ID NEP1_THEAC Reviewed; 222 AA.
AC Q9HJ48;
DT 10-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT 10-MAY-2002, sequence version 2.
DT 27-MAR-2024, 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=Ta1124;
OS Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC
OS 15155 / AMRC-C165).
OC Archaea; Candidatus Thermoplasmatota; Thermoplasmata; Thermoplasmatales;
OC Thermoplasmataceae; Thermoplasma.
OX NCBI_TaxID=273075;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165;
RX PubMed=11029001; DOI=10.1038/35035069;
RA Ruepp A., Graml W., Santos-Martinez M.-L., Koretke K.K., Volker C.,
RA Mewes H.-W., Frishman D., Stocker S., Lupas A.N., Baumeister W.;
RT "The genome sequence of the thermoacidophilic scavenger Thermoplasma
RT acidophilum.";
RL Nature 407:508-513(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 NEP1 family. {ECO:0000255|HAMAP-
CC Rule:MF_00554}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAC12251.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AL445066; CAC12251.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_010901534.1; NC_002578.1.
DR AlphaFoldDB; Q9HJ48; -.
DR SMR; Q9HJ48; -.
DR STRING; 273075.gene:9572347; -.
DR PaxDb; 273075-Ta1124m; -.
DR EnsemblBacteria; CAC12251; CAC12251; CAC12251.
DR GeneID; 1457078; -.
DR KEGG; tac:Ta1124; -.
DR eggNOG; arCOG04122; Archaea.
DR HOGENOM; CLU_055846_1_3_2; -.
DR InParanoid; Q9HJ48; -.
DR OrthoDB; 7612at2157; -.
DR Proteomes; UP000001024; 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; NEP1/MRA1; 1.
DR PANTHER; PTHR12636:SF5; RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE NEP1; 1.
DR Pfam; PF03587; EMG1; 1.
DR SUPFAM; SSF75217; alpha/beta knot; 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..222
FT /note="Ribosomal RNA small subunit methyltransferase Nep1"
FT /id="PRO_0000158624"
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; 25939 MW; 5EE70F05E4D15BB6 CRC64;
MLHLVIADAE LETIPEEMQA DPAIRRFAKK RNKRVDRMIL DSNYMHTSID RYFPNESKRR
GRPDIIYLLL EMTQESILNH KNQLRTYVHT RNNQVIRISP ITRMPKSYNR FIGLFEDLFE
KRIITNNGKE LLSMEESSLG DLINSIRRDR TILLHPKGEM RKPSEFISNA NILIVIGGFS
EGDFISDTSF INERYAIFDQ ELTIWSVANE MVANYERAVG LT
//
