ID   NEP1_SULTO              Reviewed;         219 AA.
AC   Q96YP4;
DT   10-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT   01-DEC-2001, sequence version 1.
DT   03-AUG-2022, entry version 99.
DE   RecName: Full=Ribosomal RNA small subunit methyltransferase Nep1 {ECO:0000255|HAMAP-Rule:MF_00554};
DE            EC=2.1.1.- {ECO:0000255|HAMAP-Rule:MF_00554};
DE   AltName: Full=16S rRNA (pseudouridine-N1-)-methyltransferase Nep1 {ECO:0000255|HAMAP-Rule:MF_00554};
GN   Name=nep1; OrderedLocusNames=STK_21290;
OS   Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
OS   (Sulfolobus tokodaii).
OC   Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae;
OC   Sulfurisphaera.
OX   NCBI_TaxID=273063;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 16993 / JCM 10545 / NBRC 100140 / 7;
RX   PubMed=11572479; DOI=10.1093/dnares/8.4.123;
RA   Kawarabayasi Y., Hino Y., Horikawa H., Jin-no K., Takahashi M., Sekine M.,
RA   Baba S., Ankai A., Kosugi H., Hosoyama A., Fukui S., Nagai Y.,
RA   Nishijima K., Otsuka R., Nakazawa H., Takamiya M., Kato Y., Yoshizawa T.,
RA   Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K.,
RA   Masuda S., Yanagii M., Nishimura M., Yamagishi A., Oshima T., Kikuchi H.;
RT   "Complete genome sequence of an aerobic thermoacidophilic Crenarchaeon,
RT   Sulfolobus tokodaii strain7.";
RL   DNA Res. 8:123-140(2001).
CC   -!- FUNCTION: Methyltransferase involved in ribosomal biogenesis.
CC       Specifically catalyzes the N1-methylation of the pseudouridine
CC       corresponding to position 914 in M.jannaschii 16S rRNA.
CC       {ECO:0000255|HAMAP-Rule:MF_00554}.
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; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00554};
CC   -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00554}.
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; BA000023; BAB67233.1; -; Genomic_DNA.
DR   RefSeq; WP_010980208.1; NC_003106.2.
DR   AlphaFoldDB; Q96YP4; -.
DR   SMR; Q96YP4; -.
DR   STRING; 273063.STK_21290; -.
DR   EnsemblBacteria; BAB67233; BAB67233; STK_21290.
DR   GeneID; 1460201; -.
DR   KEGG; sto:STK_21290; -.
DR   PATRIC; fig|273063.9.peg.2422; -.
DR   eggNOG; arCOG04122; Archaea.
DR   OMA; VYVHTRN; -.
DR   OrthoDB; 72065at2157; -.
DR   Proteomes; UP000001015; Chromosome.
DR   GO; GO:0070037; F:rRNA (pseudouridine) methyltransferase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0070475; P:rRNA base methylation; IEA:InterPro.
DR   CDD; cd18088; Nep1-like; 1.
DR   Gene3D; 3.40.1280.10; -; 1.
DR   HAMAP; MF_00554; NEP1; 1.
DR   InterPro; IPR029028; Alpha/beta_knot_MTases.
DR   InterPro; IPR005304; Rbsml_bgen_MeTrfase_EMG1/NEP1.
DR   InterPro; IPR023503; Ribosome_NEP1_arc.
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; Reference proteome; Ribosome biogenesis; RNA-binding;
KW   rRNA processing; rRNA-binding; S-adenosyl-L-methionine; Transferase.
FT   CHAIN           1..219
FT                   /note="Ribosomal RNA small subunit methyltransferase Nep1"
FT                   /id="PRO_0000158623"
FT   BINDING         173
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   BINDING         178
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   BINDING         194..199
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            61
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            63
FT                   /note="Stabilizes Arg-61"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            100
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            103
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            107
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
SQ   SEQUENCE   219 AA;  24974 MW;  2BDAD9C608F130EB CRC64;
     MKINLILLDS SLELVPKEIA SHPAVIRNAR KRNKKPEHTI LDISLHYHAM KNLPNWRKRG
     RPDIVHLALL MFLTEKVPIK GEVYIHTIDG KIIYVNSDMR PPKNYNRFIG LAEQLLLHGQ
     VPINDANPLM KILNIKLTDL KSKYKIGVLS EDGKKVKPEE LCNLGENWLL GVGAFPHGDF
     SEEIKGVADE YFSISNYKLE THQVICRIIS ACLQQLGWP