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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)DescriptionActionsGraphical viewLength
Sitei90Stabilizes Arg-881 Publication1
Binding sitei180S-adenosyl-L-methionine; via carbonyl oxygen2 Publications1
Binding sitei207S-adenosyl-L-methionine; via amide nitrogen2 Publications1

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 methylation Source: Reactome
  • 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.
ReactomeiR-SCE-6790901. rRNA modification in the nucleus and cytosol.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

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
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR186W.
SGDiS000004176. EMG1.

Subcellular locationi

GO - Cellular componenti

  • 90S preribosome Source: GO_Central
  • cytoplasm Source: SGD
  • nuclear microtubule Source: SGD
  • nuclear periphery Source: SGD
  • nucleolus Source: SGD
  • nucleoplasm Source: Reactome
  • 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)DescriptionActionsGraphical viewLength
Mutagenesisi88R → A: Loss of substrate rRNA binding. 1 Publication1
Mutagenesisi88R → D: Loss of substrate rRNA binding. No effect on growth. 1 Publication1
Mutagenesisi90D → G: Loses its exclusive nucleolar localization and mislocalizes to the cytoplasm. 1 Publication1
Mutagenesisi129R → A: Loss of substrate rRNA binding. 1 Publication1
Mutagenesisi132R → A: Loss of substrate rRNA binding. 1 Publication1
Mutagenesisi136R → A: Loss of substrate rRNA binding. 1 Publication1
Mutagenesisi214D → R: Almost complete loss of SAM binding. No effect on growth and ribosome biogenesis. 1 Publication1
Mutagenesisi232L → S: Almost complete loss of SAM binding. No effect on growth and ribosome biogenesis. 1 Publication1
Mutagenesisi237A → D: Almost complete loss of SAM binding. No effect on growth and ribosome biogenesis. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001586121 – 252Ribosomal RNA small subunit methyltransferase NEP1Add BLAST252

Proteomic databases

MaxQBiQ06287.
PRIDEiQ06287.
TopDownProteomicsiQ06287.

PTM databases

iPTMnetiQ06287.

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei88Interaction with substrate rRNA1 Publication1
Sitei129Interaction with substrate rRNA1 Publication1
Sitei132Interaction with substrate rRNA1 Publication1
Sitei136Interaction with substrate rRNA1 Publication1

Binary interactionsi

WithEntry#Exp.IntActNotes
NOP14Q992075EBI-11979,EBI-35157

Protein-protein interaction databases

BioGridi31456. 77 interactors.
DIPiDIP-6504N.
IntActiQ06287. 12 interactors.
MINTiMINT-658100.

Structurei

Secondary structure

1252
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi36 – 38Combined sources3
Beta strandi41 – 48Combined sources8
Beta strandi52 – 54Combined sources3
Beta strandi65 – 67Combined sources3
Turni70 – 72Combined sources3
Helixi74 – 79Combined sources6
Helixi84 – 86Combined sources3
Helixi89 – 100Combined sources12
Helixi103 – 106Combined sources4
Beta strandi110 – 116Combined sources7
Beta strandi121 – 124Combined sources4
Helixi134 – 147Combined sources14
Beta strandi148 – 152Combined sources5
Beta strandi155 – 163Combined sources9
Helixi167 – 169Combined sources3
Beta strandi173 – 180Combined sources8
Helixi189 – 194Combined sources6
Beta strandi201 – 207Combined sources7
Beta strandi209 – 211Combined sources3
Turni216 – 220Combined sources5
Beta strandi222 – 227Combined sources6
Helixi234 – 248Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5JPQelectron microscopy7.30e/f1-252[»]
ProteinModelPortaliQ06287.
SMRiQ06287.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ06287.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni212 – 214S-adenosyl-L-methionine binding2 Publications3
Regioni227 – 232S-adenosyl-L-methionine binding2 Publications6

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000000305.
InParanoidiQ06287.
KOiK14568.
OMAiTDKDSQR.
OrthoDBiEOG092C54Q4.

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)DescriptionActionsGraphical viewLength
Sequence conflicti114I → T in AAS56267 (PubMed:17322287).Curated1

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
PDB 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[»]
5JPQelectron microscopy7.30e/f1-252[»]
ProteinModelPortaliQ06287.
SMRiQ06287.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31456. 77 interactors.
DIPiDIP-6504N.
IntActiQ06287. 12 interactors.
MINTiMINT-658100.

PTM databases

iPTMnetiQ06287.

Proteomic databases

MaxQBiQ06287.
PRIDEiQ06287.
TopDownProteomicsiQ06287.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YLR186W.
SGDiS000004176. EMG1.

Phylogenomic databases

GeneTreeiENSGT00390000000305.
InParanoidiQ06287.
KOiK14568.
OMAiTDKDSQR.
OrthoDBiEOG092C54Q4.

Enzyme and pathway databases

BioCyciYEAST:G3O-32309-MONOMER.
ReactomeiR-SCE-6790901. rRNA modification in the nucleus and cytosol.
R-SCE-6791226. Major pathway of rRNA processing in the nucleolus and cytosol.

Miscellaneous databases

EvolutionaryTraceiQ06287.
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...

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: November 2, 2016
This is version 135 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

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 one 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.