NEP1_METJA
ID NEP1_METJA Reviewed; 205 AA.
AC Q57977;
DT 10-MAY-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 112.
DE RecName: Full=Ribosomal RNA small subunit methyltransferase Nep1;
DE EC=2.1.1.-;
DE AltName: Full=16S rRNA (pseudouridine-N1-)-methyltransferase Nep1;
DE AltName: Full=16S rRNA Psi914 methyltransferase;
GN Name=nep1; OrderedLocusNames=MJ0557;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP NMR STUDIES.
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=19779849; DOI=10.1007/s12104-009-9187-z;
RA Wurm J.P., Duchardt E., Meyer B., Leal B.Z., Kotter P., Entian K.D.,
RA Wohnert J.;
RT "Backbone resonance assignments of the 48 kDa dimeric putative 18S rRNA-
RT methyltransferase Nep1 from Methanocaldococcus jannaschii.";
RL Biomol. NMR. Assign. 3:251-254(2009).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, RNA-BINDING, AND RNA-BINDING SITES.
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=20047967; DOI=10.1093/nar/gkp1189;
RA Wurm J.P., Meyer B., Bahr U., Held M., Frolow O., Kotter P., Engels J.W.,
RA Heckel A., Karas M., Entian K.D., Wohnert J.;
RT "The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome
RT is a pseudouridine-N1-specific methyltransferase.";
RL Nucleic Acids Res. 38:2387-2398(2010).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF APOPROTEIN AND COMPLEXES WITH
RP S-ADENOSYL-L-HOMOCYSTEINE AND SINEFUNGIN INHIBITOR, SUBUNIT, AND
RP RNA-BINDING SITES.
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=18208838; DOI=10.1093/nar/gkm1172;
RA Taylor A.B., Meyer B., Leal B.Z., Kotter P., Schirf V., Demeler B.,
RA Hart P.J., Entian K.D., Wohnert J.;
RT "The crystal structure of Nep1 reveals an extended SPOUT-class
RT methyltransferase fold and a pre-organized SAM-binding site.";
RL Nucleic Acids Res. 36:1542-1554(2008).
CC -!- FUNCTION: Methyltransferase involved in ribosomal biogenesis.
CC Specifically catalyzes the N1-methylation of pseudouridine at position
CC 914 (Psi914) in 16S rRNA. Is not able to methylate uridine at this
CC position. {ECO:0000269|PubMed:20047967}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=pseudouridine(914) in M. jannaschii 16S rRNA + S-adenosyl-L-
CC methionine = H(+) + N(1)-methylpseudouridine(914) in M. jannaschii
CC 16S rRNA + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:46716,
CC Rhea:RHEA-COMP:11640, Rhea:RHEA-COMP:11641, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:65314,
CC ChEBI:CHEBI:74890; Evidence={ECO:0000269|PubMed:20047967};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:18208838}.
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; L77117; AAB98551.1; -; Genomic_DNA.
DR PIR; E64369; E64369.
DR RefSeq; WP_010870061.1; NC_000909.1.
DR PDB; 3BBD; X-ray; 2.15 A; A/B=1-205.
DR PDB; 3BBE; X-ray; 2.20 A; A/B=1-205.
DR PDB; 3BBH; X-ray; 2.25 A; A/B=1-205.
DR PDBsum; 3BBD; -.
DR PDBsum; 3BBE; -.
DR PDBsum; 3BBH; -.
DR AlphaFoldDB; Q57977; -.
DR BMRB; Q57977; -.
DR SMR; Q57977; -.
DR STRING; 243232.MJ_0557; -.
DR PRIDE; Q57977; -.
DR EnsemblBacteria; AAB98551; AAB98551; MJ_0557.
DR GeneID; 1451422; -.
DR KEGG; mja:MJ_0557; -.
DR eggNOG; arCOG04122; Archaea.
DR HOGENOM; CLU_055846_1_3_2; -.
DR InParanoid; Q57977; -.
DR OMA; VYVHTRN; -.
DR OrthoDB; 72065at2157; -.
DR PhylomeDB; Q57977; -.
DR BRENDA; 2.1.1.257; 3260.
DR BRENDA; 2.1.1.260; 3260.
DR EvolutionaryTrace; Q57977; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0070037; F:rRNA (pseudouridine) methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0019843; F:rRNA binding; IDA:UniProtKB.
DR GO; GO:0070475; P:rRNA base methylation; IDA:SGD.
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..205
FT /note="Ribosomal RNA small subunit methyltransferase Nep1"
FT /id="PRO_0000158616"
FT BINDING 141..143
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 162
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 167
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 185..190
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT SITE 54
FT /note="Interaction with substrate rRNA"
FT SITE 56
FT /note="Stabilizes Arg-54"
FT SITE 95
FT /note="Interaction with substrate rRNA"
FT SITE 98
FT /note="Interaction with substrate rRNA"
FT SITE 102
FT /note="Interaction with substrate rRNA"
FT STRAND 3..11
FT /evidence="ECO:0007829|PDB:3BBD"
FT HELIX 17..22
FT /evidence="ECO:0007829|PDB:3BBD"
FT HELIX 36..39
FT /evidence="ECO:0007829|PDB:3BBD"
FT TURN 40..45
FT /evidence="ECO:0007829|PDB:3BBD"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:3BBD"
FT HELIX 55..66
FT /evidence="ECO:0007829|PDB:3BBD"
FT HELIX 69..72
FT /evidence="ECO:0007829|PDB:3BBD"
FT STRAND 76..82
FT /evidence="ECO:0007829|PDB:3BBD"
FT STRAND 85..90
FT /evidence="ECO:0007829|PDB:3BBD"
FT HELIX 100..111
FT /evidence="ECO:0007829|PDB:3BBD"
FT STRAND 117..123
FT /evidence="ECO:0007829|PDB:3BBD"
FT HELIX 126..132
FT /evidence="ECO:0007829|PDB:3BBD"
FT STRAND 137..141
FT /evidence="ECO:0007829|PDB:3BBD"
FT STRAND 145..147
FT /evidence="ECO:0007829|PDB:3BBD"
FT HELIX 150..155
FT /evidence="ECO:0007829|PDB:3BBD"
FT STRAND 157..162
FT /evidence="ECO:0007829|PDB:3BBD"
FT STRAND 164..167
FT /evidence="ECO:0007829|PDB:3BBD"
FT HELIX 173..175
FT /evidence="ECO:0007829|PDB:3BBD"
FT STRAND 177..188
FT /evidence="ECO:0007829|PDB:3BBD"
FT HELIX 192..204
FT /evidence="ECO:0007829|PDB:3BBD"
SQ SEQUENCE 205 AA; 24082 MW; 8D3E8BFDCD502831 CRC64;
MTYNIILAKS ALELIPEEIK NKIRKSRVYK YDILDSNYHY KAMEKLKDKE MRGRPDIIHI
SLLNILDSPI NHEKKLNIYI HTYDDKVLKI NPETRLPRNY FRFLGVMEKV LKGERNHLIK
MEEKTLEDLL NEINAKKIAI MTKTGKLTHP KLLKEYDTFI IGGFPYGKLK INKEKVFGDI
KEISIYNKGL MAWTVCGIIC YSLSF
