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P33643

- RLUD_ECOLI

UniProt

P33643 - RLUD_ECOLI

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Protein
Ribosomal large subunit pseudouridine synthase D
Gene
rluD, sfhB, yfiI, b2594, JW2576
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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

GO - Biological processi

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

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 D
PRO_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

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.

Miscellaneous databases

EvolutionaryTraceiP33643.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini18 – 9174S4 RNA-binding
Add
BLAST

Sequence similaritiesi

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.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti271 – 32656LRKFD…EVDWL → AGVSLTARRYMQPCCVFITR SPASKWNGMRLFHKIWWS1 Publication
Add
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

« Hide 'large scale' publications
  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: July 9, 2014
This is version 129 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

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