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   02-SEP-2026, entry version 197.
DE   RecName: Full=Ribosomal large subunit pseudouridine synthase D {ECO:0000303|PubMed:9814761};
DE            EC=5.4.99.23 {ECO:0000269|PubMed:11087118, ECO:0000269|PubMed:17937767, ECO:0000269|PubMed:9814761};
DE   AltName: Full=23S rRNA pseudouridine(1911/1915/1917) synthase {ECO:0000303|PubMed:11087118};
DE   AltName: Full=Large ribosomal subunit assembly factor RluD {ECO:0000303|PubMed:33639093};
DE   AltName: Full=rRNA pseudouridylate synthase D;
DE   AltName: Full=rRNA-uridine isomerase D;
GN   Name=rluD {ECO:0000303|PubMed:9814761}; Synonyms=sfhB, yfiI;
GN   OrderedLocusNames=b2594, JW2576;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC   Enterobacterales; 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   PROTEIN SEQUENCE OF 2-31, FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION
RP   PHENOTYPE.
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   FUNCTION, CATALYTIC ACTIVITY, PROBABLE ACTIVE SITE, AND MUTAGENESIS OF
RP   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, CATALYTIC ACTIVITY, AND SUBSTRATE SPECIFICITY.
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).
RN   [10] {ECO:0007744|PDB:7BL5}
RP   STRUCTURE BY ELECTRON MICROSCOPY (3.30 ANGSTROMS) IN ASSOCIATION WITH
RP   PRE-50S RIBOSOMAL SUBUNIT, FUNCTION IN 50S RIBOSOMAL SUBUNIT BIOGENESIS,
RP   SUBUNIT, SUBCELLULAR LOCATION, AND 23S RRNA-BINDING.
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=33639093; DOI=10.1016/j.molcel.2021.02.006;
RA   Nikolay R., Hilal T., Schmidt S., Qin B., Schwefel D., Vieira-Vieira C.H.,
RA   Mielke T., Burger J., Loerke J., Amikura K., Flugel T., Ueda T.,
RA   Selbach M., Deuerling E., Spahn C.M.T.;
RT   "Snapshots of native pre-50S ribosomes reveal a biogenesis factor network
RT   and evolutionary specialization.";
RL   Mol. Cell 81:1200-1215.e9(2021).
CC   -!- FUNCTION: Responsible for synthesis of pseudouridine from uracil at
CC       positions 1911, 1915 and 1917 in 23S ribosomal RNA (PubMed:9814761,
CC       PubMed:11087118, PubMed:11453071, PubMed:17937767). Other positions are
CC       not modified (PubMed:17937767). Uridine isomerization occurs as a late
CC       step during the assembly of the large ribosomal subunit
CC       (PubMed:17937767). Member of a network of 50S ribosomal subunit
CC       biogenesis factors (ObgE, RluD, RsfS and DarP(YjgA)) which assembles
CC       along the 30S-50S interface, allowing 23S rRNA modification and
CC       preventing incorrect 23S rRNA structures from forming
CC       (PubMed:33639093). {ECO:0000269|PubMed:11087118,
CC       ECO:0000269|PubMed:11453071, ECO:0000269|PubMed:17937767,
CC       ECO:0000269|PubMed:33639093, ECO:0000269|PubMed:9814761}.
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:11453071,
CC         ECO:0000269|PubMed:17937767, ECO:0000269|PubMed:9814761};
CC   -!- SUBUNIT: In late stage pre-50S ribosomal subunit interacts with ObgE
CC       and DarP(YjgA) (PubMed:33639093). {ECO:0000269|PubMed:33639093}.
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   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:33639093}.
CC       Note=Associates with late stage pre-50S ribosomal subunits
CC       (PubMed:33639093). {ECO:0000269|PubMed:33639093}.
