ID   NEP1_THESM              Reviewed;         220 AA.
AC   C6A116;
DT   22-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-SEP-2009, sequence version 1.
DT   03-AUG-2022, entry version 68.
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 {ECO:0000255|HAMAP-Rule:MF_00554}; OrderedLocusNames=TSIB_0244;
OS   Thermococcus sibiricus (strain DSM 12597 / MM 739).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Thermococcus.
OX   NCBI_TaxID=604354;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 12597 / MM 739;
RX   PubMed=19447963; DOI=10.1128/aem.00718-09;
RA   Mardanov A.V., Ravin N.V., Svetlitchnyi V.A., Beletsky A.V.,
RA   Miroshnichenko M.L., Bonch-Osmolovskaya E.A., Skryabin K.G.;
RT   "Metabolic versatility and indigenous origin of the archaeon Thermococcus
RT   sibiricus, isolated from a siberian oil reservoir, as revealed by genome
RT   analysis.";
RL   Appl. Environ. Microbiol. 75:4580-4588(2009).
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; CP001463; ACS89311.1; -; Genomic_DNA.
DR   RefSeq; WP_012766272.1; NC_012883.1.
DR   AlphaFoldDB; C6A116; -.
DR   SMR; C6A116; -.
DR   STRING; 604354.TSIB_0244; -.
DR   EnsemblBacteria; ACS89311; ACS89311; TSIB_0244.
DR   GeneID; 8095217; -.
DR   KEGG; tsi:TSIB_0244; -.
DR   eggNOG; arCOG04122; Archaea.
DR   HOGENOM; CLU_055846_1_3_2; -.
DR   OMA; VYVHTRN; -.
DR   OrthoDB; 72065at2157; -.
DR   Proteomes; UP000009079; 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..220
FT                   /note="Ribosomal RNA small subunit methyltransferase Nep1"
FT                   /id="PRO_1000212011"
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         183
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   BINDING         196..201
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            60
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            62
FT                   /note="Stabilizes Arg-60"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            101
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            104
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            108
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
SQ   SEQUENCE   220 AA;  25184 MW;  B227F8C5DA2AB522 CRC64;
     MLHLIIADSE LELVPKELQN HPSIISHAKR RFKKPEEILL DSTYHHTALK SLKDGERRGR
     PDIVHLCLIN ALESILNKEG KLRVYVHTRN NEVIYIKPET RLPRNYNRFV GLMESLFKNR
     VIPKDLALLR IENKTLSEII GDIGPDAVFI MHENGVLMSP QSFGRKLNEY ISPAVIVGGF
     PHGDFLSVLE GEKISIYKEP LMAWSVVNEV LINYEGSLLW