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Protein

Ribosomal large subunit pseudouridine synthase D

Gene

rluD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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. pseudouridine synthase activity Source: EcoCyc
  2. RNA binding Source: UniProtKB-KW

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.
BRENDAi5.4.99.23. 2026.

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 Componenti: Chromosome UP000000625 Componenti: 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 – 107Combined sources
Helixi13 – 153Combined sources
Helixi20 – 278Combined sources
Helixi33 – 419Combined sources
Beta strandi45 – 473Combined sources
Beta strandi64 – 707Combined sources
Beta strandi86 – 894Combined sources
Beta strandi91 – 988Combined sources
Beta strandi110 – 1145Combined sources
Helixi115 – 1228Combined sources
Helixi124 – 1285Combined sources
Helixi130 – 1334Combined sources
Beta strandi143 – 1519Combined sources
Helixi152 – 16312Combined sources
Beta strandi167 – 17711Combined sources
Beta strandi183 – 1864Combined sources
Beta strandi189 – 1913Combined sources
Beta strandi199 – 2013Combined sources
Beta strandi209 – 2179Combined sources
Beta strandi219 – 22911Combined sources
Helixi235 – 2428Combined sources
Turni251 – 2544Combined sources
Helixi265 – 2739Combined sources
Beta strandi278 – 28710Combined sources
Turni289 – 2913Combined sources
Beta strandi294 – 2985Combined sources
Helixi303 – 32321Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiP33643.
KOiK06180.
OMAiTYGGRPR.
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

        10         20         30         40         50
MAQRVQLTAT VSENQLGQRL DQALAEMFPD YSRSRIKEWI LDQRVLVNGK
60 70 80 90 100
VCDKPKEKVL GGEQVAINAE IEEEARFEPQ DIPLDIVYED EDIIIINKPR
110 120 130 140 150
DLVVHPGAGN PDGTVLNALL HYYPPIADVP RAGIVHRLDK DTTGLMVVAK
160 170 180 190 200
TVPAQTRLVE SLQRREITRE YEAVAIGHMT AGGTVDEPIS RHPTKRTHMA
210 220 230 240 250
VHPMGKPAVT HYRIMEHFRV HTRLRLRLET GRTHQIRVHM AHITHPLVGD
260 270 280 290 300
PVYGGRPRPP KGASEAFIST LRKFDRQALH ATMLRLYHPI SGIEMEWHAP
310 320
IPQDMVELIE VMRADFEEHK DEVDWL
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. Curated

Experimental Info

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

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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...

Protein-protein interaction databases

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

Proteomic databases

PaxDbiP33643.
PRIDEiP33643.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EchoBASEiEB2022.
EcoGeneiEG12098. rluD.

Phylogenomic databases

eggNOGiCOG0564.
HOGENOMiHOG000275919.
InParanoidiP33643.
KOiK06180.
OMAiTYGGRPR.
OrthoDBiEOG6P070X.
PhylomeDBiP33643.

Enzyme and pathway databases

BioCyciEcoCyc:EG12098-MONOMER.
ECOL316407:JW2576-MONOMER.
MetaCyc:EG12098-MONOMER.
BRENDAi5.4.99.23. 2026.

Miscellaneous databases

EvolutionaryTraceiP33643.
PROiP33643.

Gene expression databases

GenevestigatoriP33643.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Ogura T., Tomoyasu T.
    Submitted (JAN-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(1996) [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(2005) [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(1990) [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(1997) [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(1999) [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(2000) [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(2006) [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: April 1, 2015
This is version 134 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.