NEP1_PYRHO
ID NEP1_PYRHO Reviewed; 229 AA.
AC O50087;
DT 10-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 109.
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=PH1379;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
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; BA000001; BAA30485.1; -; Genomic_DNA.
DR PIR; E71010; E71010.
DR RefSeq; WP_010885468.1; NC_000961.1.
DR AlphaFoldDB; O50087; -.
DR SMR; O50087; -.
DR STRING; 70601.3257802; -.
DR EnsemblBacteria; BAA30485; BAA30485; BAA30485.
DR GeneID; 1443706; -.
DR KEGG; pho:PH1379; -.
DR eggNOG; arCOG04122; Archaea.
DR OMA; VYVHTRN; -.
DR OrthoDB; 72065at2157; -.
DR Proteomes; UP000000752; 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..229
FT /note="Ribosomal RNA small subunit methyltransferase Nep1"
FT /id="PRO_0000158620"
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 188
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT BINDING 201..206
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT SITE 65
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT SITE 67
FT /note="Stabilizes Arg-65"
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 109
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT SITE 113
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
SQ SEQUENCE 229 AA; 26880 MW; B6DC4957106C9E29 CRC64;
MEEKKRLHLI IADAELETVP PEILDHPAIV NYAKRRKKRP EKIILDSTYH HAALRQLEDG
ERRGRPDIVH ICLLNALDSI LNKEDRLRVY VHTRNDYVIY IKPETRLPRN YNRFIGLMEN
LFEKGAVPED LELLRMEKKT LNELIEEINP DVVFIMHEEG ELMIPKNFGK LLDKFKKPTV
IVGGFPHGDF KSKVDGVKIS LYREPLMAWT IVNEVIVSYE WEVIKKFKS
