RLUD_ECOLI
ID RLUD_ECOLI Reviewed; 326 AA.
AC P33643; P77003;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 4.
DT 03-AUG-2022, entry version 179.
DE RecName: Full=Ribosomal large subunit pseudouridine synthase D;
DE EC=5.4.99.23;
DE AltName: Full=23S rRNA pseudouridine(1911/1915/1917) synthase;
DE AltName: Full=rRNA pseudouridylate synthase D;
DE AltName: Full=rRNA-uridine isomerase D;
GN Name=rluD; Synonyms=sfhB, yfiI; OrderedLocusNames=b2594, JW2576;
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 / W3110 / ATCC 27325 / DSM 5911;
RA Ogura T., Tomoyasu T.;
RL Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(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], AND SEQUENCE REVISION TO
RP 271-326.
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 40-326.
RC STRAIN=K12;
RX PubMed=1906060; DOI=10.1128/jb.173.14.4247-4253.1991;
RA Kitagawa M., Wada C., Yoshioka S., Yura T.;
RT "Expression of ClpB, an analog of the ATP-dependent protease regulatory
RT subunit in Escherichia coli, is controlled by a heat shock sigma factor
RT (sigma 32).";
RL J. Bacteriol. 173:4247-4253(1991).
RN [6]
RP CHARACTERIZATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9814761; DOI=10.1017/s1355838298981146;
RA Raychaudhuri S., Conrad J., Hall B.G., Ofengand J.;
RT "A pseudouridine synthase required for the formation of two universally
RT conserved pseudouridines in ribosomal RNA is essential for normal growth of
RT Escherichia coli.";
RL RNA 4:1407-1417(1998).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND PROTEIN SEQUENCE OF N-TERMINUS.
RX PubMed=11087118; DOI=10.1080/15216540050176566;
RA Wrzesinski J., Bakin A., Ofengand J., Lane B.G.;
RT "Isolation and properties of Escherichia coli 23S-RNA pseudouridine 1911,
RT 1915, 1917 synthase (RluD).";
RL IUBMB Life 50:33-37(2000).
RN [8]
RP MUTAGENESIS OF ASP-139.
RX PubMed=11453071; DOI=10.1017/s1355838201000243;
RA Gutgsell N.S., Del Campo M., Raychaudhuri S., Ofengand J.;
RT "A second function for pseudouridine synthases: a point mutant of RluD
RT unable to form pseudouridines 1911, 1915, and 1917 in Escherichia coli 23S
RT ribosomal RNA restores normal growth to an RluD-minus strain.";
RL RNA 7:990-998(2001).
RN [9]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=17937767; DOI=10.1111/j.1742-4658.2007.06101.x;
RA Leppik M., Peil L., Kipper K., Liiv A., Remme J.;
RT "Substrate specificity of the pseudouridine synthase RluD in Escherichia
RT coli.";
RL FEBS J. 274:5759-5766(2007).
CC -!- FUNCTION: Responsible for synthesis of pseudouridine from uracil at
CC positions 1911, 1915 and 1917 in 23S ribosomal RNA. Isomerization
CC occurs as a late step during the assembly of the large ribosomal
CC subunit. {ECO:0000269|PubMed:11087118, ECO:0000269|PubMed:17937767}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=uridine(1911/1915/1917) in 23S rRNA =
CC pseudouridine(1911/1915/1917) in 23S rRNA; Xref=Rhea:RHEA:42524,
CC Rhea:RHEA-COMP:10097, Rhea:RHEA-COMP:10098, ChEBI:CHEBI:65314,
CC ChEBI:CHEBI:65315; EC=5.4.99.23;
CC Evidence={ECO:0000269|PubMed:11087118, ECO:0000269|PubMed:17937767};
CC -!- INTERACTION:
CC P33643; P21165: pepQ; NbExp=2; IntAct=EBI-558026, EBI-552580;
CC P33643; P0A8A4: ppsR; NbExp=3; IntAct=EBI-558026, EBI-548302;
CC -!- SIMILARITY: Belongs to the pseudouridine synthase RluA family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=X57620; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U50134; AAA92957.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75643.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16479.2; -; Genomic_DNA.
DR EMBL; X57620; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; E65037; E65037.
DR RefSeq; NP_417085.1; NC_000913.3.
DR RefSeq; WP_000079100.1; NZ_STEB01000040.1.
DR PDB; 1PRZ; X-ray; 1.80 A; A=75-326.
DR PDB; 1QYU; X-ray; 2.00 A; A=2-326.
DR PDB; 1V9F; X-ray; 1.70 A; A=2-326.
DR PDB; 2IST; X-ray; 1.86 A; A=2-326.
DR PDB; 7BL5; EM; 3.30 A; 7=1-326.
DR PDBsum; 1PRZ; -.
DR PDBsum; 1QYU; -.
DR PDBsum; 1V9F; -.
DR PDBsum; 2IST; -.
DR PDBsum; 7BL5; -.
DR AlphaFoldDB; P33643; -.
DR SMR; P33643; -.
DR BioGRID; 4263197; 106.
DR DIP; DIP-10721N; -.
DR IntAct; P33643; 18.
DR STRING; 511145.b2594; -.
DR jPOST; P33643; -.
DR PaxDb; P33643; -.
DR PRIDE; P33643; -.
DR EnsemblBacteria; AAC75643; AAC75643; b2594.
DR EnsemblBacteria; BAA16479; BAA16479; BAA16479.
DR GeneID; 947087; -.
DR KEGG; ecj:JW2576; -.
DR KEGG; eco:b2594; -.
DR PATRIC; fig|1411691.4.peg.4143; -.
DR EchoBASE; EB2022; -.
DR eggNOG; COG0564; Bacteria.
