NEP1_DROME
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 03-AUG-2022, entry version 137.
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 -!- 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; 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; Q9W4J5; -.
DR PRIDE; Q9W4J5; -.
DR DNASU; 31387; -.
DR EnsemblMetazoa; FBtr0070678; FBpp0070646; FBgn0029714.
DR GeneID; 31387; -.
DR KEGG; dme:Dmel_CG3527; -.
DR UCSC; CG3527-RA; d. melanogaster.
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; CAKICSA; -.
DR OrthoDB; 1266231at2759; -.
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 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; 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:0042742; P:defense response to bacterium; IMP:FlyBase.
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; 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..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