ID   NEP1_THEKO              Reviewed;         220 AA.
AC   Q5JI44;
DT   30-AUG-2005, integrated into UniProtKB/Swiss-Prot.
DT   15-FEB-2005, sequence version 1.
DT   03-AUG-2022, entry version 87.
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=TK0876;
OS   Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS   (Pyrococcus kodakaraensis (strain KOD1)).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Thermococcus.
OX   NCBI_TaxID=69014;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX   PubMed=15710748; DOI=10.1101/gr.3003105;
RA   Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT   "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT   kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL   Genome Res. 15:352-363(2005).
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; AP006878; BAD85065.1; -; Genomic_DNA.
DR   RefSeq; WP_011249827.1; NC_006624.1.
DR   AlphaFoldDB; Q5JI44; -.
DR   SMR; Q5JI44; -.
DR   STRING; 69014.TK0876; -.
DR   EnsemblBacteria; BAD85065; BAD85065; TK0876.
DR   GeneID; 3234000; -.
DR   KEGG; tko:TK0876; -.
DR   PATRIC; fig|69014.16.peg.855; -.
DR   eggNOG; arCOG04122; Archaea.
DR   HOGENOM; CLU_055846_1_3_2; -.
DR   InParanoid; Q5JI44; -.
DR   OMA; VYVHTRN; -.
DR   OrthoDB; 72065at2157; -.
DR   PhylomeDB; Q5JI44; -.
DR   Proteomes; UP000000536; Chromosome.
DR   GO; GO:0070037; F:rRNA (pseudouridine) methyltransferase activity; IBA:GO_Central.
DR   GO; GO:0019843; F:rRNA binding; IBA:GO_Central.
DR   GO; GO:0070475; P:rRNA base methylation; IBA:GO_Central.
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_0000158621"
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;  25073 MW;  C2A07D3FF5070958 CRC64;
     MLHLIIAEAE LELVPESIRD HPAVVNYARR RKKRPEEAIL DSTYHHAALK KLPDGDRRGR
     PDIVHICLLN ALESIANKEG FLRVYVHTRN DEVIHIKPET RLPRNYNRFL GLMESLFKKG
     AVPEGLELLR IEKKPLESLI EDINPDTVFI MHEEGELIRP RSFGEILASH QNPVVVVGGF
     PHGDFMRPIE GTKVSLYREP LMAWTVVSEV IVNFEAALGL