NEP1_ARCFU
ID NEP1_ARCFU Reviewed; 219 AA.
AC O29524;
DT 10-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-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=AF_0734;
OS Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC
OS 100126 / VC-16).
OC Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae;
OC Archaeoglobus.
OX NCBI_TaxID=224325;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16;
RX PubMed=9389475; DOI=10.1038/37052;
RA Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A.,
RA Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L.,
RA Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D.,
RA Quackenbush J., Lee N.H., Sutton G.G., Gill S.R., Kirkness E.F.,
RA Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N.,
RA Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R.,
RA Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D.,
RA Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P.,
RA Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M.,
RA Smith H.O., Woese C.R., Venter J.C.;
RT "The complete genome sequence of the hyperthermophilic, sulphate-reducing
RT archaeon Archaeoglobus fulgidus.";
RL Nature 390:364-370(1997).
RN [2] {ECO:0007744|PDB:3O7B}
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE.
RX PubMed=21087996; DOI=10.1093/nar/gkq1131;
RA Thomas S.R., Keller C.A., Szyk A., Cannon J.R., Laronde-Leblanc N.A.;
RT "Structural insight into the functional mechanism of Nep1/Emg1 N1-specific
RT pseudouridine methyltransferase in ribosome biogenesis.";
RL Nucleic Acids Res. 39:2445-2457(2011).
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; AE000782; AAB90504.1; -; Genomic_DNA.
DR PIR; F69341; F69341.
DR RefSeq; WP_010878237.1; NC_000917.1.
DR PDB; 3O7B; X-ray; 1.45 A; A=1-219.
DR PDBsum; 3O7B; -.
DR AlphaFoldDB; O29524; -.
DR SMR; O29524; -.
DR STRING; 224325.AF_0734; -.
DR EnsemblBacteria; AAB90504; AAB90504; AF_0734.
DR GeneID; 24794332; -.
DR KEGG; afu:AF_0734; -.
DR eggNOG; arCOG04122; Archaea.
DR HOGENOM; CLU_055846_1_3_2; -.
DR OMA; VYVHTRN; -.
DR OrthoDB; 72065at2157; -.
DR PhylomeDB; O29524; -.
DR BRENDA; 2.1.1.260; 414.
DR Proteomes; UP000002199; 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 1: Evidence at protein level;
KW 3D-structure; Methyltransferase; Reference proteome; Ribosome biogenesis;
KW RNA-binding; rRNA processing; rRNA-binding; S-adenosyl-L-methionine;
KW Transferase.
FT CHAIN 1..219
FT /note="Ribosomal RNA small subunit methyltransferase Nep1"
FT /id="PRO_0000158615"
FT BINDING 147
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000305|PubMed:21087996,
FT ECO:0007744|PDB:3O7B"
FT BINDING 169
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554,
FT ECO:0000305|PubMed:21087996, ECO:0007744|PDB:3O7B"
FT BINDING 174
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554,
FT ECO:0000305|PubMed:21087996, ECO:0007744|PDB:3O7B"
FT BINDING 192..197
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554,
FT ECO:0000305|PubMed:21087996, ECO:0007744|PDB:3O7B"
FT SITE 61
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT SITE 63
FT /note="Stabilizes Arg-61"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT SITE 99
FT /note="Interaction with substrate rRNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT SITE 102
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 STRAND 3..11
FT /evidence="ECO:0007829|PDB:3O7B"
FT HELIX 17..19
FT /evidence="ECO:0007829|PDB:3O7B"
FT HELIX 23..32
FT /evidence="ECO:0007829|PDB:3O7B"
FT HELIX 36..38
FT /evidence="ECO:0007829|PDB:3O7B"
FT HELIX 43..46
FT /evidence="ECO:0007829|PDB:3O7B"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:3O7B"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:3O7B"
FT HELIX 63..73
FT /evidence="ECO:0007829|PDB:3O7B"
FT STRAND 79..86
FT /evidence="ECO:0007829|PDB:3O7B"
FT STRAND 91..94
FT /evidence="ECO:0007829|PDB:3O7B"
FT HELIX 104..117
FT /evidence="ECO:0007829|PDB:3O7B"
FT STRAND 118..122
FT /evidence="ECO:0007829|PDB:3O7B"
FT STRAND 125..133
FT /evidence="ECO:0007829|PDB:3O7B"
FT HELIX 135..138
FT /evidence="ECO:0007829|PDB:3O7B"
FT TURN 139..141
FT /evidence="ECO:0007829|PDB:3O7B"
FT STRAND 142..147
FT /evidence="ECO:0007829|PDB:3O7B"
FT HELIX 156..159
FT /evidence="ECO:0007829|PDB:3O7B"
FT STRAND 161..169
FT /evidence="ECO:0007829|PDB:3O7B"
FT STRAND 171..174
FT /evidence="ECO:0007829|PDB:3O7B"
FT HELIX 178..184
FT /evidence="ECO:0007829|PDB:3O7B"
FT STRAND 186..190
FT /evidence="ECO:0007829|PDB:3O7B"
FT HELIX 199..214
FT /evidence="ECO:0007829|PDB:3O7B"
SQ SEQUENCE 219 AA; 25308 MW; 8056C7AC140562FB CRC64;
MGSAFVFLEA SLELIPQKIR GHPAVRADAI RRGKRPEKIL LDDSKHHTAM KSLEFREKRG
RPDIVHQCLL LLLDSPLRDF EVYVHTLNGE IIWVNRETRL PRNYNRFVGL MEKLFEERRI
TAGDTTLIEF KDVGLRDIVR GRDVLLFREK GGRFEFSELL DGDVAVCIGA FPHGDFFEET
LRELGEFKEV SLGTESYTSL YVTSRVLCEY ERVRAHKVG
