Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei190 – 1901S-adenosyl-L-methionineUniRule annotation
Binding sitei218 – 2181S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation
Binding sitei223 – 2231S-adenosyl-L-methionineUniRule annotation
Binding sitei239 – 2391S-adenosyl-L-methionineUniRule annotation
Binding sitei299 – 2991S-adenosyl-L-methionineUniRule annotation
Active sitei324 – 3241NucleophileUniRule annotation1 Publication
Active sitei358 – 3581Proton acceptorUniRule annotation1 Publication

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi358 – 3581E → Q: Loss of catalytic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 366366tRNA/tmRNA (uracil-C(5))-methyltransferasePRO_0000161859Add
BLAST

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)LengthDescriptionGraphical viewFeature identifierActions
Sitei190 – 1901Interaction with RNA
Sitei299 – 2991Interaction with RNA
Sitei302 – 3021Interaction with RNA

Protein-protein interaction databases

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

Structurei

Secondary structure

1
366
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi8 – 103Combined sources
Helixi11 – 2616Combined sources
Turni27 – 293Combined sources
Beta strandi35 – 373Combined sources
Beta strandi41 – 433Combined sources
Beta strandi45 – 5511Combined sources
Beta strandi58 – 647Combined sources
Turni66 – 683Combined sources
Beta strandi71 – 733Combined sources
Helixi82 – 9514Combined sources
Helixi99 – 1024Combined sources
Beta strandi105 – 1128Combined sources
Beta strandi117 – 12610Combined sources
Helixi130 – 14415Combined sources
Turni145 – 1473Combined sources
Beta strandi149 – 1568Combined sources
Beta strandi159 – 1646Combined sources
Beta strandi166 – 1716Combined sources
Beta strandi180 – 1845Combined sources
Helixi193 – 20614Combined sources
Turni207 – 2093Combined sources
Beta strandi212 – 2187Combined sources
Helixi223 – 2286Combined sources
Helixi229 – 2313Combined sources
Beta strandi232 – 2387Combined sources
Helixi242 – 25413Combined sources
Beta strandi259 – 2635Combined sources
Helixi268 – 2747Combined sources
Helixi283 – 2853Combined sources
Helixi288 – 2903Combined sources
Beta strandi293 – 2986Combined sources
Helixi307 – 3137Combined sources
Beta strandi316 – 3249Combined sources
Helixi326 – 33914Combined sources
Beta strandi340 – 3489Combined sources
Beta strandi358 – 3658Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3BT7X-ray2.43A/B1-366[»]
ProteinModelPortaliP23003.
SMRiP23003. Positions 1-366.
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
EntryMethodResolution (Å)ChainPositionsPDBsum
3BT7X-ray2.43A/B1-366[»]
ProteinModelPortaliP23003.
SMRiP23003. Positions 1-366.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-11031N.
IntActiP23003. 5 interactions.
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: September 7, 2016
This is version 139 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.