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P40999

- PMT1M_SCHPO

UniProt

P40999 - PMT1M_SCHPO

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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

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
Complete GO annotation...

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
Complete GO annotation...

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.
InParanoidiP40999.
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

        10         20         30         40         50
MLSTKRLRVL ELYSGIGGMH YALNLANIPA DIVCAIDINP QANEIYNLNH
60 70 80 90 100
GKLAKHMDIS TLTAKDFDAF DCKLWTMSPS CQPFTRIGNR KDILDPRSQA
110 120 130 140 150
FLNILNVLPH VNNLPEYILI ENVQGFEESK AAEECRKVLR NCGYNLIEGI
160 170 180 190 200
LSPNQFNIPN SRSRWYGLAR LNFKGEWSID DVFQFSEVAQ KEGEVKRIRD
210 220 230 240 250
YLEIERDWSS YMVLESVLNK WGHQFDIVKP DSSSCCCFTR GYTHLVQGAG
260 270 280 290 300
SILQMSDHEN THEQFERNRM ALQLRYFTAR EVARLMGFPE SLEWSKSNVT
310 320 330
EKCMYRLLGN SINVKVVSYL ISLLLEPLNF
Length:330
Mass (Da):37,976
Last modified:February 1, 1995 - v1
Checksum:i50A7121FA7CF58A1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.
InParanoidi P40999.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 98 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