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Q12009

- TRMB_YEAST

UniProt

Q12009 - TRMB_YEAST

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Protein

tRNA (guanine-N(7)-)-methyltransferase

Gene

TRM8

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Methyltransferase that catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA, a modification required to maintain stability of tRNAs; its absence resulting in tRNA decay. Both the D-stem and T-stem structures of tRNAs are required for efficient methyltransferase activity.2 PublicationsUniRule annotation

Catalytic activityi

S-adenosyl-L-methionine + guanine(46) in tRNA = S-adenosyl-L-homocysteine + N(7)-methylguanine(46) in tRNA.1 PublicationUniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei103 – 1031S-adenosyl-L-methionine; via carbonyl oxygen1 PublicationUniRule annotation
Binding sitei181 – 1811S-adenosyl-L-methionine; via carbonyl oxygen1 PublicationUniRule annotation
Active sitei184 – 1841Curated

GO - Molecular functioni

  1. tRNA (guanine-N7-)-methyltransferase activity Source: UniProtKB-HAMAP
  2. tRNA binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. RNA (guanine-N7)-methylation Source: GOC
  2. tRNA methylation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

tRNA processing

Keywords - Ligandi

RNA-binding, S-adenosyl-L-methionine, tRNA-binding

Enzyme and pathway databases

BioCyciYEAST:YDL201W-MONOMER.
UniPathwayiUPA00989.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA (guanine-N(7)-)-methyltransferaseUniRule annotation (EC:2.1.1.33UniRule annotation)
Alternative name(s):
Transfer RNA methyltransferase 8UniRule annotation
tRNA (guanine(46)-N(7))-methyltransferaseUniRule annotation
tRNA(m7G46)-methyltransferaseUniRule annotation
Gene namesi
Name:TRM8UniRule annotation
Ordered Locus Names:YDL201W
ORF Names:D1075
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome IV

Organism-specific databases

CYGDiYDL201w.
SGDiS000002360. TRM8.

Subcellular locationi

Nucleus 1 PublicationUniRule annotation

GO - Cellular componenti

  1. nucleus Source: UniProtKB-HAMAP
  2. tRNA methyltransferase complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 286286tRNA (guanine-N(7)-)-methyltransferasePRO_0000171437Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei7 – 71Phosphoserine; by ATM or ATR1 Publication
Modified residuei59 – 591Phosphoserine2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ12009.
PaxDbiQ12009.
PeptideAtlasiQ12009.

Expressioni

Gene expression databases

GenevestigatoriQ12009.

Interactioni

Subunit structurei

Forms a complex with TRM82.1 PublicationUniRule annotation

Binary interactionsi

WithEntry#Exp.IntActNotes
TRM82Q037742EBI-19552,EBI-19486

Protein-protein interaction databases

BioGridi31845. 50 interactions.
DIPiDIP-8614N.
IntActiQ12009. 1 interaction.
MINTiMINT-2782058.
STRINGi4932.YDL201W.

Structurei

Secondary structure

1
286
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi63 – 653Combined sources
Helixi73 – 753Combined sources
Helixi78 – 803Combined sources
Helixi83 – 853Combined sources
Turni88 – 914Combined sources
Beta strandi92 – 943Combined sources
Beta strandi97 – 1026Combined sources
Helixi108 – 1169Combined sources
Beta strandi120 – 1278Combined sources
Helixi129 – 14416Combined sources
Beta strandi147 – 1504Combined sources
Turni151 – 1544Combined sources
Beta strandi155 – 1595Combined sources
Helixi166 – 1683Combined sources
Beta strandi175 – 1828Combined sources
Helixi199 – 20810Combined sources
Beta strandi209 – 22012Combined sources
Helixi222 – 23413Combined sources
Beta strandi238 – 2403Combined sources
Helixi243 – 2475Combined sources
Helixi250 – 2578Combined sources
Helixi260 – 2678Combined sources
Beta strandi273 – 2797Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2VDUX-ray2.40E/F39-286[»]
2VDVX-ray2.30E/F47-286[»]
ProteinModelPortaliQ12009.
SMRiQ12009. Positions 60-286.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ12009.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni126 – 1272S-adenosyl-L-methionine binding
Regioni161 – 1622S-adenosyl-L-methionine binding
Regioni259 – 2613S-adenosyl-L-methionine binding

