NEP1_STAMF
ID NEP1_STAMF Reviewed; 230 AA.
AC A3DNG9;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 20-MAR-2007, sequence version 1.
DT 03-AUG-2022, entry version 72.
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=Smar_1081;
OS Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / JCM 9404 / F1).
OC Archaea; Crenarchaeota; Thermoprotei; Desulfurococcales;
OC Desulfurococcaceae; Staphylothermus.
OX NCBI_TaxID=399550;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43588 / DSM 3639 / JCM 9404 / F1;
RX PubMed=19341479; DOI=10.1186/1471-2164-10-145;
RA Anderson I.J., Dharmarajan L., Rodriguez J., Hooper S., Porat I.,
RA Ulrich L.E., Elkins J.G., Mavromatis K., Sun H., Land M., Lapidus A.,
RA Lucas S., Barry K., Huber H., Zhulin I.B., Whitman W.B., Mukhopadhyay B.,
RA Woese C., Bristow J., Kyrpides N.;
RT "The complete genome sequence of Staphylothermus marinus reveals
RT differences in sulfur metabolism among heterotrophic Crenarchaeota.";
RL BMC Genomics 10:145-145(2009).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43588 / DSM 3639 / JCM 9404 / F1;
RX PubMed=21304655; DOI=10.4056/sigs.30527;
RA Anderson I.J., Sun H., Lapidus A., Copeland A., Glavina Del Rio T.,
RA Tice H., Dalin E., Lucas S., Barry K., Land M., Richardson P., Huber H.,
RA Kyrpides N.C.;
RT "Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986
RT type strain F1.";
RL Stand. Genomic Sci. 1:183-188(2009).
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; CP000575; ABN70179.1; -; Genomic_DNA.
DR RefSeq; WP_011839370.1; NC_009033.1.
DR AlphaFoldDB; A3DNG9; -.
DR SMR; A3DNG9; -.
DR STRING; 399550.Smar_1081; -.
DR EnsemblBacteria; ABN70179; ABN70179; Smar_1081.
DR GeneID; 4906949; -.
DR KEGG; smr:Smar_1081; -.
DR eggNOG; arCOG04122; Archaea.
DR HOGENOM; CLU_055846_1_3_2; -.
DR OMA; VYVHTRN; -.
DR OrthoDB; 72065at2157; -.
DR Proteomes; UP000000254; 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..230
FT /note="Ribosomal RNA small subunit methyltransferase Nep1"
FT /id="PRO_1000017931"
FT BINDING 184
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT BINDING 189
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT BINDING 205..210
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 230 AA; 26375 MW; 14D6B81453159F1E CRC64;
MNMKEPISII LLESALELVP KELWKHPAVV KNARRRGKKP GETLLDVSLH YHAMKKLKDK
EKRGRPDIVH ISLLNALESP LNKEGYLRIY IHTYPGHIIF VKPETRIPRN YNRFVGLMEQ
LLIHGKVPPD SDDPLLYVKT MTISDLLEKI NKNGIILLRE HGEKEKPENI VKYAVENNYA
IGIGGFPHGD YSQEIISISK AEFSIYNKPL TTWITISRVI VGAEHLYNII
