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Protein

Ribosomal RNA small subunit methyltransferase NEP1

Gene

EMG1

Organism
Homo sapiens (Human)
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 1248 (Psi1248) in 18S rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S rRNA. Is not able to methylate uridine at this position (PubMed:20047967). Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 during the formation of pre-ribosomes (By similarity).By similarity1 Publication

Catalytic activityi

S-adenosyl-L-methionine + pseudouridine(1248) in 18S rRNA = S-adenosyl-L-homocysteine + N(1)-methylpseudouridine(1248) in 18S rRNA.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei86 – 861Stabilizes Arg-84By similarity
Binding sitei176 – 1761S-adenosyl-L-methionine; via carbonyl oxygenBy similarity
Binding sitei201 – 2011S-adenosyl-L-methionine; via amide nitrogenBy similarity
Binding sitei206 – 2061S-adenosyl-L-methionine; via carbonyl oxygenBy similarity

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB
  • RNA binding Source: UniProtKB
  • rRNA (pseudouridine) methyltransferase activity Source: UniProtKB
  • rRNA binding Source: GO_Central

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

RNA-binding, rRNA-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.1.1.257. 2681.
ReactomeiR-HSA-6790901. rRNA modification in the nucleus.
R-HSA-6791226. Major pathway of rRNA processing in the nucleolus.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosomal RNA small subunit methyltransferase NEP11 Publication (EC:2.1.1.-1 Publication)
Alternative name(s):
18S rRNA (pseudouridine(1248)-N1)-methyltransferase1 Publication
18S rRNA Psi1248 methyltransferase1 Publication
Nucleolar protein EMG1 homologBy similarity
Protein C2f1 Publication
Ribosome biogenesis protein NEP11 Publication
Gene namesi
Name:EMG11 Publication
Synonyms:C2F1 Publication
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:16912. EMG1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Bowen-Conradi syndrome (BWCNS)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA combination of malformations characterized in newborns by low birth weight, microcephaly, mild joint restriction, a prominent nose, micrognathia, fifth finger clinodactyly, and 'rocker-bottom' feet. The syndrome is transmitted as an autosomal recessive trait. The prognosis is poor, with all infants dying within the first few months of life.
See also OMIM:211180
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti86 – 861D → G in BWCNS; studies in fibroblasts show a dramatically reduced level of EMG1 protein in a BWCNS-affected patient compared to normal fibroblasts although patient fibroblasts do not have complete EMG1 deficiency; the mutation increases dimerization of EMG1 subunits suggesting that aggregation of EMG1 leads to reduced levels of the protein. 1 Publication
VAR_062480

Keywords - Diseasei

Disease mutation

Organism-specific databases

MalaCardsiEMG1.
MIMi211180. phenotype.
Orphaneti1270. Bowen-Conradi syndrome.
PharmGKBiPA142671909.

Polymorphism and mutation databases

BioMutaiEMG1.
DMDMi20532172.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 244243Ribosomal RNA small subunit methyltransferase NEP1PRO_0000158606Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ92979.
MaxQBiQ92979.
PRIDEiQ92979.

PTM databases

iPTMnetiQ92979.
PhosphoSiteiQ92979.
SwissPalmiQ92979.

Expressioni

Gene expression databases

CleanExiHS_EMG1.
ExpressionAtlasiQ92979. baseline and differential.
GenevisibleiQ92979. HS.

Organism-specific databases

HPAiHPA039666.

Interactioni

Subunit structurei

Homodimer.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei84 – 841Interaction with substrate rRNABy similarity
Sitei125 – 1251Interaction with substrate rRNABy similarity
Sitei128 – 1281Interaction with substrate rRNABy similarity
Sitei132 – 1321Interaction with substrate rRNABy similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
FAM74A6Q5TZK33EBI-718638,EBI-10247271

Protein-protein interaction databases

BioGridi115703. 24 interactions.
IntActiQ92979. 20 interactions.
MINTiMINT-1367632.

Structurei

Secondary structure

1
244
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi42 – 509Combined sources
Beta strandi54 – 574Combined sources
Beta strandi60 – 634Combined sources
Turni66 – 683Combined sources
Helixi75 – 773Combined sources
Helixi80 – 823Combined sources
Helixi85 – 9713Combined sources
Helixi99 – 1024Combined sources
Beta strandi106 – 1127Combined sources
Beta strandi117 – 1204Combined sources
Helixi130 – 14314Combined sources
Beta strandi144 – 1474Combined sources
Beta strandi154 – 1596Combined sources
Helixi163 – 1664Combined sources
Beta strandi172 – 1765Combined sources
Beta strandi181 – 1833Combined sources
Helixi186 – 1894Combined sources
Beta strandi192 – 20110Combined sources
Beta strandi203 – 2053Combined sources
Beta strandi214 – 2185Combined sources
Helixi226 – 24116Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5FAIX-ray1.80A14-244[»]
ProteinModelPortaliQ92979.
SMRiQ92979. Positions 30-244.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni219 – 2246S-adenosyl-L-methionine bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000000305.
HOGENOMiHOG000193819.
HOVERGENiHBG029983.
InParanoidiQ92979.
KOiK14568.
OMAiCHAAEDV.
PhylomeDBiQ92979.

