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Protein

tRNA (guanine(37)-N1)-methyltransferase Trm5b

Gene

trm5b

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Specifically methylates the N1 position of guanosine-37 in various tRNAs.3 Publications

Catalytic activityi

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

Kineticsi

  1. KM=1.0 µM for S-adenosyl-L-methionine1 Publication
  2. KM=0.7 µM for tRNA1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei186S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication1
    Binding sitei265S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication1

    GO - Molecular functioni

    GO - Biological processi

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

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    tRNA processing

    Keywords - Ligandi

    S-adenosyl-L-methionine

    Enzyme and pathway databases

    BRENDAi2.1.1.228. 3260.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    tRNA (guanine(37)-N1)-methyltransferase Trm5b (EC:2.1.1.228)
    Alternative name(s):
    M1G-methyltransferase
    tRNA [GM37] methyltransferase
    Gene namesi
    Name:trm5b
    Ordered Locus Names:MJ0883
    OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
    Taxonomic identifieri243232 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
    Proteomesi
    • UP000000805 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi145R → A: 16-fold decrease in methyltransferase activity. Lack of tRNA-binding. 1 Publication1
    Mutagenesisi177Y → A: 20-fold decrease in methyltransferase activity. Reduced affinity for tRNA. 1 Publication1
    Mutagenesisi205G → A: 33-fold decrease in methyltransferase activity and reduced affinity for tRNA; when associated with A-207. 1 Publication1
    Mutagenesisi207G → A: 33-fold decrease in methyltransferase activity and reduced affinity for tRNA; when associated with A-205. 1 Publication1
    Mutagenesisi223D → A: 100-fold decrease in methyltransferase activity. Lack of tRNA-binding. 1 Publication1
    Mutagenesisi225N → A: 20-fold decrease in methyltransferase activity. 1 Publication1
    Mutagenesisi226P → A: 16-fold decrease in methyltransferase activity. 1 Publication1
    Mutagenesisi265N → A or Q: 100-fold decrease in methyltransferase activity. 1 Publication1
    Mutagenesisi265N → H: 3-fold decrease in methyltransferase activity. 1 Publication1
    Mutagenesisi267P → A: 1000-fold decrease in methyltransferase activity. No change in affinity for tRNA. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001070901 – 336tRNA (guanine(37)-N1)-methyltransferase Trm5bAdd BLAST336

    Interactioni

    Subunit structurei

    Monomer.3 Publications

    Protein-protein interaction databases

    STRINGi243232.MJ_0883.

    Structurei

    Secondary structure

    1336
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 8Combined sources6
    Helixi9 – 11Combined sources3
    Helixi12 – 21Combined sources10
    Beta strandi27 – 29Combined sources3
    Beta strandi32 – 34Combined sources3
    Beta strandi37 – 42Combined sources6
    Helixi47 – 50Combined sources4
    Turni51 – 53Combined sources3
    Beta strandi59 – 62Combined sources4
    Helixi77 – 83Combined sources7
    Helixi85 – 88Combined sources4
    Beta strandi91 – 93Combined sources3
    Beta strandi98 – 100Combined sources3
    Beta strandi103 – 106Combined sources4
    Beta strandi110 – 112Combined sources3
    Helixi114 – 127Combined sources14
    Beta strandi131 – 136Combined sources6
    Turni142 – 145Combined sources4
    Beta strandi149 – 154Combined sources6
    Beta strandi159 – 164Combined sources6
    Beta strandi167 – 172Combined sources6
    Turni173 – 175Combined sources3
    Helixi180 – 182Combined sources3
    Helixi183 – 192Combined sources10
    Beta strandi198 – 201Combined sources4
    Helixi208 – 212Combined sources5
    Turni213 – 215Combined sources3
    Beta strandi216 – 224Combined sources9
    Helixi226 – 238Combined sources13
    Turni242 – 244Combined sources3
    Beta strandi245 – 250Combined sources6
    Helixi252 – 254Combined sources3
    Beta strandi259 – 264Combined sources6
    Turni267 – 269Combined sources3
    Helixi270 – 273Combined sources4
    Helixi274 – 280Combined sources7
    Beta strandi281 – 296Combined sources16
    Helixi297 – 306Combined sources10
    Beta strandi307 – 321Combined sources15
    Beta strandi324 – 335Combined sources12

