RSMB_ECOLI
ID RSMB_ECOLI Reviewed; 429 AA.
AC P36929; P23866; Q2M6V3;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 2.
DT 03-AUG-2022, entry version 181.
DE RecName: Full=Ribosomal RNA small subunit methyltransferase B;
DE EC=2.1.1.176;
DE AltName: Full=16S rRNA m5C967 methyltransferase;
DE AltName: Full=rRNA (cytosine-C(5)-)-methyltransferase RsmB;
GN Name=rsmB; Synonyms=fmu/fmv, rrmB, sun, yhdB;
GN OrderedLocusNames=b3289, JW3250;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / K37;
RX PubMed=8432722; DOI=10.1128/jb.175.4.993-1000.1993;
RA Meinnel T., Guillon J.-M., Mechulam Y., Blanquet S.;
RT "The Escherichia coli fmt gene, encoding methionyl-tRNA(fMet)
RT formyltransferase, escapes metabolic control.";
RL J. Bacteriol. 175:993-1000(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9086272; DOI=10.1006/jmbi.1996.0835;
RA Mazel D., Coic E., Blanchard S., Saurin W., Marliere P.;
RT "A survey of polypeptide deformylase function throughout the eubacterial
RT lineage.";
RL J. Mol. Biol. 266:939-949(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 384-429.
RX PubMed=8412700; DOI=10.1111/j.1365-2958.1993.tb01714.x;
RA Schloesser A., Hamann A., Bossemeyer D., Schneider E., Bakker E.P.;
RT "NAD+ binding to the Escherichia coli K(+)-uptake protein TrkA and sequence
RT similarity between TrkA and domains of a family of dehydrogenases suggest a
RT role for NAD+ in bacterial transport.";
RL Mol. Microbiol. 9:533-543(1993).
RN [6]
RP PROTEIN SEQUENCE OF 1-23 AND 418-429, AND CHARACTERIZATION.
RX PubMed=10026269; DOI=10.1021/bi981880l;
RA Tscherne J.S., Nurse K., Popienick P., Michel H., Sochacki M., Ofengand J.;
RT "Purification, cloning, and characterization of the 16S RNA m5C967
RT methyltransferase from Escherichia coli.";
RL Biochemistry 38:1884-1892(1999).
RN [7]
RP FUNCTION.
RX PubMed=10194318; DOI=10.1021/bi982364y;
RA Gu X.R., Gustafsson C., Ku J., Yu M., Santi D.V.;
RT "Identification of the 16S rRNA m5C967 methyltransferase from Escherichia
RT coli.";
RL Biochemistry 38:4053-4057(1999).
RN [8]
RP MUTAGENESIS OF CYS-325 AND CYS-375, AND ACTIVE SITE.
RX PubMed=10899996; DOI=10.1073/pnas.97.15.8263;
RA Liu Y., Santi D.V.;
RT "m5C RNA and m5C DNA methyl transferases use different cysteine residues as
RT catalysts.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:8263-8265(2000).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE, AND MUTAGENESIS OF CYS-325 AND CYS-375.
RX PubMed=14656444; DOI=10.1016/j.str.2003.10.014;
RA Foster P.G., Nunes C.R., Greene P., Moustakas D., Stroud R.M.;
RT "The first structure of an RNA m5C methyltransferase, Fmu, provides insight
RT into catalytic mechanism and specific binding of RNA substrate.";
RL Structure 11:1609-1620(2003).
CC -!- FUNCTION: Specifically methylates the cytosine at position 967 (m5C967)
CC of 16S rRNA. {ECO:0000269|PubMed:10194318}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(967) in 16S rRNA + S-adenosyl-L-methionine = 5-
CC methylcytidine(967) in 16S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42748, Rhea:RHEA-COMP:10219, Rhea:RHEA-COMP:10220,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748; EC=2.1.1.176;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RsmB/NOP family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA58086.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAA54369.1; Type=Frameshift; Note=Was originally named Fmu and represented the N-terminal part of the RsmB protein.; Evidence={ECO:0000305};
CC Sequence=CAA54370.1; Type=Frameshift; Note=Was originally named Fmv and represented the C-terminal part of the RsmB protein.; Evidence={ECO:0000305};
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DR EMBL; X77091; CAA54369.1; ALT_FRAME; Genomic_DNA.
