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P40999

- PMT1M_SCHPO

UniProt

P40999 - PMT1M_SCHPO

Protein

tRNA (cytosine(38)-C(5))-methyltransferase

Gene

pmt1

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 97 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    Specifically methylates cytosine 38 in the anticodon loop of tRNA(Asp). Can also methylate cytosine 38 in tRNA(Glu), albeit to a lower level, but not tRNA(Lys). Pmt1-dependent tRNA methylation is induced by nitrogen limitation and depends on the nutrient-sensing protein kinase sck2. Does not have DNA-methylation activity.1 Publication

    Catalytic activityi

    S-adenosyl-L-methionine + cytosine(38) in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(38) in tRNA.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei81 – 811PROSITE-ProRule annotation

    GO - Molecular functioni

    1. tRNA (cytosine) methyltransferase activity Source: PomBase
    2. tRNA binding Source: PomBase

    GO - Biological processi

    1. tRNA methylation in response to nitrogen starvation Source: PomBase

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    tRNA processing

    Keywords - Ligandi

    RNA-binding, S-adenosyl-L-methionine

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    tRNA (cytosine(38)-C(5))-methyltransferase (EC:2.1.1.204)
    Alternative name(s):
    DNA (cytosine-5)-methyltransferase-like protein 2
    Short name:
    Dnmt2
    M.SpomI
    SpIM.SpoI
    Gene namesi
    Name:pmt1
    ORF Names:SPBC19C2.02
    OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
    Taxonomic identifieri284812 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
    ProteomesiUP000002485: Chromosome II

    Organism-specific databases

    PomBaseiSPBC19C2.02.

    Subcellular locationi

    Cytoplasm 1 Publication. Nucleus 1 Publication

    GO - Cellular componenti

    1. cytosol Source: PomBase
    2. nucleus Source: PomBase

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi81 – 811C → A: Loss of methyltransferase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 330330tRNA (cytosine(38)-C(5))-methyltransferasePRO_0000088042Add
    BLAST

    Proteomic databases

    MaxQBiP40999.

    Expressioni

    Inductioni

    Constitutively expressed at protein and RNA levels.1 Publication

    Interactioni

    Protein-protein interaction databases

    BioGridi277286. 16 interactions.
    MINTiMINT-4689975.
    STRINGi4896.SPBC19C2.02-1.

    Structurei

    3D structure databases

    ProteinModelPortaliP40999.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini7 – 330324SAM-dependent MTase C5-typePROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family.PROSITE-ProRule annotation
    Contains 1 SAM-dependent MTase C5-type domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0270.
    HOGENOMiHOG000265038.
    KOiK15336.
    OMAiFGVPYSR.
    OrthoDBiEOG71K6CK.
    PhylomeDBiP40999.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    InterProiIPR018117. C5_DNA_meth_AS.
    IPR001525. C5_MeTfrase.
    IPR029063. SAM-dependent_MTases-like.
    [Graphical view]
    PANTHERiPTHR10629. PTHR10629. 1 hit.
    PfamiPF00145. DNA_methylase. 1 hit.
    [Graphical view]
    PRINTSiPR00105. C5METTRFRASE.
    SUPFAMiSSF53335. SSF53335. 1 hit.
    TIGRFAMsiTIGR00675. dcm. 1 hit.
    PROSITEiPS00095. C5_MTASE_2. 1 hit.
    PS51679. SAM_MT_C5. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P40999-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLSTKRLRVL ELYSGIGGMH YALNLANIPA DIVCAIDINP QANEIYNLNH    50
    GKLAKHMDIS TLTAKDFDAF DCKLWTMSPS CQPFTRIGNR KDILDPRSQA 100
    FLNILNVLPH VNNLPEYILI ENVQGFEESK AAEECRKVLR NCGYNLIEGI 150
    LSPNQFNIPN SRSRWYGLAR LNFKGEWSID DVFQFSEVAQ KEGEVKRIRD 200
    YLEIERDWSS YMVLESVLNK WGHQFDIVKP DSSSCCCFTR GYTHLVQGAG 250
    SILQMSDHEN THEQFERNRM ALQLRYFTAR EVARLMGFPE SLEWSKSNVT 300
    EKCMYRLLGN SINVKVVSYL ISLLLEPLNF 330
    Length:330
    Mass (Da):37,976
    Last modified:February 1, 1995 - v1
    Checksum:i50A7121FA7CF58A1
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X82444 Genomic DNA. Translation: CAA57824.1.
    CU329671 Genomic DNA. Translation: CAB52029.1.
    PIRiS53990.
    RefSeqiNP_595687.1. NM_001021584.2.