Sequence similaritiesi

Belongs to the class I-like SAM-binding methyltransferase superfamily. TrmB family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0220.
GeneTreeiENSGT00390000017840.
HOGENOMiHOG000260965.
InParanoidiQ12009.
KOiK03439.
OMAiRAHSNPI.
OrthoDBiEOG708W9T.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
HAMAPiMF_03055. tRNA_methyltr_TrmB_euk.
InterProiIPR029063. SAM-dependent_MTases-like.
IPR025763. Trm8_euk.
IPR003358. tRNA_(Gua-N-7)_MeTrfase.
[Graphical view]
PfamiPF02390. Methyltransf_4. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
TIGRFAMsiTIGR00091. TIGR00091. 1 hit.
PROSITEiPS51625. SAM_MT_TRMB. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q12009-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MKAKPLSQDP GSKRYAYRIN KEENRKELKH VKINESSLVQ EGQKIDLPKK
60 70 80 90 100
RYYRQRAHSN PFSDHQLEYP VSPQDMDWSK LYPYYKNAEN GQMTKKVTIA
110 120 130 140 150
DIGCGFGGLM IDLSPAFPED LILGMEIRVQ VTNYVEDRII ALRNNTASKH
160 170 180 190 200
GFQNINVLRG NAMKFLPNFF EKGQLSKMFF CFPDPHFKQR KHKARIITNT
210 220 230 240 250
LLSEYAYVLK EGGVVYTITD VKDLHEWMVK HLEEHPLFER LSKEWEENDE
260 270 280
CVKIMRNATE EGKKVERKKG DKFVACFTRL PTPAIL
Length:286
Mass (Da):33,391
Last modified:November 1, 1996 - v1
Checksum:i0280B9A7B02C85B7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X99000 Genomic DNA. Translation: CAA67468.1.
Z74249 Genomic DNA. Translation: CAA98779.1.
BK006938 Genomic DNA. Translation: DAA11663.1.
PIRiS67760.
RefSeqiNP_010080.1. NM_001180261.1.

Genome annotation databases

EnsemblFungiiYDL201W; YDL201W; YDL201W.
GeneIDi851326.
KEGGisce:YDL201W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X99000 Genomic DNA. Translation: CAA67468.1 .
Z74249 Genomic DNA. Translation: CAA98779.1 .
BK006938 Genomic DNA. Translation: DAA11663.1 .
PIRi S67760.
RefSeqi NP_010080.1. NM_001180261.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2VDU X-ray 2.40 E/F 39-286 [» ]
2VDV X-ray 2.30 E/F 47-286 [» ]
ProteinModelPortali Q12009.
SMRi Q12009. Positions 60-286.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 31845. 50 interactions.
DIPi DIP-8614N.
IntActi Q12009. 1 interaction.
MINTi MINT-2782058.
STRINGi 4932.YDL201W.

Proteomic databases

MaxQBi Q12009.
PaxDbi Q12009.
PeptideAtlasi Q12009.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YDL201W ; YDL201W ; YDL201W .
GeneIDi 851326.
KEGGi sce:YDL201W.

Organism-specific databases

CYGDi YDL201w.
SGDi S000002360. TRM8.

Phylogenomic databases

eggNOGi COG0220.
GeneTreei ENSGT00390000017840.
HOGENOMi HOG000260965.
InParanoidi Q12009.
KOi K03439.
OMAi RAHSNPI.
OrthoDBi EOG708W9T.

Enzyme and pathway databases

UniPathwayi UPA00989 .
BioCyci YEAST:YDL201W-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q12009.
NextBioi 968378.
PROi Q12009.

Gene expression databases

Genevestigatori Q12009.

Family and domain databases

Gene3Di 3.40.50.150. 1 hit.
HAMAPi MF_03055. tRNA_methyltr_TrmB_euk.
InterProi IPR029063. SAM-dependent_MTases-like.
IPR025763. Trm8_euk.
IPR003358. tRNA_(Gua-N-7)_MeTrfase.
[Graphical view ]
Pfami PF02390. Methyltransf_4. 1 hit.
[Graphical view ]
SUPFAMi SSF53335. SSF53335. 1 hit.
TIGRFAMsi TIGR00091. TIGR00091. 1 hit.
PROSITEi PS51625. SAM_MT_TRMB. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV."
    Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G., Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C., Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F., Delaveau T.
    , del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M., Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T., Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C., Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S., Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L., Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H., Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M., Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M., Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A., Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G., Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E., Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S., Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D., Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V., Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E., Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X., Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A., Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T., Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L., Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E., Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L., Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M., Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K., Mewes H.-W., Zollner A., Zaccaria P.
    Nature 387:75-78(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA."
    Alexandrov A., Martzen M.R., Phizicky E.M.
    RNA 8:1253-1266(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION, INTERACTION WITH TRM82.
  4. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  5. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  6. "tRNA m7G methyltransferase Trm8p/Trm82p: evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p."
    Alexandrov A., Grayhack E.J., Phizicky E.M.
    RNA 11:821-830(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, TRNA-BINDING, INTERACTION WITH TRM82.
  7. "Rapid tRNA decay can result from lack of nonessential modifications."
    Alexandrov A., Chernyakov I., Gu W., Hiley S.L., Hughes T.R., Grayhack E.J., Phizicky E.M.
    Mol. Cell 21:87-96(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "RNA recognition mechanism of eukaryote tRNA (m7G46) methyltransferase (Trm8-Trm82 complex)."
    Matsumoto K., Toyooka T., Tomikawa C., Ochi A., Takano Y., Takayanagi N., Endo Y., Hori H.
    FEBS Lett. 581:1599-1604(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-59, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  10. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-7, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-59, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 29-286 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE AND TRM82, SUBUNIT, PROBABLE ACTIVE SITE.

Entry informationi

Entry nameiTRMB_YEAST
AccessioniPrimary (citable) accession number: Q12009
Secondary accession number(s): D6VRF3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 20, 2003
Last sequence update: November 1, 1996
Last modified: November 26, 2014
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2630 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names

External Data

Dasty 3