UniProtKB - Q06287 (NEP1_YEAST)
Protein
Ribosomal RNA small subunit methyltransferase NEP1
Gene
EMG1
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Functioni
S-adenosyl-L-methionine-dependent pseudouridine N1-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
- pseudouridine1191 in yeast 18S rRNA + S-adenosyl-L-methionine = H+ + N1-methylpseudouridine1191 in yeast 18S rRNA + S-adenosyl-L-homocysteine1 PublicationEC:2.1.1.2601 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sitei | 90 | Stabilizes Arg-881 Publication | 1 | |
Binding sitei | 180 | S-adenosyl-L-methionine; via carbonyl oxygen2 Publications | 1 | |
Binding sitei | 207 | S-adenosyl-L-methionine; via amide nitrogen2 Publications | 1 |
GO - Molecular functioni
- identical protein binding Source: IntAct
- rRNA (pseudouridine) methyltransferase activity Source: SGD
- 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
Keywordsi
Molecular function | Methyltransferase, Ribonucleoprotein, RNA-binding, rRNA-binding, Transferase |
Biological process | Ribosome biogenesis, rRNA processing |
Ligand | S-adenosyl-L-methionine |
Enzyme and pathway databases
Reactomei | 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 | Ordered Locus Names:YLR186WImported ORF Names:L9470.5 |
Organismi | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Taxonomic identifieri | 559292 [NCBI] |
Taxonomic lineagei | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › |
Proteomesi |
|
Organism-specific databases
SGDi | S000004176, EMG1 |
VEuPathDBi | FungiDB:YLR186W |
Subcellular locationi
Nucleus
- nucleolus 3 Publications
Cytoskeleton
- nuclear microtubule Source: SGD
Nucleus
- nuclear microtubule Source: SGD
- nuclear periphery Source: SGD
- nucleolus Source: SGD
- nucleoplasm Source: Reactome
- nucleus Source: SGD
Other locations
- 90S preribosome Source: GO_Central
- cytoplasm Source: SGD
- small-subunit processome Source: SGD
Keywords - Cellular componenti
NucleusPathology & 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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 88 | R → A: Loss of substrate rRNA binding. 1 Publication | 1 | |
Mutagenesisi | 88 | R → D: Loss of substrate rRNA binding. No effect on growth. 1 Publication | 1 | |
Mutagenesisi | 90 | D → G: Loses its exclusive nucleolar localization and mislocalizes to the cytoplasm. 1 Publication | 1 | |
Mutagenesisi | 129 | R → A: Loss of substrate rRNA binding. 1 Publication | 1 | |
Mutagenesisi | 132 | R → A: Loss of substrate rRNA binding. 1 Publication | 1 | |
Mutagenesisi | 136 | R → A: Loss of substrate rRNA binding. 1 Publication | 1 | |
Mutagenesisi | 214 | D → R: Almost complete loss of SAM binding. No effect on growth and ribosome biogenesis. 1 Publication | 1 | |
Mutagenesisi | 232 | L → S: Almost complete loss of SAM binding. No effect on growth and ribosome biogenesis. 1 Publication | 1 | |
Mutagenesisi | 237 | A → D: Almost complete loss of SAM binding. No effect on growth and ribosome biogenesis. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000158612 | 1 – 252 | Ribosomal RNA small subunit methyltransferase NEP1Add BLAST | 252 |
Proteomic databases
MaxQBi | Q06287 |
PaxDbi | Q06287 |
PRIDEi | Q06287 |
TopDownProteomicsi | Q06287 |
PTM databases
iPTMneti | Q06287 |
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 PublicationsSites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sitei | 88 | Interaction with substrate rRNA1 Publication | 1 | |
Sitei | 129 | Interaction with substrate rRNA1 Publication | 1 | |
Sitei | 132 | Interaction with substrate rRNA1 Publication | 1 | |
Sitei | 136 | Interaction with substrate rRNA1 Publication | 1 |
Binary interactionsi
Hide detailsQ06287
With | #Exp. | IntAct |
---|---|---|
itself | 3 | EBI-11979,EBI-11979 |
NOP14 [Q99207] | 7 | EBI-11979,EBI-35157 |
GO - Molecular functioni
- identical protein binding Source: IntAct
Protein-protein interaction databases
BioGRIDi | 31456, 449 interactors |
ComplexPortali | CPX-1604, Small ribosomal subunit processome, variant 1 CPX-1607, Small ribosomal subunit processome, variant 2 CPX-1608, Small ribosomal subunit processome, variant 3 |
DIPi | DIP-6504N |
IntActi | Q06287, 27 interactors |
STRINGi | 4932.YLR186W |
Miscellaneous databases
RNActi | Q06287, protein |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | Q06287 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q06287 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 212 – 214 | S-adenosyl-L-methionine binding2 Publications | 3 | |
Regioni | 227 – 232 | S-adenosyl-L-methionine binding2 Publications | 6 |
Sequence similaritiesi
Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase NEP1 family.Curated
Phylogenomic databases
eggNOGi | KOG3073, Eukaryota |
GeneTreei | ENSGT00390000000305 |
HOGENOMi | CLU_055846_1_1_1 |
InParanoidi | Q06287 |
OMAi | ACLETHK |
Family and domain databases
Gene3Di | 3.40.1280.10, 1 hit |
InterProi | View protein in InterPro IPR029028, Alpha/beta_knot_MTases IPR005304, Rbsml_bgen_MeTrfase_EMG1/NEP1 IPR029026, tRNA_m1G_MTases_N |
PANTHERi | PTHR12636, PTHR12636, 1 hit |
Pfami | View protein in Pfam PF03587, EMG1, 1 hit |
SUPFAMi | SSF75217, SSF75217, 1 hit |
i Sequence
Sequence statusi: Complete.