DR EMBL; X77091; CAA54370.1; ALT_FRAME; Genomic_DNA.
DR EMBL; Y10307; CAA71359.1; -; Genomic_DNA.
DR EMBL; U18997; AAA58086.1; ALT_FRAME; Genomic_DNA.
DR EMBL; U00096; AAC76314.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78003.1; -; Genomic_DNA.
DR EMBL; X52114; CAA36358.1; -; Genomic_DNA.
DR PIR; D65121; D65121.
DR RefSeq; NP_417747.1; NC_000913.3.
DR RefSeq; WP_000744778.1; NZ_SSZK01000040.1.
DR PDB; 1SQF; X-ray; 2.10 A; A=1-429.
DR PDB; 1SQG; X-ray; 1.65 A; A=1-429.
DR PDBsum; 1SQF; -.
DR PDBsum; 1SQG; -.
DR AlphaFoldDB; P36929; -.
DR SMR; P36929; -.
DR BioGRID; 4263436; 49.
DR DIP; DIP-10946N; -.
DR IntAct; P36929; 14.
DR STRING; 511145.b3289; -.
DR jPOST; P36929; -.
DR PaxDb; P36929; -.
DR PRIDE; P36929; -.
DR EnsemblBacteria; AAC76314; AAC76314; b3289.
DR EnsemblBacteria; BAE78003; BAE78003; BAE78003.
DR GeneID; 947789; -.
DR KEGG; ecj:JW3250; -.
DR KEGG; eco:b3289; -.
DR PATRIC; fig|1411691.4.peg.3443; -.
DR EchoBASE; EB2082; -.
DR eggNOG; COG0144; Bacteria.
DR eggNOG; COG0781; Bacteria.
DR HOGENOM; CLU_005316_0_4_6; -.
DR InParanoid; P36929; -.
DR OMA; RVNRQHH; -.
DR PhylomeDB; P36929; -.
DR BioCyc; EcoCyc:EG12163-MON; -.
DR BioCyc; MetaCyc:EG12163-MON; -.
DR BRENDA; 2.1.1.176; 2026.
DR EvolutionaryTrace; P36929; -.
DR PRO; PR:P36929; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0009383; F:rRNA (cytosine-C5-)-methyltransferase activity; IDA:EcoCyc.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:InterPro.
DR GO; GO:0001510; P:RNA methylation; IBA:GO_Central.
DR GO; GO:0070475; P:rRNA base methylation; IMP:EcoCyc.
DR Gene3D; 1.10.940.10; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_01856; 16SrRNA_methyltr_B; 1.
DR InterPro; IPR018314; Fmu/NOL1/Nop2p_CS.
DR InterPro; IPR001678; MeTrfase_RsmB/NOP2.
DR InterPro; IPR035926; NusB-like_sf.
DR InterPro; IPR006027; NusB_RsmB_TIM44.
DR InterPro; IPR023267; RCMT.
DR InterPro; IPR004573; rRNA_ssu_MeTfrase_B.
DR InterPro; IPR023541; rRNA_ssu_MeTfrase_B_ent.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR22807; PTHR22807; 1.
DR Pfam; PF01189; Methyltr_RsmB-F; 1.
DR Pfam; PF01029; NusB; 1.
DR PRINTS; PR02008; RCMTFAMILY.
DR SUPFAM; SSF48013; SSF48013; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00563; rsmB; 1.
DR PROSITE; PS01153; NOL1_NOP2_SUN; 1.
DR PROSITE; PS51686; SAM_MT_RSMB_NOP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Methyltransferase;
KW Reference proteome; RNA-binding; rRNA processing; S-adenosyl-L-methionine;
KW Transferase.
