ID RLUF_ECOLI Reviewed; 290 AA.
AC P32684; Q2M6T2;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 1.
DT 27-MAR-2024, entry version 169.
DE RecName: Full=Dual-specificity RNA pseudouridine synthase RluF {ECO:0000305};
DE EC=5.4.99.- {ECO:0000269|PubMed:27551044};
DE EC=5.4.99.21 {ECO:0000269|PubMed:11720289, ECO:0000269|PubMed:19298824, ECO:0000269|PubMed:27551044};
DE AltName: Full=23S rRNA pseudouridine(2604) synthase {ECO:0000305|PubMed:11720289};
DE AltName: Full=Ribosomal large subunit pseudouridine synthase F {ECO:0000305};
DE AltName: Full=rRNA pseudouridylate synthase F {ECO:0000305};
DE AltName: Full=rRNA-uridine isomerase F {ECO:0000305};
DE AltName: Full=tRNA(Tyr) pseudouridine(35) synthase {ECO:0000305};
GN Name=rluF; Synonyms=yjbC; OrderedLocusNames=b4022, JW3982;
OS Escherichia coli (strain K12).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8265357; DOI=10.1093/nar/21.23.5408;
RA Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.;
RT "Analysis of the Escherichia coli genome. IV. DNA sequence of the region
RT from 89.2 to 92.8 minutes.";
RL Nucleic Acids Res. 21:5408-5417(1993).
RN [2]
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 [3]
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 [4]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF ASP-107.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=11720289;
RA Del Campo M., Kaya Y., Ofengand J.;
RT "Identification and site of action of the remaining four putative
RT pseudouridine synthases in Escherichia coli.";
RL RNA 7:1603-1615(2001).
RN [5]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=27551044; DOI=10.1074/jbc.m116.747865;
RA Addepalli B., Limbach P.A.;
RT "Pseudouridine in the anticodon of Escherichia coli tRNATyr(QPsiA) is
RT catalyzed by the dual specificity enzyme RluF.";
RL J. Biol. Chem. 291:22327-22337(2016).
RN [6] {ECO:0007744|PDB:2GML}
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 66-290, PARTIAL PROTEIN SEQUENCE,
RP SUBUNIT, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=16712869; DOI=10.1016/j.jmb.2006.04.019;
RA Sunita S., Zhenxing H., Swaathi J., Cygler M., Matte A., Sivaraman J.;
RT "Domain organization and crystal structure of the catalytic domain of
RT E.coli RluF, a pseudouridine synthase that acts on 23S rRNA.";
RL J. Mol. Biol. 359:998-1009(2006).
RN [7] {ECO:0007744|PDB:3DH3}
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE RNA,
RP CATALYTIC ACTIVITY, AND ACTIVE SITE.
RX PubMed=19298824; DOI=10.1016/j.jmb.2009.03.029;
RA Alian A., DeGiovanni A., Griner S.L., Finer-Moore J.S., Stroud R.M.;
RT "Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the
RT key to selectivity of RluF for U2604 of the ribosome.";
RL J. Mol. Biol. 388:785-800(2009).
CC -!- FUNCTION: Dual specificity enzyme that catalyzes the synthesis of
CC pseudouridine from uracil-2604 in 23S ribosomal RNA and from uracil-35
CC in the anticodon of tRNA(Tyr) (PubMed:11720289, PubMed:27551044). Can,
CC to a small extent, also react with uracil-2605 (PubMed:11720289).
CC {ECO:0000269|PubMed:11720289, ECO:0000269|PubMed:27551044}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=uridine(2604) in 23S rRNA = pseudouridine(2604) in 23S rRNA;
CC Xref=Rhea:RHEA:38875, Rhea:RHEA-COMP:10093, Rhea:RHEA-COMP:10094,
CC ChEBI:CHEBI:65314, ChEBI:CHEBI:65315; EC=5.4.99.21;
CC Evidence={ECO:0000269|PubMed:11720289, ECO:0000269|PubMed:19298824,
CC ECO:0000269|PubMed:27551044};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=uridine(35) in tRNA(Tyr) = pseudouridine(35) in tRNA(Tyr);
CC Xref=Rhea:RHEA:60556, Rhea:RHEA-COMP:15607, Rhea:RHEA-COMP:15608,
CC ChEBI:CHEBI:65314, ChEBI:CHEBI:65315;
CC Evidence={ECO:0000269|PubMed:27551044};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:16712869,
CC ECO:0000269|PubMed:19298824}.
