ID   NEP1_THEVO              Reviewed;         222 AA.
AC   Q979E4;
DT   10-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2001, sequence version 1.
DT   03-AUG-2022, entry version 98.
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=TV1217; ORFNames=TVG1248551;
OS   Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC
OS   15438 / GSS1).
OC   Archaea; Candidatus Thermoplasmatota; Thermoplasmata; Thermoplasmatales;
OC   Thermoplasmataceae; Thermoplasma.
OX   NCBI_TaxID=273116;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1;
RX   PubMed=11121031; DOI=10.1073/pnas.97.26.14257;
RA   Kawashima T., Amano N., Koike H., Makino S., Higuchi S., Kawashima-Ohya Y.,
RA   Watanabe K., Yamazaki M., Kanehori K., Kawamoto T., Nunoshiba T.,
RA   Yamamoto Y., Aramaki H., Makino K., Suzuki M.;
RT   "Archaeal adaptation to higher temperatures revealed by genomic sequence of
RT   Thermoplasma volcanium.";
RL   Proc. Natl. Acad. Sci. U.S.A. 97:14257-14262(2000).
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; BA000011; BAB60359.1; -; Genomic_DNA.
DR   RefSeq; WP_010917449.1; NC_002689.2.
DR   AlphaFoldDB; Q979E4; -.
DR   SMR; Q979E4; -.
DR   STRING; 273116.14325455; -.
DR   EnsemblBacteria; BAB60359; BAB60359; BAB60359.
DR   GeneID; 1441331; -.
DR   KEGG; tvo:TVG1248551; -.
DR   eggNOG; arCOG04122; Archaea.
DR   HOGENOM; CLU_055846_1_3_2; -.
DR   OMA; VYVHTRN; -.
DR   OrthoDB; 72065at2157; -.
DR   PhylomeDB; Q979E4; -.
DR   Proteomes; UP000001017; 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; Ribosome biogenesis; RNA-binding; rRNA processing;
KW   rRNA-binding; S-adenosyl-L-methionine; Transferase.
FT   CHAIN           1..222
FT                   /note="Ribosomal RNA small subunit methyltransferase Nep1"
FT                   /id="PRO_0000158625"
FT   BINDING         177
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   BINDING         182
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   BINDING         197..202
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            62
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            64
FT                   /note="Stabilizes Arg-62"
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            106
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            110
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
SQ   SEQUENCE   222 AA;  25904 MW;  19207A69EEB0D2D3 CRC64;
     MLHLIVADSE LETIPEEMLD DPGVRRFAKK RNKRVDRMIL DSNYMHAFID KYYPGESKRR
     GRPDIIYILL EMAQESILNR KNLLRTYIHT RNDFVIKISP ITRMPKSYNR FIGLFEDLFE
     KEIITNNGKT LLSLERMKLD ELLESLKKDR TILLHPKGEF KKPSEFISTE DIAAIIGGFS
     EGDFRSDVSN IPEKYSIFRD ELTIWSVGLE IVASYERAIG LL