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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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei186 – 1861S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication
    Binding sitei265 – 2651S-adenosyl-L-methioninePROSITE-ProRule annotation1 Publication

    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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi145 – 1451R → A: 16-fold decrease in methyltransferase activity. Lack of tRNA-binding. 1 Publication
    Mutagenesisi177 – 1771Y → A: 20-fold decrease in methyltransferase activity. Reduced affinity for tRNA. 1 Publication
    Mutagenesisi205 – 2051G → A: 33-fold decrease in methyltransferase activity and reduced affinity for tRNA; when associated with A-207. 1 Publication
    Mutagenesisi207 – 2071G → A: 33-fold decrease in methyltransferase activity and reduced affinity for tRNA; when associated with A-205. 1 Publication
    Mutagenesisi223 – 2231D → A: 100-fold decrease in methyltransferase activity. Lack of tRNA-binding. 1 Publication
    Mutagenesisi225 – 2251N → A: 20-fold decrease in methyltransferase activity. 1 Publication
    Mutagenesisi226 – 2261P → A: 16-fold decrease in methyltransferase activity. 1 Publication
    Mutagenesisi265 – 2651N → A or Q: 100-fold decrease in methyltransferase activity. 1 Publication
    Mutagenesisi265 – 2651N → H: 3-fold decrease in methyltransferase activity. 1 Publication
    Mutagenesisi267 – 2671P → A: 1000-fold decrease in methyltransferase activity. No change in affinity for tRNA. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 336336tRNA (guanine(37)-N1)-methyltransferase Trm5bPRO_0000107090Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.3 Publications

    Protein-protein interaction databases

    STRINGi243232.MJ_0883.

    Structurei

    Secondary structure

    1
    336
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 86Combined sources
    Helixi9 – 113Combined sources
    Helixi12 – 2110Combined sources
    Beta strandi27 – 293Combined sources
    Beta strandi32 – 343Combined sources
    Beta strandi37 – 426Combined sources
    Helixi47 – 504Combined sources
    Turni51 – 533Combined sources
    Beta strandi59 – 624Combined sources
    Helixi77 – 837Combined sources
    Helixi85 – 884Combined sources
    Beta strandi91 – 933Combined sources
    Beta strandi98 – 1003Combined sources
    Beta strandi103 – 1064Combined sources
    Beta strandi110 – 1123Combined sources
    Helixi114 – 12714Combined sources
    Beta strandi131 – 1366Combined sources
    Turni142 – 1454Combined sources
    Beta strandi149 – 1546Combined sources
    Beta strandi159 – 1646Combined sources
    Beta strandi167 – 1726Combined sources
    Turni173 – 1753Combined sources
    Helixi180 – 1823Combined sources
    Helixi183 – 19210Combined sources
    Beta strandi198 – 2014Combined sources
    Helixi208 – 2125Combined sources
    Turni213 – 2153Combined sources
    Beta strandi216 – 2249Combined sources
    Helixi226 – 23813Combined sources
    Turni242 – 2443Combined sources
    Beta strandi245 – 2506Combined sources
    Helixi252 – 2543Combined sources
    Beta strandi259 – 2646Combined sources
    Turni267 – 2693Combined sources
    Helixi270 – 2734Combined sources
    Helixi274 – 2807Combined sources
    Beta strandi281 – 29616Combined sources
    Helixi297 – 30610Combined sources
    Beta strandi307 – 32115Combined sources
    Beta strandi324 – 33512Combined sources

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiQ58293.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni223 – 2242S-adenosyl-L-methionine binding
    Regioni251 – 2522S-adenosyl-L-methionine binding

    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.

    Genome annotation databases

    EnsemblBacteriaiAAB98887; AAB98887; MJ_0883.
    KEGGimja:MJ_0883.

    Cross-referencesi

    Sequence databases

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

    3D structure databases

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

    Protein-protein interaction databases

    STRINGi243232.MJ_0883.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAB98887; AAB98887; MJ_0883.
    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.

    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...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
    2. "Distinct origins of tRNA(m1G37) methyltransferase."
      Christian T., Evilia C., Williams S., Hou Y.M.
      J. Mol. Biol. 339:707-719(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBUNIT.
    3. "Catalysis by the second class of tRNA(m1G37) methyl transferase requires a conserved proline."
      Christian T., Evilia C., Hou Y.M.
      Biochemistry 45:7463-7473(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF ARG-145; TYR-177; GLY-205; GLY-207; ASP-223; ASN-225; PRO-226; ASN-265 AND PRO-267.
    4. "Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5."
      Christian T., Lahoud G., Liu C., Hoffmann K., Perona J.J., Hou Y.M.
      RNA 16:2484-2492(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    5. "Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5."
      Goto-Ito S., Ito T., Ishii R., Muto Y., Bessho Y., Yokoyama S.
      Proteins 72:1274-1289(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), SUBUNIT.
    6. "Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation."
      Goto-Ito S., Ito T., Kuratani M., Bessho Y., Yokoyama S.
      Nat. Struct. Mol. Biol. 16:1109-1115(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS) IN COMPLEX WITH S-ADENOSYL-L-METHIONINE AND TRNA.

    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: December 9, 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. 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.