NEP1_THEON
ID NEP1_THEON Reviewed; 219 AA.
AC B6YTM6;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 20-JAN-2009, sequence version 1.
DT 03-AUG-2022, entry version 76.
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=TON_0428;
OS Thermococcus onnurineus (strain NA1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Thermococcus.
OX NCBI_TaxID=523850;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NA1;
RX PubMed=18790866; DOI=10.1128/jb.00746-08;
RA Lee H.S., Kang S.G., Bae S.S., Lim J.K., Cho Y., Kim Y.J., Jeon J.H.,
RA Cha S.-S., Kwon K.K., Kim H.-T., Park C.-J., Lee H.-W., Kim S.I., Chun J.,
RA Colwell R.R., Kim S.-J., Lee J.-H.;
RT "The complete genome sequence of Thermococcus onnurineus NA1 reveals a
RT mixed heterotrophic and carboxydotrophic metabolism.";
RL J. Bacteriol. 190:7491-7499(2008).
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; CP000855; ACJ15913.1; -; Genomic_DNA.
DR RefSeq; WP_012571385.1; NC_011529.1.
DR AlphaFoldDB; B6YTM6; -.
DR SMR; B6YTM6; -.
DR STRING; 523850.TON_0428; -.
DR EnsemblBacteria; ACJ15913; ACJ15913; TON_0428.
DR GeneID; 7016723; -.
DR KEGG; ton:TON_0428; -.
DR PATRIC; fig|523850.10.peg.430; -.
DR eggNOG; arCOG04122; Archaea.
DR HOGENOM; CLU_055846_1_3_2; -.
DR OMA; VYVHTRN; -.
DR OrthoDB; 72065at2157; -.
DR Proteomes; UP000002727; 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..219
FT /note="Ribosomal RNA small subunit methyltransferase Nep1"
FT /id="PRO_1000129103"
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 219 AA; 24908 MW; CC477C652FB7A964 CRC64;
MLHLVIADSE LELAPKSIVD HPAIVNYAKR RNKKPEEVLL DSTYHHSALK KLEDGERRGR
PDIVHVCLLN ALESIANKEG KLRVYVHTRN DEVIYIKPET RIPRNYNRFV GLMESLFKNG
VVPEGLELLR MEEKSLAELI DEIKPDGVFV MHENGESMKP QEFGKVLAGL QSPLVVVGGF
PHGDFRSEIP GKKISLYKAP LMAWTVVNEI IINFEHWVL