    Genome annotation databases

    EnsemblFungiiSPBC19C2.02.1; SPBC19C2.02.1:pep; SPBC19C2.02.
    GeneIDi2540766.
    KEGGispo:SPBC19C2.02.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X82444 Genomic DNA. Translation: CAA57824.1 .
    CU329671 Genomic DNA. Translation: CAB52029.1 .
    PIRi S53990.
    RefSeqi NP_595687.1. NM_001021584.2.

    3D structure databases

    ProteinModelPortali P40999.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 277286. 16 interactions.
    MINTi MINT-4689975.
    STRINGi 4896.SPBC19C2.02-1.

    Proteomic databases

    MaxQBi P40999.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii SPBC19C2.02.1 ; SPBC19C2.02.1:pep ; SPBC19C2.02 .
    GeneIDi 2540766.
    KEGGi spo:SPBC19C2.02.

    Organism-specific databases

    PomBasei SPBC19C2.02.

    Phylogenomic databases

    eggNOGi COG0270.
    HOGENOMi HOG000265038.
    KOi K15336.
    OMAi FGVPYSR.
    OrthoDBi EOG71K6CK.
    PhylomeDBi P40999.

    Miscellaneous databases

    NextBioi 20801885.
    PROi P40999.

    Family and domain databases

    Gene3Di 3.40.50.150. 1 hit.
    InterProi IPR018117. C5_DNA_meth_AS.
    IPR001525. C5_MeTfrase.
    IPR029063. SAM-dependent_MTases-like.
    [Graphical view ]
    PANTHERi PTHR10629. PTHR10629. 1 hit.
    Pfami PF00145. DNA_methylase. 1 hit.
    [Graphical view ]
    PRINTSi PR00105. C5METTRFRASE.
    SUPFAMi SSF53335. SSF53335. 1 hit.
    TIGRFAMsi TIGR00675. dcm. 1 hit.
    PROSITEi PS00095. C5_MTASE_2. 1 hit.
    PS51679. SAM_MT_C5. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The fission yeast gene pmt1+ encodes a DNA methyltransferase homologue."
      Wilkinson C.R.M., Bartlett R., Nurse P., Bird A.P.
      Nucleic Acids Res. 23:203-210(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
      Strain: 972 / ATCC 24843.
    2. "The genome sequence of Schizosaccharomyces pombe."
      Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
      , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
      Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 972 / ATCC 24843.
    3. "Activation of a yeast pseudo DNA methyltransferase by deletion of a single amino acid."
      Pinarbasi E., Elliott J., Hornby D.P.
      J. Mol. Biol. 257:804-813(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    4. "ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe."
      Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S., Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S., Yoshida M.
      Nat. Biotechnol. 24:841-847(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    5. "Pmt1, a Dnmt2 homolog in Schizosaccharomyces pombe, mediates tRNA methylation in response to nutrient signaling."
      Becker M., Muller S., Nellen W., Jurkowski T.P., Jeltsch A., Ehrenhofer-Murray A.E.
      Nucleic Acids Res. 40:11648-11658(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF CYS-81, INDUCTION.

    Entry informationi

    Entry nameiPMT1M_SCHPO
    AccessioniPrimary (citable) accession number: P40999
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 97 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Caution

    Was originally thought not to have cytosine-5 methyltransferase activity, and this was attributed to the insertion of a Ser residue between the Pro-Cys motif found at the active site of C5 MTases (PubMed:8636983). When this serine is deleted it becomes catalytically active and recognizes and methylates the sequence CC[AT]GG. This was in agreement with S.pombe lacking m5C DNA-methylation. However, it has later been shown that it has tRNA-methyltransferase activity despite this sequence variation (PubMed:23074192).2 Publications

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Schizosaccharomyces pombe
      Schizosaccharomyces pombe: entries and gene names
    2. Restriction enzymes and methylases
      Classification of restriction enzymes and methylases and list of entries
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3