Q06287-1 [UniParc]FASTAAdd to basket
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
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 114 | I → T in AAS56267 (PubMed:17322287).Curated | 1 |
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 |
PIRi | S51431 |
RefSeqi | NP_013287.1, NM_001182073.1 |
Genome annotation databases
EnsemblFungii | YLR186W_mRNA; YLR186W; YLR186W |
GeneIDi | 850883 |
KEGGi | sce:YLR186W |
Similar proteinsi
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 |
PIRi | S51431 |
RefSeqi | NP_013287.1, NM_001182073.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB 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 | [»] | |
5JPQ | electron microscopy | 7.30 | e/f | 1-252 | [»] | |
5TZS | electron microscopy | 5.10 | j/k | 1-252 | [»] | |
5WLC | electron microscopy | 3.80 | SJ/SK | 1-252 | [»] | |
5WYJ | electron microscopy | 8.70 | E1/E2 | 1-252 | [»] | |
5WYK | electron microscopy | 4.50 | E1/E2 | 1-252 | [»] | |
6KE6 | electron microscopy | 3.40 | RG/RH | 1-252 | [»] | |
6LQP | electron microscopy | 3.20 | RG/RH | 1-252 | [»] | |
6LQQ | electron microscopy | 4.10 | RG/RH | 1-252 | [»] | |
6LQR | electron microscopy | 8.60 | RG/RH | 1-252 | [»] | |
6LQS | electron microscopy | 3.80 | RG/RH | 1-252 | [»] | |
6LQT | electron microscopy | 4.90 | RH | 1-252 | [»] | |
6LQU | electron microscopy | 3.70 | RG/RH | 1-252 | [»] | |
6LQV | electron microscopy | 4.80 | RG/RH | 1-252 | [»] | |
6ZQA | electron microscopy | 4.40 | JF/JG | 1-252 | [»] | |
6ZQB | electron microscopy | 3.90 | JF/JG | 1-252 | [»] | |
6ZQC | electron microscopy | 3.80 | JF/JG | 1-252 | [»] | |
6ZQD | electron microscopy | 3.80 | JF/JG | 1-252 | [»] | |
6ZQE | electron microscopy | 7.10 | JF/JG | 1-252 | [»] | |
6ZQF | electron microscopy | 4.90 | JF/JG | 1-252 | [»] | |
6ZQG | electron microscopy | 3.50 | JF/JG | 1-252 | [»] | |
SMRi | Q06287 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 31456, 449 interactors |
ComplexPortali | CPX-1604, Small ribosomal subunit processome, variant 1 CPX-1607, Small ribosomal subunit processome, variant 2 CPX-1608, Small ribosomal subunit processome, variant 3 |
DIPi | DIP-6504N |
IntActi | Q06287, 27 interactors |
STRINGi | 4932.YLR186W |
PTM databases
iPTMneti | Q06287 |
Proteomic databases
MaxQBi | Q06287 |
PaxDbi | Q06287 |
PRIDEi | Q06287 |
TopDownProteomicsi | Q06287 |
Genome annotation databases
EnsemblFungii | YLR186W_mRNA; YLR186W; YLR186W |
GeneIDi | 850883 |
KEGGi | sce:YLR186W |
Organism-specific databases
SGDi | S000004176, EMG1 |
VEuPathDBi | FungiDB:YLR186W |
Phylogenomic databases
eggNOGi | KOG3073, Eukaryota |
GeneTreei | ENSGT00390000000305 |
HOGENOMi | CLU_055846_1_1_1 |
InParanoidi | Q06287 |
OMAi | ACLETHK |
Enzyme and pathway databases
Reactomei | R-SCE-6791226, Major pathway of rRNA processing in the nucleolus and cytosol |
Miscellaneous databases
EvolutionaryTracei | Q06287 |
PROi | PR:Q06287 |
RNActi | Q06287, protein |
Family and domain databases
Gene3Di | 3.40.1280.10, 1 hit |
InterProi | View protein in InterPro IPR029028, Alpha/beta_knot_MTases IPR005304, Rbsml_bgen_MeTrfase_EMG1/NEP1 IPR029026, tRNA_m1G_MTases_N |
PANTHERi | PTHR12636, PTHR12636, 1 hit |
Pfami | View protein in Pfam PF03587, EMG1, 1 hit |
SUPFAMi | SSF75217, SSF75217, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | NEP1_YEAST | |
Accessioni | Q06287Primary (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: | February 10, 2021 | |
This is version 167 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Fungal Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD - Yeast chromosome XII
Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families