIRVDSFPAA SELINQLMTA MIAGVRNNPV
110 120 130 140 150
LRHKLFQIDY LTTLSNQAVV SLLYHKKLDD EWRQEAEALR DALRAQNLNV
160 170 180 190 200
HLIGRATKTK IELDQDYIDE RLPVAGKEMI YRQVENSFTQ PNAAMNIQML
210 220 230 240 250
EWALDVTKGS KGDLLELYCG NGNFSLALAR NFDRVLATEI AKPSVAAAQY
260 270 280 290 300
NIAANHIDNV QIIRMAAEEF TQAMNGVREF NRLQGIDLKS YQCETIFVDP
310 320 330 340 350
PRSGLDSETE KMVQAYPRIL YISCNPETLC KNLETLSQTH KVERLALFDQ
360
FPYTHHMECG VLLTAK
Length:366
Mass (Da):41,967
Last modified:August 1, 1991 - v1
Checksum:iA7A65FD98380D27D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M57568 Genomic DNA. Translation: AAA24691.1.
U00006 Genomic DNA. Translation: AAC43071.1.
U00096 Genomic DNA. Translation: AAC76947.1.
AP009048 Genomic DNA. Translation: BAE77346.1.
X66026 Genomic DNA. Translation: CAA46825.1.
PIRiA37321.
RefSeqiNP_418400.1. NC_000913.3.
WP_000187022.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76947; AAC76947; b3965.
BAE77346; BAE77346; BAE77346.
GeneIDi947143.
KEGGiecj:JW3937.
eco:b3965.
PATRICi32123451. VBIEscCol129921_4086.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M57568 Genomic DNA. Translation: AAA24691.1.
U00006 Genomic DNA. Translation: AAC43071.1.
U00096 Genomic DNA. Translation: AAC76947.1.
AP009048 Genomic DNA. Translation: BAE77346.1.
X66026 Genomic DNA. Translation: CAA46825.1.
PIRiA37321.
RefSeqiNP_418400.1. NC_000913.3.
WP_000187022.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BT7X-ray2.43A/B1-366[»]
ProteinModelPortaliP23003.
SMRiP23003.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-11031N.
IntActiP23003. 5 interactors.
MINTiMINT-1223595.
STRINGi511145.b3965.

Proteomic databases

PaxDbiP23003.
PRIDEiP23003.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76947; AAC76947; b3965.
BAE77346; BAE77346; BAE77346.
GeneIDi947143.
KEGGiecj:JW3937.
eco:b3965.
PATRICi32123451. VBIEscCol129921_4086.

Organism-specific databases

EchoBASEiEB1015.
EcoGeneiEG11022. trmA.

Phylogenomic databases

eggNOGiENOG4107R9T. Bacteria.
COG2265. LUCA.
HOGENOMiHOG000218626.
InParanoidiP23003.
KOiK00557.
OMAiESAQYNI.
PhylomeDBiP23003.

Enzyme and pathway databases

BioCyciEcoCyc:EG11022-MONOMER.
ECOL316407:JW3937-MONOMER.
MetaCyc:EG11022-MONOMER.
BRENDAi2.1.1.35. 2026.

Miscellaneous databases

EvolutionaryTraceiP23003.
PROiP23003.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_01011. RNA_methyltr_TrmA. 1 hit.
InterProiIPR030390. MeTrfase_TrmA_AS.
IPR030391. MeTrfase_TrmA_CS.
IPR029063. SAM-dependent_MTases.
IPR011869. TrmA_MeTrfase.
IPR010280. U5_MeTrfase_fam.
[Graphical view]
PfamiPF05958. tRNA_U5-meth_tr. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR02143. trmA_only. 1 hit.
PROSITEiPS51687. SAM_MT_RNA_M5U. 1 hit.
PS01230. TRMA_1. 1 hit.
PS01231. TRMA_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTRMA_ECOLI
AccessioniPrimary (citable) accession number: P23003
Secondary accession number(s): Q2M8R0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: August 1, 1991
Last modified: November 2, 2016
This is version 141 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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.