Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P33643

- RLUD_ECOLI

UniProt

P33643 - RLUD_ECOLI

Protein

Ribosomal large subunit pseudouridine synthase D

Gene

rluD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 130 (01 Oct 2014)
      Sequence version 4 (23 Jan 2007)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    Functioni

    Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA. Isomerization occurs as a late step during the assembly of the large ribosomal subunit.2 Publications

    Catalytic activityi

    23S rRNA uridine(1911)/uridine(1915)/uridine(1917) = 23S rRNA pseudouridine(1911)/pseudouridine(1915)/pseudouridine(1917).2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei139 – 1391

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. pseudouridine synthase activity Source: EcoCyc
    3. RNA binding Source: UniProtKB-KW

    GO - Biological processi

    1. enzyme-directed rRNA pseudouridine synthesis Source: EcoCyc
    2. ribosomal large subunit assembly Source: EcoCyc

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    rRNA processing

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG12098-MONOMER.
    ECOL316407:JW2576-MONOMER.
    MetaCyc:EG12098-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribosomal large subunit pseudouridine synthase D (EC:5.4.99.23)
    Alternative name(s):
    23S rRNA pseudouridine(1911/1915/1917) synthase
    rRNA pseudouridylate synthase D
    rRNA-uridine isomerase D
    Gene namesi
    Name:rluD
    Synonyms:sfhB, yfiI
    Ordered Locus Names:b2594, JW2576
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG12098. rluD.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi139 – 1391D → N or T: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed
    Chaini2 – 326325Ribosomal large subunit pseudouridine synthase DPRO_0000162688Add
    BLAST

    Proteomic databases

    PaxDbiP33643.
    PRIDEiP33643.

    Expressioni

    Gene expression databases

    GenevestigatoriP33643.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ppsRP0A8A42EBI-558026,EBI-548302

    Protein-protein interaction databases

    DIPiDIP-10721N.
    IntActiP33643. 18 interactions.
    STRINGi511145.b2594.

    Structurei

    Secondary structure

    1
    326
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 107
    Helixi13 – 153
    Helixi20 – 278
    Helixi33 – 419
    Beta strandi45 – 473
    Beta strandi64 – 707
    Beta strandi86 – 894
    Beta strandi91 – 988
    Beta strandi110 – 1145
    Helixi115 – 1228
    Helixi124 – 1285
    Helixi130 – 1334
    Beta strandi143 – 1519
    Helixi152 – 16312
    Beta strandi167 – 17711
    Beta strandi183 – 1864
    Beta strandi189 – 1913
    Beta strandi199 – 2013
    Beta strandi209 – 2179
    Beta strandi219 – 22911
    Helixi235 – 2428
    Turni251 – 2544
    Helixi265 – 2739
    Beta strandi278 – 28710
    Turni289 – 2913
    Beta strandi294 – 2985
    Helixi303 – 32321

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1PRZX-ray1.80A75-326[»]
    1QYUX-ray2.00A2-326[»]
    1V9FX-ray1.70A2-326[»]
    2ISTX-ray1.86A2-326[»]
    ProteinModelPortaliP33643.
    SMRiP33643. Positions 2-326.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP33643.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini18 – 9174S4 RNA-bindingPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the pseudouridine synthase RluA family.Curated
    Contains 1 S4 RNA-binding domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0564.
    HOGENOMiHOG000275919.
    KOiK06180.
    OMAiRDIVHGG.
    OrthoDBiEOG6P070X.
    PhylomeDBiP33643.

    Family and domain databases

    Gene3Di3.10.290.10. 1 hit.
    InterProiIPR020103. PsdUridine_synth_cat_dom.
    IPR006225. PsdUridine_synth_RluC/D.
    IPR006224. PsdUridine_synth_RluC/D_CS.
    IPR006145. PsdUridine_synth_RsuA/RluD.
    IPR002942. S4_RNA-bd.
    [Graphical view]
    PfamiPF00849. PseudoU_synth_2. 1 hit.
    PF01479. S4. 1 hit.
    [Graphical view]
    SMARTiSM00363. S4. 1 hit.
    [Graphical view]
    SUPFAMiSSF55120. SSF55120. 1 hit.
    TIGRFAMsiTIGR00005. rluA_subfam. 1 hit.
    PROSITEiPS01129. PSI_RLU. 1 hit.
    PS50889. S4. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P33643-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAQRVQLTAT VSENQLGQRL DQALAEMFPD YSRSRIKEWI LDQRVLVNGK    50
    VCDKPKEKVL GGEQVAINAE IEEEARFEPQ DIPLDIVYED EDIIIINKPR 100
    DLVVHPGAGN PDGTVLNALL HYYPPIADVP RAGIVHRLDK DTTGLMVVAK 150
    TVPAQTRLVE SLQRREITRE YEAVAIGHMT AGGTVDEPIS RHPTKRTHMA 200
    VHPMGKPAVT HYRIMEHFRV HTRLRLRLET GRTHQIRVHM AHITHPLVGD 250
    PVYGGRPRPP KGASEAFIST LRKFDRQALH ATMLRLYHPI SGIEMEWHAP 300
    IPQDMVELIE VMRADFEEHK DEVDWL 326
    Length:326
    Mass (Da):37,122
    Last modified:January 23, 2007 - v4
    Checksum:i39672B8BB559D14C
    GO

