SubmitCancel

Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

Q06287

- NEP1_YEAST

UniProt

Q06287 - NEP1_YEAST

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein
Ribosomal RNA small subunit methyltransferase NEP1
Gene
EMG1, NEP1, YLR186W, L9470.5
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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. rRNA base methylation Source: SGD
  5. rRNA processing Source: SGD
  6. ribosomal small subunit biogenesis 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 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
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. 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 NEP1
PRO_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

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.

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.

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti114 – 1141I → T in AAS56267. 1 Publication

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

« 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 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: June 11, 2014
This is version 116 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