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2YX1X-ray2.20A/B1-336[»]
    2ZZMX-ray2.65A1-336[»]
    2ZZNX-ray2.95A/B1-336[»]
    3AY0X-ray3.05A/B1-336[»]
    ProteinModelPortaliQ58293.
    SMRiQ58293.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ58293.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni223 – 224S-adenosyl-L-methionine binding2
    Regioni251 – 252S-adenosyl-L-methionine binding2

    Sequence similaritiesi

    Belongs to the class I-like SAM-binding methyltransferase superfamily. TRM5/TYW2 family.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiarCOG00033. Archaea.
    COG2520. LUCA.
    InParanoidiQ58293.
    KOiK15429.
    OMAiVIMNLPK.
    PhylomeDBiQ58293.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    InterProiIPR030382. MeTrfase_TRM5/TYW2.
    IPR029063. SAM-dependent_MTases.
    [Graphical view]
    PfamiPF02475. Met_10. 1 hit.
    [Graphical view]
    SUPFAMiSSF53335. SSF53335. 1 hit.
    PROSITEiPS51684. SAM_MT_TRM5_TYW2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q58293-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MPLCLKINKK HGEQTRRILI ENNLLNKDYK ITSEGNYLYL PIKDVDEDIL
    60 70 80 90 100
    KSILNIEFEL VDKELEEKKI IKKPSFREII SKKYRKEIDE GLISLSYDVV
    110 120 130 140 150
    GDLVILQISD EVDEKIRKEI GELAYKLIPC KGVFRRKSEV KGEFRVRELE
    160 170 180 190 200
    HLAGENRTLT IHKENGYRLW VDIAKVYFSP RLGGERARIM KKVSLNDVVV
    210 220 230 240 250
    DMFAGVGPFS IACKNAKKIY AIDINPHAIE LLKKNIKLNK LEHKIIPILS
    260 270 280 290 300
    DVREVDVKGN RVIMNLPKFA HKFIDKALDI VEEGGVIHYY TIGKDFDKAI
    310 320 330
    KLFEKKCDCE VLEKRIVKSY APREYILALD FKINKK
    Length:336
    Mass (Da):39,000
    Last modified:November 1, 1996 - v1
    Checksum:i3E4811F0932EE95F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L77117 Genomic DNA. Translation: AAB98887.1.
    PIRiC64410.
    RefSeqiWP_010870397.1. NC_000909.1.

    Genome annotation databases

    EnsemblBacteriaiAAB98887; AAB98887; MJ_0883.
    GeneIDi1451772.
    KEGGimja:MJ_0883.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L77117 Genomic DNA. Translation: AAB98887.1.
    PIRiC64410.
    RefSeqiWP_010870397.1. NC_000909.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2YX1X-ray2.20A/B1-336[»]
    2ZZMX-ray2.65A1-336[»]
    2ZZNX-ray2.95A/B1-336[»]
    3AY0X-ray3.05A/B1-336[»]
    ProteinModelPortaliQ58293.
    SMRiQ58293.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi243232.MJ_0883.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAB98887; AAB98887; MJ_0883.
    GeneIDi1451772.
    KEGGimja:MJ_0883.

    Phylogenomic databases

    eggNOGiarCOG00033. Archaea.
    COG2520. LUCA.
    InParanoidiQ58293.
    KOiK15429.
    OMAiVIMNLPK.
    PhylomeDBiQ58293.

    Enzyme and pathway databases

    BRENDAi2.1.1.228. 3260.

    Miscellaneous databases

    EvolutionaryTraceiQ58293.
    PROiQ58293.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    InterProiIPR030382. MeTrfase_TRM5/TYW2.
    IPR029063. SAM-dependent_MTases.
    [Graphical view]
    PfamiPF02475. Met_10. 1 hit.
    [Graphical view]
    SUPFAMiSSF53335. SSF53335. 1 hit.
    PROSITEiPS51684. SAM_MT_TRM5_TYW2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiTRM5B_METJA
    AccessioniPrimary (citable) accession number: Q58293
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: November 1, 1996
    Last modified: November 2, 2016
    This is version 90 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. Methanococcus jannaschii
      Methanococcus jannaschii: entries and gene names
    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.