CC   -!- DISRUPTION PHENOTYPE: Severe growth inhibition, makes only very small
CC       colonies (PubMed:9814761). No longer synthesizes pseudouridine at
CC       positions 199, 1915 and 1917 in 23S rRNA (PubMed:9814761). In this
CC       strain a miniTn10(cam) insertion has occurred; the first 196 residues
CC       are present followed by 12 extra residues before a premature stop codon
CC       (PubMed:9814761). {ECO:0000269|PubMed:9814761}.
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_CP009789.1.
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   AlphaFoldDB; P33643; -.
DR   EMDB; EMD-12218; -.
DR   MDposit; P33643; -.
DR   SMR; P33643; -.
DR   BioGRID; 4263197; 123.
DR   DIP; DIP-10721N; -.
DR   FunCoup; P33643; 887.
DR   IntAct; P33643; 17.
DR   STRING; 511145.b2594; -.
DR   jPOST; P33643; -.
DR   PaxDb; 511145-b2594; -.
DR   EnsemblBacteria; AAC75643; AAC75643; b2594.
DR   GeneID; 947087; -.
DR   KEGG; ecj:JW2576; -.
DR   KEGG; eco:b2594; -.
DR   KEGG; ecoc:C3026_14375; -.
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; KSERAYT; -.
DR   OrthoDB; 9807829at2; -.
DR   PhylomeDB; P33643; -.
DR   BioCyc; EcoCyc:EG12098-MONOMER; -.
DR   BioCyc; MetaCyc:EG12098-MONOMER; -.
DR   BRENDA; 5.4.99.23; 2026.
DR   EvolutionaryTrace; P33643; -.
DR   PRO; PR:P33643; -.
DR   Proteomes; UP000000625; Chromosome.
DR   AbasyAtlas; P33643; -.
DR   GO; GO:0005737; C:cytoplasm; EXP:UniProtKB.
DR   GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR   GO; GO:0160140; F:23S rRNA pseudouridine(1911/1915/1917) synthase activity; EXP:UniProtKB.
DR   GO; GO:0009982; F:pseudouridine synthase activity; IBA:GO_Central.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
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   FunFam; 3.10.290.10:FF:000011; Pseudouridine synthase; 1.
DR   FunFam; 3.30.2350.10:FF:000004; Pseudouridine synthase; 1.
DR   Gene3D; 6.10.140.230; -; 1.
DR   Gene3D; 3.30.2350.10; Pseudouridine synthase; 1.
DR   Gene3D; 3.10.290.10; RNA-binding S4 domain; 1.
DR   InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR   InterPro; IPR006224; PsdUridine_synth_RluA-like_CS.
DR   InterPro; IPR006225; PsdUridine_synth_RluC/D.
DR   InterPro; IPR006145; PsdUridine_synth_RsuA/RluA.
DR   InterPro; IPR050188; RluA_PseudoU_synthase.
DR   InterPro; IPR002942; S4_RNA-bd.
DR   InterPro; IPR036986; S4_RNA-bd_sf.
DR   NCBIfam; NF008385; PRK11180.1; 1.
DR   NCBIfam; TIGR00005; rluA_subfam; 1.
DR   PANTHER; PTHR21600; MITOCHONDRIAL RNA PSEUDOURIDINE SYNTHASE; 1.
DR   PANTHER; PTHR21600:SF44; RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE D; 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; PS01129; PSI_RLU; 1.
DR   PROSITE; PS50889; S4; 1.
DR   PDBsum; 1PRZ; -.
DR   PDBsum; 1QYU; -.
DR   PDBsum; 1V9F; -.
DR   PDBsum; 2IST; -.
DR   PDBsum; 7BL5; -.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Direct protein sequencing; Isomerase;
KW   Reference proteome; Ribosome biogenesis; RNA-binding; rRNA processing;
KW   rRNA-binding.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000269|PubMed:11087118,
FT                   ECO:0000269|PubMed:9814761"
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                   /evidence="ECO:0000305|PubMed:11453071"
FT   MUTAGEN         139
FT                   /note="D->N,T: Loss of activity."
FT                   /evidence="ECO:0000269|PubMed:11453071"
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   HELIX           77..79
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           257..260
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           300..302
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
//