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Q06287 (NEP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 114. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:EMG1
Synonyms:NEP1
Ordered Locus Names:YLR186W
ORF Names:L9470.5
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length252 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.4 Ref.5 Ref.6 Ref.9

Catalytic activity

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

Subunit structure

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. Ref.4 Ref.6 Ref.8

Subcellular location

Nucleusnucleolus Ref.4 Ref.6.

Disruption phenotype

Depletion of EMG1 affects growth and leads to strong ribosome biogenesis defects, with defects in 20S pre-rRNA and mature 18S rRNA species. Ref.8

Sequence similarities

Belongs to the NEP1 family.

Ontologies

Keywords
   Biological processRibosome biogenesis
rRNA processing
   Cellular componentNucleus
   LigandRNA-binding
rRNA-binding
S-adenosyl-L-methionine
   Molecular functionMethyltransferase
Ribonucleoprotein
Transferase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processendonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Inferred from mutant phenotype Ref.6. 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)

Inferred from mutant phenotype Ref.6. Source: SGD

endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Inferred from mutant phenotype Ref.6. Source: SGD

rRNA base methylation

Inferred from mutant phenotype PubMed 20972225. Source: SGD

rRNA processing

Inferred from mutant phenotype Ref.4. Source: SGD

ribosomal small subunit biogenesis

Inferred from mutant phenotype Ref.4. Source: SGD

   Cellular_componentcytoplasm

Inferred from direct assay Ref.4. Source: SGD

nuclear microtubule

Inferred from direct assay Ref.5. Source: SGD

nucleolus

Inferred from direct assay Ref.6. Source: SGD

nucleus

Inferred from direct assay Ref.4Ref.5. Source: SGD

small-subunit processome

Inferred from direct assay Ref.6. Source: SGD

   Molecular_functionrRNA (pseudouridine) methyltransferase activity

Traceable author statement Ref.9. Source: UniProtKB

rRNA binding

Inferred from direct assay Ref.9. Source: UniProtKB

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

CHZ1P400191EBI-11979,EBI-22480

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 252252Ribosomal RNA small subunit methyltransferase NEP1
PRO_0000158612

Regions

Region212 – 2143S-adenosyl-L-methionine binding
Region227 – 2326S-adenosyl-L-methionine binding

Sites

Binding site1801S-adenosyl-L-methionine; via carbonyl oxygen
Binding site2071S-adenosyl-L-methionine; via amide nitrogen
Site881Interaction with substrate rRNA
Site901Stabilizes Arg-88
Site1291Interaction with substrate rRNA
Site1321Interaction with substrate rRNA
Site1361Interaction with substrate rRNA

Experimental info

Mutagenesis881R → A: Loss of substrate rRNA binding. Ref.7 Ref.8
Mutagenesis881R → D: Loss of substrate rRNA binding. No effect on growth. Ref.7 Ref.8
Mutagenesis1291R → A: Loss of substrate rRNA binding. Ref.7
Mutagenesis1321R → A: Loss of substrate rRNA binding. Ref.7
Mutagenesis1361R → A: Loss of substrate rRNA binding. Ref.7
Mutagenesis2141D → R: Almost complete loss of SAM binding. No effect on growth and ribosome biogenesis. Ref.8
Mutagenesis2321L → S: Almost complete loss of SAM binding. No effect on growth and ribosome biogenesis. Ref.8
Mutagenesis2371A → D: Almost complete loss of SAM binding. No effect on growth and ribosome biogenesis. Ref.8
Sequence conflict1141I → T in AAS56267. Ref.3

Secondary structure

............................................ 252
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q06287 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 4A8FCDA812051AD1

FASTA25227,895
        10         20         30         40         50         60 
MVEDSRVRDA LKGGDQKALP ASLVPQAPPV LTSKDKITKR MIVVLAMASL ETHKISSNGP 

        70         80         90        100        110        120 
GGDKYVLLNC DDHQGLLKKM GRDISEARPD ITHQCLLTLL DSPINKAGKL QVYIQTSRGI 

       130        140        150        160        170        180 
LIEVNPTVRI PRTFKRFSGL MVQLLHKLSI RSVNSEEKLL KVIKNPITDH LPTKCRKVTL 

       190        200        210        220        230        240 
SFDAPVIRVQ DYIEKLDDDE SICVFVGAMA RGKDNFADEY VDEKVGLSNY PLSASVACSK 

       250 
FCHGAEDAWN IL 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[3]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U17246 Genomic DNA. Translation: AAB67457.1.
AY557941 Genomic DNA. Translation: AAS56267.1.
BK006945 Genomic DNA. Translation: DAA09505.1.
PIRS51431.
RefSeqNP_013287.1. NM_001182073.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalQ06287.
SMRQ06287. Positions 28-252.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31456. 102 interactions.
DIPDIP-6504N.
IntActQ06287. 12 interactions.
MINTMINT-658100.
STRING4932.YLR186W.

Proteomic databases

PaxDbQ06287.
PeptideAtlasQ06287.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYLR186W; YLR186W; YLR186W.
GeneID850883.
KEGGsce:YLR186W.

Organism-specific databases

CYGDYLR186w.
SGDS000004176. EMG1.

Phylogenomic databases

eggNOGCOG1756.
GeneTreeENSGT00390000000305.
KOK14568.
OMADSPINKA.
OrthoDBEOG7FV415.

Enzyme and pathway databases

BioCycYEAST:G3O-32309-MONOMER.

Gene expression databases

GenevestigatorQ06287.

Family and domain databases

InterProIPR005304. Rbsml_bgen_MeTrfase_EMG1/NEP1.
[Graphical view]
PANTHERPTHR12636. PTHR12636. 1 hit.
PfamPF03587. EMG1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ06287.
NextBio967239.
PROQ06287.

Entry information

Entry nameNEP1_YEAST
AccessionPrimary (citable) accession number: Q06287
Secondary accession number(s): D6VYI9, E9P8U2
Entry history
Integrated into UniProtKB/Swiss-Prot: May 10, 2002
Last sequence update: November 1, 1996
Last modified: April 16, 2014
This is version 114 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XII

Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references