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Protein

tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI

Gene

trmI

Organism
Pyrococcus abyssi (strain GE5 / Orsay)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenosine at position(s) 57 (m1A57) and 58 (m1A58) in the T-loop of some tRNAs. Methylates the first adenine of an AA sequence.2 Publications

Catalytic activityi

2 S-adenosyl-L-methionine + adenine(57)/adenine(58) in tRNA = 2 S-adenosyl-L-homocysteine + N(1)-methyladenine(57)/N(1)-methyladenine(58) in tRNA.PROSITE-ProRule annotation2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei125 – 1251S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication
Binding sitei153 – 1531S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication
Binding sitei169 – 1691S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-16690.
BRENDAi2.1.1.219. 5242.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI (EC:2.1.1.219)
Alternative name(s):
tRNA(m1A57/58)-methyltransferase
Gene namesi
Name:trmI
Synonyms:pimT-like
Ordered Locus Names:PYRAB04300
ORF Names:PAB0283
OrganismiPyrococcus abyssi (strain GE5 / Orsay)
Taxonomic identifieri272844 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000810 Componenti: Chromosome
  • UP000009139 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi78 – 781H → Y: Decreases efficiency of the dimethylation reaction. 1 Publication
Mutagenesisi196 – 1961C → S: Decreases stability of TrmI at extreme temperatures; when associated with S-233. 1 Publication
Mutagenesisi233 – 2331C → S: Decreases stability of TrmI at extreme temperatures; when associated with S-196. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 253253tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmIPRO_0000407310Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi196 – 196Interchain (with C-233)
Disulfide bondi233 – 233Interchain (with C-196)

Keywords - PTMi

Disulfide bond

Interactioni

Subunit structurei

Homotetramer composed of a dimer of dimers; disulfide-linked. Disulfide bonds are important for the stability of TrmI at extreme temperatures.2 Publications

Protein-protein interaction databases

STRINGi272844.PAB0283.

Structurei

Secondary structure

1
253
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 115Combined sources
Beta strandi17 – 215Combined sources
Beta strandi24 – 296Combined sources
Beta strandi32 – 354Combined sources
Helixi36 – 394Combined sources
Beta strandi47 – 493Combined sources
Beta strandi55 – 595Combined sources
Helixi63 – 697Combined sources
Helixi79 – 8810Combined sources
Beta strandi96 – 1005Combined sources
Helixi106 – 11510Combined sources
Beta strandi119 – 1246Combined sources
Helixi128 – 14114Combined sources
Turni144 – 1463Combined sources
Beta strandi147 – 1504Combined sources
Helixi154 – 1563Combined sources
Beta strandi162 – 1687Combined sources
Helixi173 – 1764Combined sources
Helixi177 – 1837Combined sources
Beta strandi184 – 19613Combined sources
Helixi197 – 20913Combined sources
Helixi211 – 2133Combined sources
Beta strandi218 – 2203Combined sources
Beta strandi227 – 2304Combined sources
Beta strandi233 – 2364Combined sources
Beta strandi238 – 2414Combined sources
Beta strandi246 – 2527Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3LGAX-ray2.05A/B/C/D1-253[»]
3LHDX-ray2.59A/B/C/D1-253[»]
3MB5X-ray1.60A1-253[»]
ProteinModelPortaliQ9V1J7.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9V1J7.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni104 – 1074S-adenosyl-L-methionine binding

Domaini

Contains a large catalytic C-terminal domain that binds S-adenosyl-L-methionine and a smaller N-terminal domain that may play a role in tRNA recognition. Domains are connected by a linker region.1 Publication