CC -!- SIMILARITY: Belongs to the pseudouridine synthase RsuA family.
CC {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U00006; AAC43116.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76992.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78024.1; -; Genomic_DNA.
DR PIR; E65209; E65209.
DR RefSeq; NP_418446.1; NC_000913.3.
DR RefSeq; WP_000936377.1; NZ_SSZK01000049.1.
DR PDB; 2GML; X-ray; 2.60 A; A/B=66-290.
DR PDB; 3DH3; X-ray; 3.00 A; A/B/C/D=1-290.
DR PDBsum; 2GML; -.
DR PDBsum; 3DH3; -.
DR AlphaFoldDB; P32684; -.
DR SMR; P32684; -.
DR BioGRID; 4261777; 60.
DR IntAct; P32684; 9.
DR STRING; 511145.b4022; -.
DR jPOST; P32684; -.
DR PaxDb; 511145-b4022; -.
DR EnsemblBacteria; AAC76992; AAC76992; b4022.
DR GeneID; 948519; -.
DR KEGG; ecj:JW3982; -.
DR KEGG; eco:b4022; -.
DR PATRIC; fig|1411691.4.peg.2691; -.
DR EchoBASE; EB1865; -.
DR eggNOG; COG1187; Bacteria.
DR HOGENOM; CLU_024979_6_1_6; -.
DR InParanoid; P32684; -.
DR OMA; YHKPKGE; -.
DR OrthoDB; 9807213at2; -.
DR PhylomeDB; P32684; -.
DR BioCyc; EcoCyc:EG11921-MONOMER; -.
DR BioCyc; MetaCyc:EG11921-MONOMER; -.
DR BRENDA; 5.4.99.21; 2026.
DR EvolutionaryTrace; P32684; -.
DR PRO; PR:P32684; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0009982; F:pseudouridine synthase activity; IDA:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0120159; F:rRNA pseudouridine synthase activity; IDA:EcoCyc.
DR GO; GO:0106029; F:tRNA pseudouridine synthase activity; IDA:EcoCyc.
DR GO; GO:0000455; P:enzyme-directed rRNA pseudouridine synthesis; IMP:EcoCyc.
DR GO; GO:0031119; P:tRNA pseudouridine synthesis; IMP:EcoCyc.
DR CDD; cd02554; PseudoU_synth_RluF; 1.
DR CDD; cd00165; S4; 1.
DR DisProt; DP02011; -.
DR Gene3D; 3.30.70.1560; Alpha-L RNA-binding motif; 1.
DR Gene3D; 3.30.70.580; Pseudouridine synthase I, catalytic domain, N-terminal subdomain; 1.
DR Gene3D; 3.10.290.10; RNA-binding S4 domain; 1.
DR InterPro; IPR042092; PsdUridine_s_RsuA/RluB/E/F_cat.
DR InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR InterPro; IPR006145; PsdUridine_synth_RsuA/RluA.
DR InterPro; IPR000748; PsdUridine_synth_RsuA/RluB/E/F.
DR InterPro; IPR018496; PsdUridine_synth_RsuA/RluB_CS.
DR InterPro; IPR002942; S4_RNA-bd.
DR InterPro; IPR036986; S4_RNA-bd_sf.
DR InterPro; IPR020094; TruA/RsuA/RluB/E/F_N.
DR NCBIfam; TIGR00093; pseudouridine synthase; 1.
DR PANTHER; PTHR47683; PSEUDOURIDINE SYNTHASE FAMILY PROTEIN-RELATED; 1.
DR PANTHER; PTHR47683:SF2; S4 DOMAIN-CONTAINING PROTEIN; 1.
