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Protein

Ribosomal RNA small subunit methyltransferase NEP1

Gene

EMG1

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

Functioni

S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates pseudouridine at position 1189 (Psi1189) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. N1-methylation is independent on acp-modification at the N3-position of U1191. Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 (RPS19A/RPS19B) during the formation of pre-ribosomes.5 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.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei88 – 881Interaction with substrate rRNA1 Publication
Sitei90 – 901Stabilizes Arg-881 Publication
Sitei129 – 1291Interaction with substrate rRNA1 Publication
Sitei132 – 1321Interaction with substrate rRNA1 Publication
Sitei136 – 1361Interaction with substrate rRNA1 Publication
Binding sitei180 – 1801S-adenosyl-L-methionine; via carbonyl oxygen2 Publications
Binding sitei207 – 2071S-adenosyl-L-methionine; via amide nitrogen2 Publications

GO - Molecular functioni

  • rRNA (pseudouridine) methyltransferase activity Source: UniProtKB
  • rRNA binding Source: UniProtKB

GO - Biological processi

  • endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • 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
  • endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Source: SGD
  • ribosomal small subunit biogenesis Source: SGD
  • rRNA base methylation Source: SGD
  • rRNA processing Source: SGD
Complete GO annotation...

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 NEP11 Publication (EC:2.1.1.2601 Publication)
Alternative name(s):
18S rRNA (pseudouridine(1189)-N1)-methyltransferase1 Publication
Short name:
18S rRNA Psi1189 methyltransferase1 Publication
Essential for mitotic growth protein 11 Publication
Nucleolar essential protein 11 Publication
Gene namesi
Name:EMG11 Publication
Synonyms:NEP11 Publication
Ordered Locus Names:YLR186WImported
ORF Names:L9470.5
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome XII

Organism-specific databases

CYGDiYLR186w.
EuPathDBiFungiDB:YLR186W.
SGDiS000004176. EMG1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: SGD
  • nuclear microtubule Source: SGD
  • nuclear periphery Source: SGD
  • nucleolus Source: SGD
  • nucleus Source: SGD
  • small-subunit processome Source: SGD
Complete GO annotation...

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. 1 Publication
Mutagenesisi88 – 881R → D: Loss of substrate rRNA binding. No effect on growth. 1 Publication
Mutagenesisi90 – 901D → G: Loses its exclusive nucleolar localization and mislocalizes to the cytoplasm. 1 Publication
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.

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

Protein-protein interaction databases

BioGridi31456. 103 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 – 383Combined sources
Beta strandi41 – 488Combined sources
Beta strandi52 – 543Combined sources
Beta strandi65 – 673Combined sources
Turni70 – 723Combined sources
Helixi74 – 796Combined sources
Helixi84 – 863Combined sources
Helixi89 – 10012Combined sources
Helixi103 – 1064Combined sources
Beta strandi110 – 1167Combined sources
Beta strandi121 – 1244Combined sources
Helixi134 – 14714Combined sources
Beta strandi148 – 1525Combined sources
Beta strandi155 – 1639Combined sources
Helixi167 – 1693Combined sources
Beta strandi173 – 1808Combined sources
Helixi189 – 1946Combined sources
Beta strandi201 – 2077Combined sources
Beta strandi209 – 2113Combined sources
Turni216 – 2205Combined sources
Beta strandi222 – 2276Combined sources
Helixi234 – 24815Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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 binding2 Publications
Regioni227 – 2326S-adenosyl-L-methionine binding2 Publications

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1756.
GeneTreeiENSGT00390000000305.
InParanoidiQ06287.
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

        10         20         30         40         50
MVEDSRVRDA LKGGDQKALP ASLVPQAPPV LTSKDKITKR MIVVLAMASL
60 70 80 90 100
ETHKISSNGP GGDKYVLLNC DDHQGLLKKM GRDISEARPD ITHQCLLTLL
110 120 130 140 150
DSPINKAGKL QVYIQTSRGI LIEVNPTVRI PRTFKRFSGL MVQLLHKLSI
160 170 180 190 200
RSVNSEEKLL KVIKNPITDH LPTKCRKVTL SFDAPVIRVQ DYIEKLDDDE
210 220 230 240 250
SICVFVGAMA RGKDNFADEY VDEKVGLSNY PLSASVACSK FCHGAEDAWN

IL
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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...

Protein-protein interaction databases

BioGridi31456. 103 interactions.
DIPiDIP-6504N.
IntActiQ06287. 12 interactions.
MINTiMINT-658100.
STRINGi4932.YLR186W.

Proteomic databases

MaxQBiQ06287.
PaxDbiQ06287.
PeptideAtlasiQ06287.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CYGDiYLR186w.
EuPathDBiFungiDB:YLR186W.
SGDiS000004176. EMG1.

Phylogenomic databases

eggNOGiCOG1756.
GeneTreeiENSGT00390000000305.
InParanoidiQ06287.
KOiK14568.
OMAiDSPINKA.
OrthoDBiEOG7FV415.

Enzyme and pathway databases

BioCyciYEAST:G3O-32309-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ06287.
NextBioi967239.
PROiQ06287.

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.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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 Bowen-Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Psi1191 in yeast 18S rRNA."
    Meyer B., Wurm J.P., Kotter P., Leisegang M.S., Schilling V., Buchhaupt M., Held M., Bahr U., Karas M., Heckel A., Bohnsack M.T., Wohnert J., Entian K.D.
    Nucleic Acids Res. 39:1526-1537(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, MUTAGENESIS OF ASP-90.
  9. "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.
  10. "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-ADENOSYL-L-HOMOCYSTEINE 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: June 24, 2015
This is version 122 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

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 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.