RSMF_THET8
ID RSMF_THET8 Reviewed; 456 AA.
AC Q5SII2;
DT 07-JAN-2015, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=Ribosomal RNA small subunit methyltransferase F {ECO:0000250|UniProtKB:P76273};
DE EC=2.1.1.- {ECO:0000269|PubMed:20558545};
DE EC=2.1.1.178 {ECO:0000269|PubMed:20558545};
DE AltName: Full=rRNA (cytosine-C(5)-)-methyltransferase RsmF {ECO:0000250|UniProtKB:P76273};
GN Name=rsmF {ECO:0000303|PubMed:20558545};
GN OrderedLocusNames=TTHA1387 {ECO:0000312|EMBL:BAD71210.1};
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.30 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE, FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RX PubMed=20558545; DOI=10.1261/rna.2088310;
RA Demirci H., Larsen L.H., Hansen T., Rasmussen A., Cadambi A., Gregory S.T.,
RA Kirpekar F., Jogl G.;
RT "Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus
RT thermophilus.";
RL RNA 16:1584-1596(2010).
CC -!- FUNCTION: Specifically methylates the cytosines at positions 1400
CC (m5C1400), 1404 (m5C1404) and 1407 (m5C1407) of 16S rRNA. C1400, C1404
CC and C1407 are methylated in a 30S subunit substrate, but only C1400 and
CC C1404 are methylated when naked 16S rRNA is the substrate. Methylation
CC by RsmF may facilitate growth at temperatures outside the optimal
CC growth temperature. {ECO:0000269|PubMed:20558545}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(1400) in 16S rRNA + S-adenosyl-L-methionine = 5-
CC methylcytidine(1400) in 16S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:47732, Rhea:RHEA-COMP:11892, Rhea:RHEA-COMP:11893,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000269|PubMed:20558545};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(1404) in 16S rRNA + S-adenosyl-L-methionine = 5-
CC methylcytidine(1404) in 16S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:47736, Rhea:RHEA-COMP:11894, Rhea:RHEA-COMP:11895,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000269|PubMed:20558545};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(1407) in 16S rRNA + S-adenosyl-L-methionine = 5-
CC methylcytidine(1407) in 16S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42756, Rhea:RHEA-COMP:10223, Rhea:RHEA-COMP:10224,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.178;
CC Evidence={ECO:0000269|PubMed:20558545};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P76273}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RsmB/NOP family. {ECO:0000255|PROSITE-ProRule:PRU01023}.
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DR EMBL; AP008226; BAD71210.1; -; Genomic_DNA.
DR RefSeq; WP_011228642.1; NC_006461.1.
DR RefSeq; YP_144653.1; NC_006461.1.
DR PDB; 3M6U; X-ray; 1.40 A; A/B=1-456.
DR PDB; 3M6V; X-ray; 1.82 A; A/B=1-456.
DR PDB; 3M6W; X-ray; 1.30 A; A=1-456.
DR PDB; 3M6X; X-ray; 1.68 A; A=1-456.
DR PDBsum; 3M6U; -.
DR PDBsum; 3M6V; -.
DR PDBsum; 3M6W; -.
DR PDBsum; 3M6X; -.
DR AlphaFoldDB; Q5SII2; -.
DR SMR; Q5SII2; -.
DR STRING; 300852.55772769; -.
DR DrugBank; DB02899; N-Carboxymethionine.
DR EnsemblBacteria; BAD71210; BAD71210; BAD71210.
DR GeneID; 3168094; -.
DR KEGG; ttj:TTHA1387; -.
DR PATRIC; fig|300852.9.peg.1363; -.
DR eggNOG; COG0144; Bacteria.
DR eggNOG; COG3270; Bacteria.
DR HOGENOM; CLU_005316_6_1_0; -.
DR OMA; PWCAEGF; -.
DR PhylomeDB; Q5SII2; -.
DR EvolutionaryTrace; Q5SII2; -.
DR Proteomes; UP000000532; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0001510; P:RNA methylation; IEA:InterPro.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR031341; Methyltr_RsmF_N.
DR InterPro; IPR001678; MeTrfase_RsmB/NOP2.
DR InterPro; IPR023267; RCMT.
DR InterPro; IPR031340; RsmF_methylt_CI.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR22807; PTHR22807; 1.
DR Pfam; PF01189; Methyltr_RsmB-F; 1.
DR Pfam; PF17125; Methyltr_RsmF_N; 1.
DR Pfam; PF17126; RsmF_methylt_CI; 1.
DR PRINTS; PR02008; RCMTFAMILY.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51686; SAM_MT_RSMB_NOP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Methyltransferase; Reference proteome;
KW RNA-binding; rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..456
FT /note="Ribosomal RNA small subunit methyltransferase F"
FT /id="PRO_0000431481"
FT ACT_SITE 230
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 109..115
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:20558545"
FT BINDING 133
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:20558545"
FT BINDING 138
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:20558545"
FT BINDING 177
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:20558545"
FT HELIX 4..14
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 15..17
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 18..26
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 33..36
FT /evidence="ECO:0007829|PDB:3M6W"
FT TURN 38..40
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 43..49
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 55..57
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 60..65
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 73..75
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 76..79
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 82..85
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 92..97
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 104..109
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 114..122
FT /evidence="ECO:0007829|PDB:3M6W"
FT TURN 123..125
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 127..132
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 136..149
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 154..156
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 160..167
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 171..177
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 183..185
FT /evidence="ECO:0007829|PDB:3M6W"
FT TURN 186..188
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 193..195
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 200..216
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 219..230
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 234..236
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 238..247
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 251..254
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 262..264
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 267..269
FT /evidence="ECO:0007829|PDB:3M6W"
FT TURN 270..272
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 274..278
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 279..282
FT /evidence="ECO:0007829|PDB:3M6W"
FT TURN 284..286
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 287..290
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 292..299
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 317..330
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 338..341
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 344..347
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 361..371
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 374..378
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 379..384
FT /evidence="ECO:0007829|PDB:3M6W"
FT TURN 386..388
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 393..395
FT /evidence="ECO:0007829|PDB:3M6U"
FT STRAND 397..400
FT /evidence="ECO:0007829|PDB:3M6W"
FT HELIX 405..411
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 423..432
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 435..445
FT /evidence="ECO:0007829|PDB:3M6W"
FT STRAND 448..451
FT /evidence="ECO:0007829|PDB:3M6W"
SQ SEQUENCE 456 AA; 49740 MW; C440940306A6683E CRC64;
MLPKAFLSRM AELLGEEFPA FLKALTEGKR TYGLRVNTLK LPPEAFQRIS PWPLRPIPWC
QEGFYYPEEA RPGPHPFFYA GLYYIQEPSA QAVGVLLDPK PGERVLDLAA APGGKTTHLA
ARMGGKGLLL ANEVDGKRVR GLLENVERWG APLAVTQAPP RALAEAFGTY FHRVLLDAPC
SGEGMFRKDR EAARHWGPSA PKRMAEVQKA LLAQASRLLG PGGVLVYSTC TFAPEENEGV
VAHFLKAHPE FRLEDARLHP LFAPGVPEWG EGNPELLKTA RLWPHRLEGE GHFLARFRKE
GGAWSTPRLE RPSPLSQEAL RAFRGFLEEA GLTLEGPVLD RAGHLYLLPE GLPTLLGLKA
PAPGLYLGKV QKGRFLPARA LALAFGATLP WPEGLPRLAL TPEDPRALAF ATGEGVAWEG
EDHPLALVVL KTAAGEFPLD FGKAKRGVLR PVGVGL
