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Q06287

- NEP1_YEAST

UniProt

Q06287 - NEP1_YEAST

Protein

Ribosomal RNA small subunit methyltransferase NEP1

Gene

EMG1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 117 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      Previous versions | rss
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    Functioni

    Has an essential role in 40S ribosomal subunit biogenesis and 18S rRNA processing. Probably catalyzes the N1-methylation of pseudouridine at position 1189 (Psi1189) in 18S rRNA. Thus, is most likely the methyltransferase involved in the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) in position 1189 in 18S rRNA. Is also involved in ribosome assembly.4 Publications

    Catalytic activityi

    S-adenosyl-L-methionine + pseudouridine(1191) in yeast 18S rRNA = S-adenosyl-L-homocysteine + N(1)-methylpseudouridine(1191) in yeast 18S rRNA.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei88 – 881Interaction with substrate rRNA
    Sitei90 – 901Stabilizes Arg-88
    Sitei129 – 1291Interaction with substrate rRNA
    Sitei132 – 1321Interaction with substrate rRNA
    Sitei136 – 1361Interaction with substrate rRNA
    Binding sitei180 – 1801S-adenosyl-L-methionine; via carbonyl oxygen
    Binding sitei207 – 2071S-adenosyl-L-methionine; via amide nitrogen

    GO - Molecular functioni

    1. protein binding Source: HGNC
    2. rRNA (pseudouridine) methyltransferase activity Source: UniProtKB
    3. rRNA binding Source: UniProtKB

    GO - Biological processi

    1. endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
    2. endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
    3. endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
    4. ribosomal small subunit biogenesis Source: SGD
    5. rRNA base methylation Source: SGD
    6. rRNA processing Source: SGD

    Keywords - Molecular functioni

    Methyltransferase, Ribonucleoprotein, Transferase

    Keywords - Biological processi

    Ribosome biogenesis, rRNA processing

    Keywords - Ligandi

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

    Enzyme and pathway databases

    BioCyciYEAST:G3O-32309-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribosomal RNA small subunit methyltransferase NEP1 (EC:2.1.1.260)
    Alternative name(s):
    18S rRNA (pseudouridine-N1-)-methyltransferase NEP1
    18S rRNA Psi1189 methyltransferase
    Essential for mitotic growth 1
    Nucleolar essential protein 1
    Gene namesi
    Name:EMG1
    Synonyms:NEP1
    Ordered Locus Names:YLR186W
    ORF Names:L9470.5
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XII

    Organism-specific databases

    CYGDiYLR186w.
    SGDiS000004176. EMG1.

    Subcellular locationi

    Nucleusnucleolus 2 Publications

    GO - Cellular componenti

    1. cytoplasm Source: SGD
    2. nuclear microtubule Source: SGD
    3. nucleolus Source: SGD
    4. nucleus Source: SGD
    5. small-subunit processome Source: SGD

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    Depletion of EMG1 affects growth and leads to strong ribosome biogenesis defects, with defects in 20S pre-rRNA and mature 18S rRNA species.1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi88 – 881R → A: Loss of substrate rRNA binding. 2 Publications
    Mutagenesisi88 – 881R → D: Loss of substrate rRNA binding. No effect on growth. 2 Publications
    Mutagenesisi129 – 1291R → A: Loss of substrate rRNA binding. 1 Publication
    Mutagenesisi132 – 1321R → A: Loss of substrate rRNA binding. 1 Publication
    Mutagenesisi136 – 1361R → A: Loss of substrate rRNA binding. 1 Publication
    Mutagenesisi214 – 2141D → R: Almost complete loss of SAM binding. No effect on growth and ribosome biogenesis. 1 Publication
    Mutagenesisi232 – 2321L → S: Almost complete loss of SAM binding. No effect on growth and ribosome biogenesis. 1 Publication
    Mutagenesisi237 – 2371A → D: Almost complete loss of SAM binding. No effect on growth and ribosome biogenesis. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 252252Ribosomal RNA small subunit methyltransferase NEP1PRO_0000158612Add
    BLAST

    Proteomic databases

    MaxQBiQ06287.
    PaxDbiQ06287.
    PeptideAtlasiQ06287.

