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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei86 – 861S-adenosyl-L-methionine
Binding sitei113 – 1131S-adenosyl-L-methionine; via amide nitrogenBy similarity
Active sitei169 – 1691Proton acceptorSequence analysis

GO - Molecular functioni

  • 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity Source: GO_Central
  • identical protein binding Source: IntAct
  • 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi59 – 591G → A: Loss of activity. 1 Publication
Mutagenesisi91 – 911G → A: Loss of activity; no effect on tRNA binding. 1 Publication
Mutagenesisi114 – 1141R → A: Loss of activity. 1 Publication
Mutagenesisi115 – 1151Y → A: Increases Km for S-adenosyl-L-methionine 24-fold. 1 Publication
Mutagenesisi117 – 1171G → A: Loss of activity. 1 Publication
Mutagenesisi119 – 1191D → A: Loss of activity. 1 Publication
Mutagenesisi121 – 1211R → A: Loss of activity; no effect on tRNA binding. 1 Publication
Mutagenesisi128 – 1281D → A: Loss of activity. 1 Publication
Mutagenesisi135 – 1351D → A: Loss of activity; no effect on tRNA binding. 1 Publication
Mutagenesisi136 – 1361Y → A: Increases Km for S-adenosyl-L-methionine 68-fold. 1 Publication
Mutagenesisi141 – 1411G → A: Increases Km for S-adenosyl-L-methionine 82-fold. 1 Publication
Mutagenesisi154 – 1541R → A: Loss of activity; no effect on tRNA binding. 1 Publication
Mutagenesisi169 – 1691D → A: Loss of activity. 1 Publication
Mutagenesisi171 – 1711F → A: Loss of activity. 1 Publication
Mutagenesisi184 – 1841P → A: Loss of activity; no effect on tRNA binding. 1 Publication
Mutagenesisi192 – 1921V → A: Loss of activity; no effect on tRNA binding. 1 Publication
Mutagenesisi193 – 1931P → A: Loss of activity; no effect on tRNA binding. 1 Publication
Mutagenesisi196 – 1961L → A: Loss of activity; no effect on tRNA binding. 1 Publication
Mutagenesisi197 – 1971L → A: Loss of activity; no effect on tRNA binding. 1 Publication
Mutagenesisi204 – 2041I → A: Loss of activity; no effect on tRNA binding. 1 Publication
Mutagenesisi207 – 2071W → A: Loss of activity; no effect on tRNA binding. 1 Publication
Mutagenesisi207 – 2071W → F or H: Small decrease in activity. 1 Publication
Mutagenesisi208 – 2081R → A: Loss of activity; no effect on tRNA binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 255255tRNA (guanine-N(1)-)-methyltransferasePRO_0000060375Add
BLAST

Proteomic databases

EPDiP0A873.
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

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi4263072. 18 interactions.
DIPiDIP-48264N.
IntActiP0A873. 1 interaction.
STRINGi511145.b2607.

Structurei

Secondary structure

1
255
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 65Combined sources
Helixi10 – 134Combined sources
Helixi14 – 174Combined sources
Helixi20 – 278Combined sources
Beta strandi32 – 365Combined sources
Helixi38 – 414Combined sources
Helixi64 – 7815Combined sources
Beta strandi83 – 875Combined sources
Beta strandi91 – 933Combined sources
Helixi96 – 1038Combined sources
Beta strandi106 – 1116Combined sources
Helixi120 – 1267Combined sources
Beta strandi128 – 1369Combined sources
Helixi142 – 15312Combined sources
Turni157 – 1593Combined sources
Beta strandi185 – 1873Combined sources
Helixi194 – 1974Combined sources
Helixi201 – 21919Combined sources
Helixi221 – 2255Combined sources
Helixi231 – 24515Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1P9PX-ray2.50A1-255[»]
ProteinModelPortaliP0A873.
SMRiP0A873. Positions 1-246.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A873.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni133 – 1386S-adenosyl-L-methionine binding

Sequence similaritiesi

Belongs to the RNA methyltransferase TrmD family.Curated

Phylogenomic databases

eggNOGiENOG4105D6X. Bacteria.
COG0336. LUCA.
HOGENOMiHOG000016242.
InParanoidiP0A873.
KOiK00554.
OMAiYKGVDQR.
OrthoDBiEOG6J48RZ.
PhylomeDBiP0A873.

Family and domain databases

Gene3Di1.10.1270.20. 1 hit.
3.40.1280.10. 1 hit.
HAMAPiMF_00605. TrmD.
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
EntryMethodResolution (Å)ChainPositionsPDBsum
1P9PX-ray2.50A1-255[»]
ProteinModelPortaliP0A873.
SMRiP0A873. Positions 1-246.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263072. 18 interactions.
DIPiDIP-48264N.
IntActiP0A873. 1 interaction.
STRINGi511145.b2607.

Proteomic databases

EPDiP0A873.
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.
OrthoDBiEOG6J48RZ.
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.
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...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of an Escherichia coli operon containing genes for the tRNA(m1G)methyltransferase, the ribosomal proteins S16 and L19 and a 21-K polypeptide."
    Bystroem A.S., Hjalmarsson K.J., Wikstroem P.M., Bjoerk G.R.
    EMBO J. 2:899-905(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], OPERON STRUCTURE.
    Strain: K12.
  2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
    Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
    , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
    DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Purification and characterization of transfer RNA (guanine-1)methyltransferase from Escherichia coli."
    Hjalmarsson K.J., Bystroem A.S., Bjoerk G.R.
    J. Biol. Chem. 258:1343-1351(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, PROTEIN SEQUENCE OF 1-10.
  6. Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, FUNCTION, SUBUNIT, MUTAGENESIS OF GLY-59; GLY-91; ARG-114; TYR-115; GLY-117; ASP-119; ARG-121; ASP-128; ASP-135; TYR-136; GLY-141; ARG-154; ASP-169; PHE-171; PRO-184; VAL-192; PRO-193; LEU-196; LEU-197; ILE-204; TRP-207 AND ARG-208.

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: June 8, 2016
This is version 95 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.