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. TRM61 family.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiarCOG00978. Archaea.
COG2519. LUCA.
HOGENOMiHOG000245274.
KOiK07442.
OMAiRPDHRMI.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR029063. SAM-dependent_MTases.
IPR014816. tRNA_MeTrfase_Gcd14.
[Graphical view]
PfamiPF08704. GCD14. 1 hit.
[Graphical view]
PIRSFiPIRSF017269. GCD14. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51620. SAM_TRM61. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9V1J7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIREGDKVVL VDPRGKRYLI TVSKRDFHTD LGILKLEEII GRNFGEAIKS
60 70 80 90 100
HKGHEFKILR PRIVDYLDKM KRGPQIVHPK DAALIVAYAG ISPGDFIVEA
110 120 130 140 150
GVGSGALTLF LANIVGPEGR VVSYEIREDF AKLAWENIKW AGFDDRVTIK
160 170 180 190 200
LKDIYEGIEE ENVDHVILDL PQPERVVEHA AKALKPGGFF VAYTPCSNQV
210 220 230 240 250
MRLHEKLREF KDYFMKPRTI NVLVFDQEVK KECMRPRTTA LVHTGYITFA

RRI
Length:253
Mass (Da):28,873
Last modified:May 1, 2000 - v1
Checksum:iAFE9CB4FA59470C1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248284 Genomic DNA. Translation: CAB49352.1.
HE613800 Genomic DNA. Translation: CCE69811.1.
PIRiA75159.
RefSeqiWP_010867553.1. NC_000868.1.

Genome annotation databases

EnsemblBacteriaiCAB49352; CAB49352; PAB0283.
GeneIDi1495324.
KEGGipab:PAB0283.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ248284 Genomic DNA. Translation: CAB49352.1.
HE613800 Genomic DNA. Translation: CCE69811.1.
PIRiA75159.
RefSeqiWP_010867553.1. NC_000868.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3LGAX-ray2.05A/B/C/D1-253[»]
3LHDX-ray2.59A/B/C/D1-253[»]
3MB5X-ray1.60A1-253[»]
ProteinModelPortaliQ9V1J7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272844.PAB0283.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB49352; CAB49352; PAB0283.
GeneIDi1495324.
KEGGipab:PAB0283.

Phylogenomic databases

eggNOGiarCOG00978. Archaea.
COG2519. LUCA.
HOGENOMiHOG000245274.
KOiK07442.
OMAiRPDHRMI.

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-16690.
BRENDAi2.1.1.219. 5242.

Miscellaneous databases

EvolutionaryTraceiQ9V1J7.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR029063. SAM-dependent_MTases.
IPR014816. tRNA_MeTrfase_Gcd14.
[Graphical view]
PfamiPF08704. GCD14. 1 hit.
[Graphical view]
PIRSFiPIRSF017269. GCD14. 1 hit.
SUPFAMiSSF53335. SSF53335. 1 hit.
PROSITEiPS51620. SAM_TRM61. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: GE5 / Orsay.
  2. "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and Pyrococcus furiosus DSM 3638."
    Gao J., Wang J.
    Curr. Microbiol. 64:118-129(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENOME REANNOTATION.
    Strain: GE5 / Orsay.
  3. "A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase."
    Roovers M., Wouters J., Bujnicki J.M., Tricot C., Stalon V., Grosjean H., Droogmans L.
    Nucleic Acids Res. 32:465-476(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, DISULFIDE BONDS, MUTAGENESIS OF CYS-196 AND CYS-233.
    Strain: GE5 / Orsay.
  4. "Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase."
    Guelorget A., Roovers M., Guerineau V., Barbey C., Li X., Golinelli-Pimpaneau B.
    Nucleic Acids Res. 38:6206-6218(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE AND S-ADENOSYL-L-METHIONINE, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, DISULFIDE BONDS, DOMAIN, MUTAGENESIS OF HIS-78.

Entry informationi

Entry nameiTRMI_PYRAB
AccessioniPrimary (citable) accession number: Q9V1J7
Secondary accession number(s): G8ZGD2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 3, 2011
Last sequence update: May 1, 2000
Last modified: November 11, 2015
This is version 87 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, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.