DR HOGENOM; CLU_016902_4_0_6; -.
DR InParanoid; P33643; -.
DR OMA; AHPSPGW; -.
DR PhylomeDB; P33643; -.
DR BioCyc; EcoCyc:EG12098-MON; -.
DR BioCyc; MetaCyc:EG12098-MON; -.
DR BRENDA; 5.4.99.23; 2026.
DR EvolutionaryTrace; P33643; -.
DR PRO; PR:P33643; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0009982; F:pseudouridine synthase activity; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0120159; F:rRNA pseudouridine synthase activity; IDA:EcoCyc.
DR GO; GO:0000455; P:enzyme-directed rRNA pseudouridine synthesis; IMP:EcoCyc.
DR GO; GO:0000027; P:ribosomal large subunit assembly; IMP:EcoCyc.
DR CDD; cd02869; PseudoU_synth_RluA_like; 1.
DR CDD; cd00165; S4; 1.
DR Gene3D; 3.10.290.10; -; 1.
DR InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR InterPro; IPR006225; PsdUridine_synth_RluC/D.
DR InterPro; IPR006224; PsdUridine_synth_RluC/D_CS.
DR InterPro; IPR006145; PsdUridine_synth_RsuA/RluA.
DR InterPro; IPR002942; S4_RNA-bd.
DR InterPro; IPR036986; S4_RNA-bd_sf.
DR Pfam; PF00849; PseudoU_synth_2; 1.
DR Pfam; PF01479; S4; 1.
DR SMART; SM00363; S4; 1.
DR SUPFAM; SSF55120; SSF55120; 1.
DR TIGRFAMs; TIGR00005; rluA_subfam; 1.
DR PROSITE; PS01129; PSI_RLU; 1.
DR PROSITE; PS50889; S4; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Isomerase; Reference proteome;
KW RNA-binding; rRNA processing.
FT INIT_MET 1
FT /note="Removed"
FT CHAIN 2..326
FT /note="Ribosomal large subunit pseudouridine synthase D"
FT /id="PRO_0000162688"
FT DOMAIN 18..91
FT /note="S4 RNA-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00182"
FT ACT_SITE 139
FT MUTAGEN 139
FT /note="D->N,T: Loss of activity."
FT /evidence="ECO:0000269|PubMed:11453071"
FT CONFLICT 271..326
FT /note="LRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEHKDE
FT VDWL -> AGVSLTARRYMQPCCVFITRSPASKWNGMRLFHKIWWS (in Ref. 2)"
FT /evidence="ECO:0000305"
FT STRAND 4..10
FT /evidence="ECO:0007829|PDB:2IST"
FT HELIX 13..15
FT /evidence="ECO:0007829|PDB:2IST"
FT HELIX 20..27
FT /evidence="ECO:0007829|PDB:2IST"
FT HELIX 33..41
FT /evidence="ECO:0007829|PDB:2IST"
FT STRAND 45..47
FT /evidence="ECO:0007829|PDB:2IST"
FT STRAND 64..70
FT /evidence="ECO:0007829|PDB:2IST"
FT STRAND 86..89
FT /evidence="ECO:0007829|PDB:1V9F"
FT STRAND 91..98
FT /evidence="ECO:0007829|PDB:1V9F"
FT STRAND 110..114
FT /evidence="ECO:0007829|PDB:1V9F"
FT HELIX 115..122
FT /evidence="ECO:0007829|PDB:1V9F"
FT HELIX 124..128
FT /evidence="ECO:0007829|PDB:1V9F"
FT HELIX 130..133
FT /evidence="ECO:0007829|PDB:1V9F"
FT STRAND 143..151
FT /evidence="ECO:0007829|PDB:1V9F"
FT HELIX 152..163
FT /evidence="ECO:0007829|PDB:1V9F"
FT STRAND 167..177
FT /evidence="ECO:0007829|PDB:1V9F"
FT STRAND 183..186
FT /evidence="ECO:0007829|PDB:1V9F"
FT STRAND 189..191
FT /evidence="ECO:0007829|PDB:1V9F"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:1V9F"
FT STRAND 209..217
FT /evidence="ECO:0007829|PDB:1V9F"
FT STRAND 219..229
FT /evidence="ECO:0007829|PDB:1V9F"
FT HELIX 235..242
FT /evidence="ECO:0007829|PDB:1V9F"
FT TURN 251..254
FT /evidence="ECO:0007829|PDB:1V9F"
FT HELIX 265..273
FT /evidence="ECO:0007829|PDB:1V9F"
FT STRAND 278..287
FT /evidence="ECO:0007829|PDB:1V9F"
FT TURN 289..291
FT /evidence="ECO:0007829|PDB:1V9F"
FT STRAND 294..298
FT /evidence="ECO:0007829|PDB:1V9F"
FT HELIX 303..323
FT /evidence="ECO:0007829|PDB:1V9F"
SQ SEQUENCE 326 AA; 37122 MW; 39672B8BB559D14C CRC64;
MAQRVQLTAT VSENQLGQRL DQALAEMFPD YSRSRIKEWI LDQRVLVNGK VCDKPKEKVL
GGEQVAINAE IEEEARFEPQ DIPLDIVYED EDIIIINKPR DLVVHPGAGN PDGTVLNALL
HYYPPIADVP RAGIVHRLDK DTTGLMVVAK TVPAQTRLVE SLQRREITRE YEAVAIGHMT
AGGTVDEPIS RHPTKRTHMA VHPMGKPAVT HYRIMEHFRV HTRLRLRLET GRTHQIRVHM
AHITHPLVGD PVYGGRPRPP KGASEAFIST LRKFDRQALH ATMLRLYHPI SGIEMEWHAP
IPQDMVELIE VMRADFEEHK DEVDWL