    Sequence cautioni

    The sequence X57620 differs from that shown. Reason: Frameshift at position 134.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti271 – 32656LRKFD…EVDWL → AGVSLTARRYMQPCCVFITR SPASKWNGMRLFHKIWWS(PubMed:9205837)CuratedAdd
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U50134 Genomic DNA. Translation: AAA92957.1.
    U00096 Genomic DNA. Translation: AAC75643.1.
    AP009048 Genomic DNA. Translation: BAA16479.2.
    X57620 Genomic DNA. No translation available.
    PIRiE65037.
    RefSeqiNP_417085.1. NC_000913.3.
    YP_490818.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75643; AAC75643; b2594.
    BAA16479; BAA16479; BAA16479.
    GeneIDi12934203.
    947087.
    KEGGiecj:Y75_p2543.
    eco:b2594.
    PATRICi32120591. VBIEscCol129921_2694.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U50134 Genomic DNA. Translation: AAA92957.1 .
    U00096 Genomic DNA. Translation: AAC75643.1 .
    AP009048 Genomic DNA. Translation: BAA16479.2 .
    X57620 Genomic DNA. No translation available.
    PIRi E65037.
    RefSeqi NP_417085.1. NC_000913.3.
    YP_490818.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1PRZ X-ray 1.80 A 75-326 [» ]
    1QYU X-ray 2.00 A 2-326 [» ]
    1V9F X-ray 1.70 A 2-326 [» ]
    2IST X-ray 1.86 A 2-326 [» ]
    ProteinModelPortali P33643.
    SMRi P33643. Positions 2-326.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10721N.
    IntActi P33643. 18 interactions.
    STRINGi 511145.b2594.

    Proteomic databases

    PaxDbi P33643.
    PRIDEi P33643.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75643 ; AAC75643 ; b2594 .
    BAA16479 ; BAA16479 ; BAA16479 .
    GeneIDi 12934203.
    947087.
    KEGGi ecj:Y75_p2543.
    eco:b2594.
    PATRICi 32120591. VBIEscCol129921_2694.

    Organism-specific databases

    EchoBASEi EB2022.
    EcoGenei EG12098. rluD.

    Phylogenomic databases

    eggNOGi COG0564.
    HOGENOMi HOG000275919.
    KOi K06180.
    OMAi RDIVHGG.
    OrthoDBi EOG6P070X.
    PhylomeDBi P33643.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG12098-MONOMER.
    ECOL316407:JW2576-MONOMER.
    MetaCyc:EG12098-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P33643.
    PROi P33643.

    Gene expression databases

    Genevestigatori P33643.

    Family and domain databases

    Gene3Di 3.10.290.10. 1 hit.
    InterProi IPR020103. PsdUridine_synth_cat_dom.
    IPR006225. PsdUridine_synth_RluC/D.
    IPR006224. PsdUridine_synth_RluC/D_CS.
    IPR006145. PsdUridine_synth_RsuA/RluD.
    IPR002942. S4_RNA-bd.
    [Graphical view ]
    Pfami PF00849. PseudoU_synth_2. 1 hit.
    PF01479. S4. 1 hit.
    [Graphical view ]
    SMARTi SM00363. S4. 1 hit.
    [Graphical view ]
    SUPFAMi SSF55120. SSF55120. 1 hit.
    TIGRFAMsi TIGR00005. rluA_subfam. 1 hit.
    PROSITEi PS01129. PSI_RLU. 1 hit.
    PS50889. S4. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Ogura T., Tomoyasu T.
      Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
      Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
      , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
      DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION TO 271-326.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "Expression of ClpB, an analog of the ATP-dependent protease regulatory subunit in Escherichia coli, is controlled by a heat shock sigma factor (sigma 32)."
      Kitagawa M., Wada C., Yoshioka S., Yura T.
      J. Bacteriol. 173:4247-4253(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 40-326.
      Strain: K12.
    6. "A pseudouridine synthase required for the formation of two universally conserved pseudouridines in ribosomal RNA is essential for normal growth of Escherichia coli."
      Raychaudhuri S., Conrad J., Hall B.G., Ofengand J.
      RNA 4:1407-1417(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
      Strain: K12 / MG1655 / ATCC 47076.
    7. "Isolation and properties of Escherichia coli 23S-RNA pseudouridine 1911, 1915, 1917 synthase (RluD)."
      Wrzesinski J., Bakin A., Ofengand J., Lane B.G.
      IUBMB Life 50:33-37(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, PROTEIN SEQUENCE OF N-TERMINUS.
    8. "A second function for pseudouridine synthases: a point mutant of RluD unable to form pseudouridines 1911, 1915, and 1917 in Escherichia coli 23S ribosomal RNA restores normal growth to an RluD-minus strain."
      Gutgsell N.S., Del Campo M., Raychaudhuri S., Ofengand J.
      RNA 7:990-998(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF ASP-139.
    9. "Substrate specificity of the pseudouridine synthase RluD in Escherichia coli."
      Leppik M., Peil L., Kipper K., Liiv A., Remme J.
      FEBS J. 274:5759-5766(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
      Strain: K12 / MG1655 / ATCC 47076.

    Entry informationi

    Entry nameiRLUD_ECOLI
    AccessioniPrimary (citable) accession number: P33643
    Secondary accession number(s): P77003
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1994
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 130 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3