DR Pfam; PF00849; PseudoU_synth_2; 1.
DR Pfam; PF01479; S4; 1.
DR SMART; SM00363; S4; 1.
DR SUPFAM; SSF55174; Alpha-L RNA-binding motif; 1.
DR SUPFAM; SSF55120; Pseudouridine synthase; 1.
DR PROSITE; PS01149; PSI_RSU; 1.
DR PROSITE; PS50889; S4; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Isomerase; Reference proteome;
KW rRNA processing; tRNA processing.
FT CHAIN 1..290
FT /note="Dual-specificity RNA pseudouridine synthase RluF"
FT /id="PRO_0000100016"
FT DOMAIN 7..72
FT /note="S4 RNA-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00182"
FT REGION 105..108
FT /note="Interaction with RNA"
FT /evidence="ECO:0000269|PubMed:19298824"
FT REGION 187..190
FT /note="Interaction with RNA"
FT /evidence="ECO:0000269|PubMed:19298824"
FT REGION 243..290
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 257..272
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 107
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:19298824"
FT MUTAGEN 107
FT /note="D->N,T: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11720289"
FT HELIX 9..14
FT /evidence="ECO:0007829|PDB:3DH3"
FT TURN 15..17
FT /evidence="ECO:0007829|PDB:3DH3"
FT HELIX 21..29
FT /evidence="ECO:0007829|PDB:3DH3"
FT STRAND 33..35
FT /evidence="ECO:0007829|PDB:3DH3"
FT STRAND 52..54
FT /evidence="ECO:0007829|PDB:3DH3"
FT STRAND 57..59
FT /evidence="ECO:0007829|PDB:3DH3"
FT HELIX 64..66
FT /evidence="ECO:0007829|PDB:3DH3"
FT STRAND 69..74
FT /evidence="ECO:0007829|PDB:2GML"
FT STRAND 82..85
FT /evidence="ECO:0007829|PDB:2GML"
FT STRAND 87..89
FT /evidence="ECO:0007829|PDB:2GML"
FT HELIX 90..93
FT /evidence="ECO:0007829|PDB:2GML"
FT STRAND 101..104
FT /evidence="ECO:0007829|PDB:2GML"
FT STRAND 111..118
FT /evidence="ECO:0007829|PDB:2GML"
FT HELIX 120..132
FT /evidence="ECO:0007829|PDB:2GML"
FT STRAND 135..143
FT /evidence="ECO:0007829|PDB:2GML"
FT HELIX 147..153
FT /evidence="ECO:0007829|PDB:2GML"
FT STRAND 160..163
FT /evidence="ECO:0007829|PDB:3DH3"
FT STRAND 168..173
FT /evidence="ECO:0007829|PDB:2GML"
FT STRAND 176..181
FT /evidence="ECO:0007829|PDB:2GML"
FT HELIX 188..195
FT /evidence="ECO:0007829|PDB:2GML"
FT STRAND 200..208
FT /evidence="ECO:0007829|PDB:2GML"
FT STRAND 221..223
FT /evidence="ECO:0007829|PDB:2GML"
FT HELIX 226..233
FT /evidence="ECO:0007829|PDB:2GML"
SQ SEQUENCE 290 AA; 32477 MW; C88C830CBE5DF2FA CRC64;
MLPDSSVRLN KYISESGICS RREADRYIEQ GNVFLNGKRA TIGDQVKPGD VVKVNGQLIE
PREAEDLVLI ALNKPVGIVS TTEDGERDNI VDFVNHSKRV FPIGRLDKDS QGLIFLTNHG
DLVNKILRAG NDHEKEYLVT VDKPITEEFI RGMSAGVPIL GTVTKKCKVK KEAPFVFRIT
LVQGLNRQIR RMCEHFGYEV KKLERTRIMN VSLSGIPLGE WRDLTDDELI DLFKLIENSS
SEVKPKAKAK PKTAGIKRPV VKMEKTAEKG GRPASNGKRF TSPGRKKKGR
//