    Expressioni

    Gene expression databases

    GenevestigatoriQ06287.

    Interactioni

    Subunit structurei

    Homodimer. Interacts with snoRNA U3. Interacts with NOP14 and MPP10. Component of the ribosomal small subunit (SSU) processome composed of at least 40 protein subunits and snoRNA U3.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CHZ1P400191EBI-11979,EBI-22480

    Protein-protein interaction databases

    BioGridi31456. 102 interactions.
    DIPiDIP-6504N.
    IntActiQ06287. 12 interactions.
    MINTiMINT-658100.
    STRINGi4932.YLR186W.

    Structurei

    Secondary structure

    1
    252
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi36 – 383
    Beta strandi41 – 488
    Beta strandi52 – 543
    Beta strandi65 – 673
    Turni70 – 723
    Helixi74 – 796
    Helixi84 – 863
    Helixi89 – 10012
    Helixi103 – 1064
    Beta strandi110 – 1167
    Beta strandi121 – 1244
    Helixi134 – 14714
    Beta strandi148 – 1525
    Beta strandi155 – 1639
    Helixi167 – 1693
    Beta strandi173 – 1808
    Helixi189 – 1946
    Beta strandi201 – 2077
    Beta strandi209 – 2113
    Turni216 – 2205
    Beta strandi222 – 2276
    Helixi234 – 24815

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2V3JX-ray2.00A1-252[»]
    2V3KX-ray2.00A1-252[»]
    3OIIX-ray1.85A/B1-252[»]
    3OIJX-ray3.00A/B1-252[»]
    3OINX-ray1.90A/B1-252[»]
    ProteinModelPortaliQ06287.
    SMRiQ06287. Positions 28-252.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ06287.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni212 – 2143S-adenosyl-L-methionine binding
    Regioni227 – 2326S-adenosyl-L-methionine binding

    Sequence similaritiesi

    Belongs to the NEP1 family.Curated

    Phylogenomic databases

    eggNOGiCOG1756.
    GeneTreeiENSGT00390000000305.
    KOiK14568.
    OMAiDSPINKA.
    OrthoDBiEOG7FV415.

    Family and domain databases

    InterProiIPR029028. Alpha/beta_knot_MTases.
    IPR005304. Rbsml_bgen_MeTrfase_EMG1/NEP1.
    [Graphical view]
    PANTHERiPTHR12636. PTHR12636. 1 hit.
    PfamiPF03587. EMG1. 1 hit.
    [Graphical view]
    SUPFAMiSSF75217. SSF75217. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q06287-1 [UniParc]FASTAAdd to Basket

    « Hide

    MVEDSRVRDA LKGGDQKALP ASLVPQAPPV LTSKDKITKR MIVVLAMASL    50
    ETHKISSNGP GGDKYVLLNC DDHQGLLKKM GRDISEARPD ITHQCLLTLL 100
    DSPINKAGKL QVYIQTSRGI LIEVNPTVRI PRTFKRFSGL MVQLLHKLSI 150
    RSVNSEEKLL KVIKNPITDH LPTKCRKVTL SFDAPVIRVQ DYIEKLDDDE 200
    SICVFVGAMA RGKDNFADEY VDEKVGLSNY PLSASVACSK FCHGAEDAWN 250
    IL 252
    Length:252
    Mass (Da):27,895
    Last modified:November 1, 1996 - v1
    Checksum:i4A8FCDA812051AD1
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti114 – 1141I → T in AAS56267. (PubMed:17322287)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U17246 Genomic DNA. Translation: AAB67457.1.
    AY557941 Genomic DNA. Translation: AAS56267.1.
    BK006945 Genomic DNA. Translation: DAA09505.1.
    PIRiS51431.
    RefSeqiNP_013287.1. NM_001182073.1.

