NEP1_CAEEL
ID NEP1_CAEEL Reviewed; 231 AA.
AC Q9XX15;
DT 10-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 114.
DE RecName: Full=Ribosomal RNA small subunit methyltransferase nep-1 {ECO:0000250|UniProtKB:Q92979};
DE EC=2.1.1.- {ECO:0000250|UniProtKB:Q92979};
DE AltName: Full=18S rRNA (pseudouridine-N1)-methyltransferase {ECO:0000250|UniProtKB:Q92979};
DE AltName: Full=Ribosome biogenesis protein nep-1 {ECO:0000250|UniProtKB:Q92979};
GN ORFNames=Y39A1A.14;
OS Caenorhabditis elegans.
OC Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida;
OC Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae;
OC Caenorhabditis.
OX NCBI_TaxID=6239;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Bristol N2;
RX PubMed=9851916; DOI=10.1126/science.282.5396.2012;
RG The C. elegans sequencing consortium;
RT "Genome sequence of the nematode C. elegans: a platform for investigating
RT biology.";
RL Science 282:2012-2018(1998).
CC -!- FUNCTION: S-adenosyl-L-methionine-dependent pseudouridine N(1)-
CC methyltransferase that methylates a pseudouridine in 18S rRNA. Involved
CC the biosynthesis of the hypermodified N1-methyl-N3-(3-amino-3-
CC carboxypropyl) pseudouridine (m1acp3-Psi) conserved in eukaryotic 18S
CC rRNA. Has also an essential role in 40S ribosomal subunit biogenesis
CC independent on its methyltransferase activity, facilitating the
CC incorporation of ribosomal protein S19 during the formation of pre-
CC ribosomes. {ECO:0000250|UniProtKB:Q06287,
CC ECO:0000250|UniProtKB:Q92979}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a pseudouridine in 16S/18S rRNA + S-adenosyl-L-methionine = an
CC N(1)-methylpseudouridine in 16S/18S rRNA + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:46696, Rhea:RHEA-COMP:11633, Rhea:RHEA-
CC COMP:11634, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65314, ChEBI:CHEBI:74890;
CC Evidence={ECO:0000250|UniProtKB:Q92979};
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:Q06287}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:Q92979}.
CC -!- SIMILARITY: Belongs to the class IV-like SAM-binding methyltransferase
CC superfamily. RNA methyltransferase NEP1 family. {ECO:0000305}.
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DR EMBL; AL031633; CAA21025.1; -; Genomic_DNA.
DR PIR; T26736; T26736.
DR RefSeq; NP_499349.1; NM_066948.3.
DR AlphaFoldDB; Q9XX15; -.
DR SMR; Q9XX15; -.
DR BioGRID; 41677; 13.
DR IntAct; Q9XX15; 1.
DR STRING; 6239.Y39A1A.14; -.
DR EPD; Q9XX15; -.
DR PaxDb; Q9XX15; -.
DR PeptideAtlas; Q9XX15; -.
DR EnsemblMetazoa; Y39A1A.14.1; Y39A1A.14.1; WBGene00012652.
DR GeneID; 176488; -.
DR UCSC; Y39A1A.14; c. elegans.
DR CTD; 176488; -.
DR WormBase; Y39A1A.14; CE19133; WBGene00012652; -.
DR eggNOG; KOG3073; Eukaryota.
DR GeneTree; ENSGT00390000000305; -.
DR HOGENOM; CLU_055846_1_1_1; -.
DR InParanoid; Q9XX15; -.
DR OMA; CAKICSA; -.
DR OrthoDB; 1266231at2759; -.
DR PhylomeDB; Q9XX15; -.
DR Reactome; R-CEL-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR PRO; PR:Q9XX15; -.
DR Proteomes; UP000001940; Chromosome III.
DR Bgee; WBGene00012652; Expressed in germ line (C elegans) and 4 other tissues.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0032040; C:small-subunit processome; IBA:GO_Central.
DR GO; GO:0070037; F:rRNA (pseudouridine) methyltransferase activity; ISS:UniProtKB.
DR GO; GO:0019843; F:rRNA binding; IBA:GO_Central.
DR GO; GO:0070475; P:rRNA base methylation; IBA:GO_Central.
DR CDD; cd18088; Nep1-like; 1.
DR Gene3D; 3.40.1280.10; -; 1.
DR InterPro; IPR029028; Alpha/beta_knot_MTases.
DR InterPro; IPR005304; Rbsml_bgen_MeTrfase_EMG1/NEP1.
DR InterPro; IPR029026; tRNA_m1G_MTases_N.
DR PANTHER; PTHR12636; PTHR12636; 1.
DR Pfam; PF03587; EMG1; 1.
DR SUPFAM; SSF75217; SSF75217; 1.
PE 3: Inferred from homology;
KW Methyltransferase; Nucleus; Reference proteome; Ribosome biogenesis;
KW RNA-binding; rRNA processing; rRNA-binding; S-adenosyl-L-methionine;
KW Transferase.
FT CHAIN 1..231
FT /note="Ribosomal RNA small subunit methyltransferase nep-1"
FT /id="PRO_0000158608"
FT BINDING 161
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT BINDING 188
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT BINDING 193
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT BINDING 206..211
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT SITE 69
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT SITE 71
FT /note="Stabilizes Arg-69"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT SITE 110
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT SITE 113
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT SITE 117
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
SQ SEQUENCE 231 AA; 25765 MW; 48A242B186C40D43 CRC64;
MSHEYDTVAP PNAKRMKTDN QLEDKKILYV VLEGCSLETA KVGGEYAILS SDKHANFLRK
QKKDPADYRP DILHQCLLNL LDSPLNRAGK LRVFFRTSKN VLVDVSPQCR IPRTFDRFCG
LMVQLLHKLS IRAAETTQKL MSVVKNPVSN HLPVGSRKML MSFNVPELTM ANKLVAPETD
EPLVLIIGGI ARGKIVVDYN DSETKISNYP LSAALTCAKV TSGLEEIWGI I