FT CHAIN 1..429
FT /note="Ribosomal RNA small subunit methyltransferase B"
FT /id="PRO_0000211792"
FT ACT_SITE 375
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 254..260
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 277
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:14656444"
FT BINDING 303
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:14656444"
FT BINDING 322
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:14656444"
FT MUTAGEN 325
FT /note="C->A: Reduces activity 3-fold."
FT /evidence="ECO:0000269|PubMed:10899996,
FT ECO:0000269|PubMed:14656444"
FT MUTAGEN 375
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:10899996,
FT ECO:0000269|PubMed:14656444"
FT CONFLICT 3
FT /note="K -> C (in Ref. 6; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 3
FT /note="K -> W (in Ref. 6; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 105..106
FT /note="GA -> RR (in Ref. 1; CAA54369)"
FT /evidence="ECO:0000305"
FT HELIX 7..21
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 25..33
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 38..65
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 72..74
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 75..90
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 95..108
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 112..114
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 115..136
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 140..143
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 147..156
FT /evidence="ECO:0007829|PDB:1SQG"
FT TURN 158..160
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 161..168
FT /evidence="ECO:0007829|PDB:1SQG"
FT STRAND 174..178
FT /evidence="ECO:0007829|PDB:1SQG"
FT TURN 180..182
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 185..194
FT /evidence="ECO:0007829|PDB:1SQG"
FT STRAND 208..213
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 217..219
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 223..225
FT /evidence="ECO:0007829|PDB:1SQG"
FT STRAND 227..230
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 233..236
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 238..242
FT /evidence="ECO:0007829|PDB:1SQG"
FT STRAND 249..254
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 259..267
FT /evidence="ECO:0007829|PDB:1SQG"
FT STRAND 272..279
FT /evidence="ECO:0007829|PDB:1SQG"
FT TURN 280..282
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 283..292
FT /evidence="ECO:0007829|PDB:1SQG"
FT STRAND 298..301
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 308..311
FT /evidence="ECO:0007829|PDB:1SQG"
FT STRAND 316..322
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 328..330
FT /evidence="ECO:0007829|PDB:1SQG"
FT TURN 331..333
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 337..340
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 345..360
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 361..363
FT /evidence="ECO:0007829|PDB:1SQG"
FT STRAND 364..375
FT /evidence="ECO:0007829|PDB:1SQG"
FT TURN 379..382
FT /evidence="ECO:0007829|PDB:1SQG"
FT HELIX 383..392
FT /evidence="ECO:0007829|PDB:1SQG"
FT STRAND 400..402
FT /evidence="ECO:0007829|PDB:1SQG"
FT STRAND 404..411
FT /evidence="ECO:0007829|PDB:1SQG"
FT STRAND 420..427
FT /evidence="ECO:0007829|PDB:1SQG"
SQ SEQUENCE 429 AA; 48348 MW; 1F516223C84D80F8 CRC64;
MKKQRNLRSM AAQAVEQVVE QGQSLSNILP PLQQKVSDKD KALLQELCFG VLRTLSQLDW
LINKLMARPM TGKQRTVHYL IMVGLYQLLY TRIPPHAALA ETVEGAIAIK RPQLKGLING
VLRQFQRQQE ELLAEFNASD ARYLHPSWLL KRLQKAYPEQ WQSIVEANNQ RPPMWLRINR
THHSRDSWLA LLDEAGMKGF PHADYPDAVR LETPAPVHAL PGFEDGWVTV QDASAQGCMT
WLAPQNGEHI LDLCAAPGGK TTHILEVAPE AQVVAVDIDE QRLSRVYDNL KRLGMKATVK
QGDGRYPSQW CGEQQFDRIL LDAPCSATGV IRRHPDIKWL RRDRDIPELA QLQSEILDAI
WPHLKTGGTL VYATCSVLPE ENSLQIKAFL QRTADAELCE TGTPEQPGKQ NLPGAEEGDG
FFYAKLIKK