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.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q92979-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAPSDGFKP RERSGGEQAQ DWDALPPKRP RLGAGNKIGG RRLIVVLEGA
60 70 80 90 100
SLETVKVGKT YELLNCDKHK SILLKNGRDP GEARPDITHQ SLLMLMDSPL
110 120 130 140 150
NRAGLLQVYI HTQKNVLIEV NPQTRIPRTF DRFCGLMVQL LHKLSVRAAD
160 170 180 190 200
GPQKLLKVIK NPVSDHFPVG CMKVGTSFSI PVVSDVRELV PSSDPIVFVV
210 220 230 240
GAFAHGKVSV EYTEKMVSIS NYPLSAALTC AKLTTAFEEV WGVI
Length:244
Mass (Da):26,720
Last modified:January 23, 2007 - v4
Checksum:i922F6CF49B4EFD11
GO

Sequence cautioni

The sequence AAB51325.1 differs from that shown. Reason: Erroneous initiation. Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti34 – 341A → G.
Corresponds to variant rs11064480 [ dbSNP | Ensembl ].
VAR_050237
Natural varianti86 – 861D → G in BWCNS; studies in fibroblasts show a dramatically reduced level of EMG1 protein in a BWCNS-affected patient compared to normal fibroblasts although patient fibroblasts do not have complete EMG1 deficiency; the mutation increases dimerization of EMG1 subunits suggesting that aggregation of EMG1 leads to reduced levels of the protein. 1 Publication
VAR_062480

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U47924 Genomic DNA. Translation: AAB51325.1. Different initiation.
U72514 mRNA. Translation: AAC51641.1.
BC055314 mRNA. Translation: AAH55314.1.
CCDSiCCDS73430.1.
RefSeqiNP_001306978.1. NM_001320049.1.
NP_006322.4. NM_006331.7.
UniGeneiHs.558447.
Hs.744040.

Genome annotation databases

EnsembliENST00000599672; ENSP00000470560; ENSG00000126749.
GeneIDi10436.
KEGGihsa:10436.
UCSCiuc031ysa.2. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U47924 Genomic DNA. Translation: AAB51325.1. Different initiation.
U72514 mRNA. Translation: AAC51641.1.
BC055314 mRNA. Translation: AAH55314.1.
CCDSiCCDS73430.1.
RefSeqiNP_001306978.1. NM_001320049.1.
NP_006322.4. NM_006331.7.
UniGeneiHs.558447.
Hs.744040.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5FAIX-ray1.80A14-244[»]
ProteinModelPortaliQ92979.
SMRiQ92979. Positions 30-244.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115703. 24 interactions.
IntActiQ92979. 20 interactions.
MINTiMINT-1367632.

PTM databases

iPTMnetiQ92979.
PhosphoSiteiQ92979.
SwissPalmiQ92979.

Polymorphism and mutation databases

BioMutaiEMG1.
DMDMi20532172.

Proteomic databases

EPDiQ92979.
MaxQBiQ92979.
PRIDEiQ92979.

Protocols and materials databases

DNASUi10436.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000599672; ENSP00000470560; ENSG00000126749.
GeneIDi10436.
KEGGihsa:10436.
UCSCiuc031ysa.2. human.

Organism-specific databases

CTDi10436.
GeneCardsiEMG1.
HGNCiHGNC:16912. EMG1.
HPAiHPA039666.
MalaCardsiEMG1.
MIMi211180. phenotype.
611531. gene.
neXtProtiNX_Q92979.
Orphaneti1270. Bowen-Conradi syndrome.
PharmGKBiPA142671909.
GenAtlasiSearch...

Phylogenomic databases

GeneTreeiENSGT00390000000305.
HOGENOMiHOG000193819.
HOVERGENiHBG029983.
InParanoidiQ92979.
KOiK14568.
OMAiCHAAEDV.
PhylomeDBiQ92979.

Enzyme and pathway databases

BRENDAi2.1.1.257. 2681.
ReactomeiR-HSA-6790901. rRNA modification in the nucleus.
R-HSA-6791226. Major pathway of rRNA processing in the nucleolus.

Miscellaneous databases

ChiTaRSiEMG1. human.
GeneWikiiEMG1.
GenomeRNAii10436.
PROiQ92979.
SOURCEiSearch...

Gene expression databases

CleanExiHS_EMG1.
ExpressionAtlasiQ92979. baseline and differential.
GenevisibleiQ92979. HS.

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. "Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination."
    Ansari-Lari M.A., Shen Y., Muzny D.M., Lee W., Gibbs R.A.
    Genome Res. 7:268-280(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Testis.
  3. Bienvenut W.V.
    Submitted (OCT-2004) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 2-11, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY.
    Tissue: Cervix carcinoma.
  4. "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: SUBCELLULAR LOCATION.
  5. "The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase."
    Wurm J.P., Meyer B., Bahr U., Held M., Frolow O., Kotter P., Engels J.W., Heckel A., Karas M., Entian K.D., Wohnert J.
    Nucleic Acids Res. 38:2387-2398(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. Cited for: VARIANT BWCNS GLY-86, CHARACTERIZATION OF VARIANT BWCNS GLY-86.

Entry informationi

Entry nameiNEP1_HUMAN
AccessioniPrimary (citable) accession number: Q92979
Secondary accession number(s): O00675, O00726
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2002
Last sequence update: January 23, 2007
Last modified: June 8, 2016
This is version 146 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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.