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P33643 (RLUD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 126. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:rluD
Synonyms:sfhB, yfiI
Ordered Locus Names:b2594, JW2576
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length326 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.7 Ref.9

Catalytic activity

23S rRNA uridine(1911)/uridine(1915)/uridine(1917) = 23S rRNA pseudouridine(1911)/pseudouridine(1915)/pseudouridine(1917). Ref.7 Ref.9

Sequence similarities

Belongs to the pseudouridine synthase RluA family.

Contains 1 S4 RNA-binding domain.

Sequence caution

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

Binary interactions

With

Entry

#Exp.

IntAct

Notes

ppsRP0A8A42EBI-558026,EBI-548302

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed
Chain2 – 326325Ribosomal large subunit pseudouridine synthase D
PRO_0000162688

Regions

Domain18 – 9174S4 RNA-binding

Sites

Active site1391

Experimental info

Mutagenesis1391D → N or T: Loss of activity. Ref.8
Sequence conflict271 – 32656LRKFD…EVDWL → AGVSLTARRYMQPCCVFITR SPASKWNGMRLFHKIWWS Ref.2

Secondary structure

..................................................... 326
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P33643 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: 39672B8BB559D14C

FASTA32637,122
        10         20         30         40         50         60 
MAQRVQLTAT VSENQLGQRL DQALAEMFPD YSRSRIKEWI LDQRVLVNGK VCDKPKEKVL 

        70         80         90        100        110        120 
GGEQVAINAE IEEEARFEPQ DIPLDIVYED EDIIIINKPR DLVVHPGAGN PDGTVLNALL 

       130        140        150        160        170        180 
HYYPPIADVP RAGIVHRLDK DTTGLMVVAK TVPAQTRLVE SLQRREITRE YEAVAIGHMT 

       190        200        210        220        230        240 
AGGTVDEPIS RHPTKRTHMA VHPMGKPAVT HYRIMEHFRV HTRLRLRLET GRTHQIRVHM 

       250        260        270        280        290        300 
AHITHPLVGD PVYGGRPRPP KGASEAFIST LRKFDRQALH ATMLRLYHPI SGIEMEWHAP 

       310        320 
IPQDMVELIE VMRADFEEHK DEVDWL 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U50134 Genomic DNA. Translation: AAA92957.1.
U00096 Genomic DNA. Translation: AAC75643.1.
AP009048 Genomic DNA. Translation: BAA16479.2.
X57620 Genomic DNA. No translation available.
PIRE65037.
RefSeqNP_417085.1. NC_000913.3.
YP_490818.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1PRZX-ray1.80A75-326[»]
1QYUX-ray2.00A2-325[»]
1V9FX-ray1.70A2-325[»]
2ISTX-ray1.86A2-325[»]
ProteinModelPortalP33643.
SMRP33643. Positions 2-326.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10721N.
IntActP33643. 18 interactions.
STRING511145.b2594.

Proteomic databases

PaxDbP33643.
PRIDEP33643.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75643; AAC75643; b2594.
BAA16479; BAA16479; BAA16479.
GeneID12934203.
947087.
KEGGecj:Y75_p2543.
eco:b2594.
PATRIC32120591. VBIEscCol129921_2694.

Organism-specific databases

EchoBASEEB2022.
EcoGeneEG12098. rluD.

Phylogenomic databases

eggNOGCOG0564.
HOGENOMHOG000275919.
KOK06180.
OMANALLHHV.
OrthoDBEOG6P070X.
PhylomeDBP33643.
ProtClustDBPRK11180.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP33643.

Family and domain databases

Gene3D3.10.290.10. 1 hit.
InterProIPR020103. 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]
PfamPF00849. PseudoU_synth_2. 1 hit.
PF01479. S4. 1 hit.
[Graphical view]
SMARTSM00363. S4. 1 hit.
[Graphical view]
SUPFAMSSF55120. SSF55120. 1 hit.
TIGRFAMsTIGR00005. rluA_subfam. 1 hit.
PROSITEPS01129. PSI_RLU. 1 hit.
PS50889. S4. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP33643.
PROP33643.

Entry information

Entry nameRLUD_ECOLI
AccessionPrimary (citable) accession number: P33643
Secondary accession number(s): P77003
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: January 23, 2007
Last modified: April 16, 2014
This is version 126 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene