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Protein

tRNA (guanine-N(1)-)-methyltransferase

Gene

trmD

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

Functioni

Specifically methylates guanosine-37 in various tRNAs.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei86S-adenosyl-L-methionine1
Binding sitei113S-adenosyl-L-methionine; via amide nitrogenBy similarity1
Active sitei169Proton acceptorSequence analysis1

GO - Molecular functioni

  • 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity Source: GO_Central
  • magnesium ion binding Source: EcoCyc
  • tRNA (guanine(37)-N(1))-methyltransferase activity Source: EcoCyc
  • tRNA (guanine-N1-)-methyltransferase activity Source: EcoCyc

GO - Biological processi

  • tRNA methylation Source: EcoCyc
  • tRNA N1-guanine 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:EG11023-MONOMER.
ECOL316407:JW2588-MONOMER.
MetaCyc:EG11023-MONOMER.
BRENDAi2.1.1.228. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA (guanine-N(1)-)-methyltransferase (EC:2.1.1.228)
Alternative name(s):
M1G-methyltransferase
tRNA [GM37] methyltransferase
Gene namesi
Name:trmD
Ordered Locus Names:b2607, JW2588
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11023. trmD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi59G → A: Loss of activity. 1 Publication1
Mutagenesisi91G → A: Loss of activity; no effect on tRNA binding. 1 Publication1
Mutagenesisi114R → A: Loss of activity. 1 Publication1
Mutagenesisi115Y → A: Increases Km for S-adenosyl-L-methionine 24-fold. 1 Publication1
Mutagenesisi117G → A: Loss of activity. 1 Publication1
Mutagenesisi119D → A: Loss of activity. 1 Publication1
Mutagenesisi121R → A: Loss of activity; no effect on tRNA binding. 1 Publication1
Mutagenesisi128D → A: Loss of activity. 1 Publication1
Mutagenesisi135D → A: Loss of activity; no effect on tRNA binding. 1 Publication1
Mutagenesisi136Y → A: Increases Km for S-adenosyl-L-methionine 68-fold. 1 Publication1
Mutagenesisi141G → A: Increases Km for S-adenosyl-L-methionine 82-fold. 1 Publication1
Mutagenesisi154R → A: Loss of activity; no effect on tRNA binding. 1 Publication1
Mutagenesisi169D → A: Loss of activity. 1 Publication1
Mutagenesisi171F → A: Loss of activity. 1 Publication1
Mutagenesisi184P → A: Loss of activity; no effect on tRNA binding. 1 Publication1
Mutagenesisi192V → A: Loss of activity; no effect on tRNA binding. 1 Publication1
Mutagenesisi193P → A: Loss of activity; no effect on tRNA binding. 1 Publication1
Mutagenesisi196L → A: Loss of activity; no effect on tRNA binding. 1 Publication1
Mutagenesisi197L → A: Loss of activity; no effect on tRNA binding. 1 Publication1
Mutagenesisi204I → A: Loss of activity; no effect on tRNA binding. 1 Publication1
Mutagenesisi207W → A: Loss of activity; no effect on tRNA binding. 1 Publication1
Mutagenesisi207W → F or H: Small decrease in activity. 1 Publication1
Mutagenesisi208R → A: Loss of activity; no effect on tRNA binding. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000603751 – 255tRNA (guanine-N(1)-)-methyltransferaseAdd BLAST255

Proteomic databases

PaxDbiP0A873.
PRIDEiP0A873.

Expressioni

Inductioni

Part of the rpsP-rimM-trmD-rplS operon.

Interactioni

Subunit structurei

Homodimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-1129132,EBI-1129132

Protein-protein interaction databases

BioGridi4263072. 18 interactors.
DIPiDIP-48264N.
IntActiP0A873. 1 interactor.
STRINGi511145.b2607.

Structurei

Secondary structure

1255
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 6Combined sources5
Helixi10 – 13Combined sources4
Helixi14 – 17Combined sources4
Helixi20 – 27Combined sources8
Beta strandi32 – 36Combined sources5
Helixi38 – 41Combined sources4
Helixi64 – 78Combined sources15
Beta strandi83 – 87Combined sources5
Beta strandi91 – 93Combined sources3
Helixi96 – 103Combined sources8
Beta strandi106 – 111Combined sources6
Helixi120 – 126Combined sources7
Beta strandi128 – 136Combined sources9
Helixi142 – 153Combined sources12
Turni157 – 159Combined sources3
Beta strandi185 – 187Combined sources3
Helixi194 – 197Combined sources4
Helixi201 – 219Combined sources19
Helixi221 – 225Combined sources5
Helixi231 – 245Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1P9PX-ray2.50A1-255[»]
ProteinModelPortaliP0A873.
SMRiP0A873.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A873.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni133 – 138S-adenosyl-L-methionine binding6

Sequence similaritiesi

Belongs to the RNA methyltransferase TrmD family.Curated

Phylogenomic databases

eggNOGiENOG4105D6X. Bacteria.
COG0336. LUCA.
HOGENOMiHOG000016242.
InParanoidiP0A873.
KOiK00554.
OMAiYKGVDQR.
PhylomeDBiP0A873.

Family and domain databases

Gene3Di1.10.1270.20. 1 hit.
3.40.1280.10. 1 hit.
HAMAPiMF_00605. TrmD. 1 hit.
InterProiIPR029028. Alpha/beta_knot_MTases.
IPR002649. tRNA_m1G_MeTrfase_bac.
IPR023148. tRNA_m1G_MeTrfase_C.
IPR029026. tRNA_m1G_MTases_N.
IPR016009. tRNA_MeTrfase_TRMD/TRM10.
[Graphical view]
PfamiPF01746. tRNA_m1G_MT. 1 hit.
[Graphical view]
PIRSFiPIRSF000386. tRNA_mtase. 1 hit.
SUPFAMiSSF75217. SSF75217. 1 hit.
TIGRFAMsiTIGR00088. trmD. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A873-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MWIGIISLFP EMFRAITDYG VTGRAVKNGL LSIQSWSPRD FTHDRHRTVD
60 70 80 90 100
DRPYGGGPGM LMMVQPLRDA IHAAKAAAGE GAKVIYLSPQ GRKLDQAGVS
110 120 130 140 150
ELATNQKLIL VCGRYEGIDE RVIQTEIDEE WSIGDYVLSG GELPAMTLID
160 170 180 190 200
SVSRFIPGVL GHEASATEDS FAEGLLDCPH YTRPEVLEGM EVPPVLLSGN
210 220 230 240 250
HAEIRRWRLK QSLGRTWLRR PELLENLALT EEQARLLAEF KTEHAQQQHK

HDGMA
Length:255
Mass (Da):28,422
Last modified:April 1, 1988 - v1
Checksum:iB101087229B4CDBD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01818 Genomic DNA. Translation: CAA25959.1.
U00096 Genomic DNA. Translation: AAC75656.1.
AP009048 Genomic DNA. Translation: BAA16492.1.
PIRiA30380. XYECG1.
RefSeqiNP_417098.1. NC_000913.3.
WP_000264777.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75656; AAC75656; b2607.
BAA16492; BAA16492; BAA16492.
GeneIDi947099.
KEGGiecj:JW2588.
eco:b2607.
PATRICi32120613. VBIEscCol129921_2705.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01818 Genomic DNA. Translation: CAA25959.1.
U00096 Genomic DNA. Translation: AAC75656.1.
AP009048 Genomic DNA. Translation: BAA16492.1.
PIRiA30380. XYECG1.
RefSeqiNP_417098.1. NC_000913.3.
WP_000264777.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1P9PX-ray2.50A1-255[»]
ProteinModelPortaliP0A873.
SMRiP0A873.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263072. 18 interactors.
DIPiDIP-48264N.
IntActiP0A873. 1 interactor.
STRINGi511145.b2607.

Proteomic databases

PaxDbiP0A873.
PRIDEiP0A873.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75656; AAC75656; b2607.
BAA16492; BAA16492; BAA16492.
GeneIDi947099.
KEGGiecj:JW2588.
eco:b2607.
PATRICi32120613. VBIEscCol129921_2705.

Organism-specific databases

EchoBASEiEB1016.
EcoGeneiEG11023. trmD.

Phylogenomic databases

eggNOGiENOG4105D6X. Bacteria.
COG0336. LUCA.
HOGENOMiHOG000016242.
InParanoidiP0A873.
KOiK00554.
OMAiYKGVDQR.
PhylomeDBiP0A873.

Enzyme and pathway databases

BioCyciEcoCyc:EG11023-MONOMER.
ECOL316407:JW2588-MONOMER.
MetaCyc:EG11023-MONOMER.
BRENDAi2.1.1.228. 2026.

Miscellaneous databases

EvolutionaryTraceiP0A873.
PROiP0A873.

Family and domain databases

Gene3Di1.10.1270.20. 1 hit.
3.40.1280.10. 1 hit.
HAMAPiMF_00605. TrmD. 1 hit.
InterProiIPR029028. Alpha/beta_knot_MTases.
IPR002649. tRNA_m1G_MeTrfase_bac.
IPR023148. tRNA_m1G_MeTrfase_C.
IPR029026. tRNA_m1G_MTases_N.
IPR016009. tRNA_MeTrfase_TRMD/TRM10.
[Graphical view]
PfamiPF01746. tRNA_m1G_MT. 1 hit.
[Graphical view]
PIRSFiPIRSF000386. tRNA_mtase. 1 hit.
SUPFAMiSSF75217. SSF75217. 1 hit.
TIGRFAMsiTIGR00088. trmD. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiTRMD_ECOLI
AccessioniPrimary (citable) accession number: P0A873
Secondary accession number(s): P07020
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: April 1, 1988
Last modified: November 2, 2016
This is version 97 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The specific activity of this enzyme increases only slightly with increased growth rate.
This enzyme is present at ca. 80 molecules/genome.

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.