    Genome annotation databases

    EnsemblFungiiYLR186W; YLR186W; YLR186W.
    GeneIDi850883.
    KEGGisce:YLR186W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U17246 Genomic DNA. Translation: AAB67457.1 .
    AY557941 Genomic DNA. Translation: AAS56267.1 .
    BK006945 Genomic DNA. Translation: DAA09505.1 .
    PIRi S51431.
    RefSeqi NP_013287.1. NM_001182073.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2V3J X-ray 2.00 A 1-252 [» ]
    2V3K X-ray 2.00 A 1-252 [» ]
    3OII X-ray 1.85 A/B 1-252 [» ]
    3OIJ X-ray 3.00 A/B 1-252 [» ]
    3OIN X-ray 1.90 A/B 1-252 [» ]
    ProteinModelPortali Q06287.
    SMRi Q06287. Positions 28-252.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 31456. 102 interactions.
    DIPi DIP-6504N.
    IntActi Q06287. 12 interactions.
    MINTi MINT-658100.
    STRINGi 4932.YLR186W.

    Proteomic databases

    MaxQBi Q06287.
    PaxDbi Q06287.
    PeptideAtlasi Q06287.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YLR186W ; YLR186W ; YLR186W .
    GeneIDi 850883.
    KEGGi sce:YLR186W.

    Organism-specific databases

    CYGDi YLR186w.
    SGDi S000004176. EMG1.

    Phylogenomic databases

    eggNOGi COG1756.
    GeneTreei ENSGT00390000000305.
    KOi K14568.
    OMAi DSPINKA.
    OrthoDBi EOG7FV415.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-32309-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q06287.
    NextBioi 967239.
    PROi Q06287.

    Gene expression databases

    Genevestigatori Q06287.

    Family and domain databases

    InterProi IPR029028. Alpha/beta_knot_MTases.
    IPR005304. Rbsml_bgen_MeTrfase_EMG1/NEP1.
    [Graphical view ]
    PANTHERi PTHR12636. PTHR12636. 1 hit.
    Pfami PF03587. EMG1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF75217. SSF75217. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
      Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H.
      , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
      Nature 387:87-90(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. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. "Novel stress-responsive genes EMG1 and NOP14 encode conserved, interacting proteins required for 40S ribosome biogenesis."
      Liu P.C., Thiele D.J.
      Mol. Biol. Cell 12:3644-3657(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH NOP14, SUBCELLULAR LOCATION.
    5. "Nep1p (Emg1p), a novel protein conserved in eukaryotes and archaea, is involved in ribosome biogenesis."
      Eschrich D., Buchhaupt M., Koetter P., Entian K.-D.
      Curr. Genet. 40:326-338(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    6. "The small-subunit processome is a ribosome assembly intermediate."
      Bernstein K.A., Gallagher J.E.G., Mitchell B.M., Granneman S., Baserga S.J.
      Eukaryot. Cell 3:1619-1626(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH MPP10 AND SNORNA U3, IDENTIFICATION IN SSU PROCESSOME, SUBCELLULAR LOCATION.
    7. "The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site."
      Taylor A.B., Meyer B., Leal B.Z., Kotter P., Schirf V., Demeler B., Hart P.J., Entian K.D., Wohnert J.
      Nucleic Acids Res. 36:1542-1554(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ARG-88; ARG-129; ARG-132 AND ARG-136.
    8. "The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases."
      Leulliot N., Bohnsack M.T., Graille M., Tollervey D., Van Tilbeurgh H.
      Nucleic Acids Res. 36:629-639(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF APOPROTEIN AND COMPLEX WITH SAM, RNA-BINDING, SUBUNIT, DISRUPTION PHENOTYPE, MUTAGENESIS OF ARG-88; ASP-214; LEU-232 AND ALA-237.
      Strain: ATCC 204511 / S288c / AB972.
    9. "Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis."
      Thomas S.R., Keller C.A., Szyk A., Cannon J.R., Laronde-Leblanc N.A.
      Nucleic Acids Res. 39:2445-2457(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) IN COMPLEXES WITH S-ADENOSYLHOMOCYSTEINE AND COGNATE RNA, FUNCTION.

    Entry informationi

    Entry nameiNEP1_YEAST
    AccessioniPrimary (citable) accession number: Q06287
    Secondary accession number(s): D6VYI9, E9P8U2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 10, 2002
    Last sequence update: November 1, 1996
    Last modified: October 1, 2014
    This is version 117 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

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

    External Data

    Dasty 3