ID   NEP1_METTP              Reviewed;         226 AA.
AC   A0B5L3;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   28-NOV-2006, sequence version 1.
DT   03-AUG-2022, entry version 80.
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=Mthe_0188;
OS   Methanothrix thermoacetophila (strain DSM 6194 / JCM 14653 / NBRC 101360 /
OS   PT) (Methanosaeta thermophila).
OC   Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC   Methanotrichales; Methanotrichaceae; Methanothrix.
OX   NCBI_TaxID=349307;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 6194 / JCM 14653 / NBRC 101360 / PT;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Pitluck S., Chain P.,
RA   Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA   Hauser L., Kyrpides N., Kim E., Smith K.S., Ingram-Smith C., Richardson P.;
RT   "Complete sequence of Methanosaeta thermophila PT.";
RL   Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
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; CP000477; ABK13987.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0B5L3; -.
DR   SMR; A0B5L3; -.
DR   STRING; 349307.Mthe_0188; -.
DR   EnsemblBacteria; ABK13987; ABK13987; Mthe_0188.
DR   KEGG; mtp:Mthe_0188; -.
DR   HOGENOM; CLU_055846_1_3_2; -.
DR   OMA; VYVHTRN; -.
DR   Proteomes; UP000000674; 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..226
FT                   /note="Ribosomal RNA small subunit methyltransferase Nep1"
FT                   /id="PRO_1000017927"
FT   BINDING         176
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   BINDING         181
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            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   226 AA;  25401 MW;  CB2065F18A0A0553 CRC64;
     MISMLLADSE LELVPREIVG YPAVRLNARK RNKSPAKSIL DASLHHSAMR ALPMGDRRGR
     PDIVHVFLLV ALESVLNRVG QLRVYIHTRN NEMITIDPTT RIPKNYPRFV GLMESLFEKG
     SVPEREPLIV MQRDRDIGAC IGEIPHEKVI LLSPKGRRVR LSDYVKECDN ALFILGGFPK
     GEFISDVLSE ADDTISIYEE SLSVWTVASE ILVNYENHVL EASAPS