ID NEP1_DROME Reviewed; 252 AA.
AC Q9W4J5;
DT 10-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT 28-FEB-2003, sequence version 2.
DT 24-JAN-2024, entry version 142.
DE RecName: Full=Ribosomal RNA small subunit methyltransferase NEP1 {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 NEP1 {ECO:0000250|UniProtKB:Q92979};
GN ORFNames=CG3527;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
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 -!- FUNCTION: S-adenosyl-L-methionine-dependent pseudouridine N(1)-
CC methyltransferase that methylates pseudouridine at position in 18S
CC rRNA. Involved the biosynthesis of the hypermodified N1-methyl-N3-(3-
CC amino-3-carboxypropyl) pseudouridine (m1acp3-Psi) conserved in
CC eukaryotic 18S rRNA. Is not able to methylate uridine at this position
CC (By similarity). Has also an essential role in 40S ribosomal subunit
CC biogenesis independent on its methyltransferase activity, facilitating
CC the incorporation of ribosomal protein S19 during the formation of pre-
CC ribosomes (By similarity). Part of the small subunit (SSU) processome,
CC first precursor of the small eukaryotic ribosomal subunit. During the
CC assembly of the SSU processome in the nucleolus, many ribosome
CC biogenesis factors, an RNA chaperone and ribosomal proteins associate
CC with the nascent pre-rRNA and work in concert to generate RNA folding,
CC modifications, rearrangements and cleavage as well as targeted
CC degradation of pre-ribosomal RNA by the RNA exosome (By similarity).
CC {ECO:0000250|UniProtKB:Q06287, 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. Part of the small subunit (SSU) processome,
CC composed of more than 70 proteins and the RNA chaperone small nucleolar
CC RNA (snoRNA) U3. {ECO:0000250|UniProtKB:Q06287,
CC ECO:0000250|UniProtKB:Q92979}.
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; AE014298; AAF45956.2; -; Genomic_DNA.
DR RefSeq; NP_572170.1; NM_131942.3.
DR AlphaFoldDB; Q9W4J5; -.
DR SMR; Q9W4J5; -.
DR BioGRID; 57904; 2.
DR DIP; DIP-23557N; -.
DR STRING; 7227.FBpp0070646; -.
DR PaxDb; 7227-FBpp0070646; -.
DR DNASU; 31387; -.
DR EnsemblMetazoa; FBtr0070678; FBpp0070646; FBgn0029714.
DR GeneID; 31387; -.
DR KEGG; dme:Dmel_CG3527; -.
DR UCSC; CG3527-RA; d. melanogaster.
DR AGR; FB:FBgn0029714; -.
DR FlyBase; FBgn0029714; CG3527.
DR VEuPathDB; VectorBase:FBgn0029714; -.
DR eggNOG; KOG3073; Eukaryota.
DR GeneTree; ENSGT00390000000305; -.
DR HOGENOM; CLU_055846_1_1_1; -.
DR InParanoid; Q9W4J5; -.
DR OMA; VHNTFEL; -.
DR OrthoDB; 275493at2759; -.
DR PhylomeDB; Q9W4J5; -.
DR Reactome; R-DME-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR BioGRID-ORCS; 31387; 1 hit in 1 CRISPR screen.
DR GenomeRNAi; 31387; -.
DR PRO; PR:Q9W4J5; -.
DR Proteomes; UP000000803; Chromosome X.
DR Bgee; FBgn0029714; Expressed in adult abdomen and 24 other cell types or tissues.
DR ExpressionAtlas; Q9W4J5; baseline and differential.
DR Genevisible; Q9W4J5; DM.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0032040; C:small-subunit processome; ISS:UniProtKB.
DR GO; GO:0070037; F:rRNA (pseudouridine) methyltransferase activity; ISS:UniProtKB.
DR GO; GO:0019843; F:rRNA binding; IBA:GO_Central.
DR GO; GO:0042742; P:defense response to bacterium; IMP:FlyBase.
DR GO; GO:0042274; P:ribosomal small subunit biogenesis; ISS:UniProtKB.
DR GO; GO:0070475; P:rRNA base methylation; IBA:GO_Central.
DR GO; GO:0031167; P:rRNA methylation; ISS:FlyBase.
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; NEP1/MRA1; 1.
DR PANTHER; PTHR12636:SF5; RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE NEP1; 1.
DR Pfam; PF03587; EMG1; 1.
DR SUPFAM; SSF75217; alpha/beta knot; 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..252
FT /note="Ribosomal RNA small subunit methyltransferase NEP1"
FT /id="PRO_0000158609"
FT BINDING 176
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT BINDING 209
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT BINDING 214
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT BINDING 227..232
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT SITE 84
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT SITE 86
FT /note="Stabilizes Arg-84"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT SITE 125
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT SITE 128
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
FT SITE 132
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000250|UniProtKB:Q06287"
SQ SEQUENCE 252 AA; 28359 MW; BE5B490E0DA778FA CRC64;
MGGQGKAINR KRKFVGRKAD DPEFDLDKKQ FKVLHLNATE KRLIIVLEGA QLETVKVHNT
FELLNCDDHA GIMRKNQRDP GSCRPDITHQ CLLMLFDSPL NRAGLLQVFV RTEHNVLIEI
NPQTRIPRTF KRFAGLMVQL LHKFQIRAND SSRRLMSVIK NPITDHVPVG CKKYAMSFSG
KLLPNCRDLV PHGDETSASY DEPVVIVIGA FAHGVLKTDY TEELFSISNY PLSAAIACSK
ICSAFEEVWG VV
//
