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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)DescriptionActionsGraphical viewLength
Active sitei1391

GO - Molecular functioni

  • pseudouridine synthase activity Source: EcoCyc
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

  • enzyme-directed rRNA pseudouridine synthesis Source: EcoCyc
  • 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12098. rluD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi139D → N or T: Loss of activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved
ChainiPRO_00001626882 – 326Ribosomal large subunit pseudouridine synthase DAdd BLAST325

Proteomic databases

PaxDbiP33643.
PRIDEiP33643.

Interactioni

Binary interactionsi

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

Protein-protein interaction databases

BioGridi4263197. 29 interactors.
DIPiDIP-10721N.
IntActiP33643. 18 interactors.
STRINGi511145.b2594.

Structurei

Secondary structure

1326
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 10Combined sources7
Helixi13 – 15Combined sources3
Helixi20 – 27Combined sources8
Helixi33 – 41Combined sources9
Beta strandi45 – 47Combined sources3
Beta strandi64 – 70Combined sources7
Beta strandi86 – 89Combined sources4
Beta strandi91 – 98Combined sources8
Beta strandi110 – 114Combined sources5
Helixi115 – 122Combined sources8
Helixi124 – 128Combined sources5
Helixi130 – 133Combined sources4
Beta strandi143 – 151Combined sources9
Helixi152 – 163Combined sources12
Beta strandi167 – 177Combined sources11
Beta strandi183 – 186Combined sources4
Beta strandi189 – 191Combined sources3
Beta strandi199 – 201Combined sources3
Beta strandi209 – 217Combined sources9
Beta strandi219 – 229Combined sources11
Helixi235 – 242Combined sources8
Turni251 – 254Combined sources4
Helixi265 – 273Combined sources9
Beta strandi278 – 287Combined sources10
Turni289 – 291Combined sources3
Beta strandi294 – 298Combined sources5
Helixi303 – 323Combined sources21

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP33643.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini18 – 91S4 RNA-bindingPROSITE-ProRule annotationAdd BLAST74

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C34. Bacteria.
COG0564. LUCA.
HOGENOMiHOG000275919.
InParanoidiP33643.
KOiK06180.
OMAiSRIYECI.
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)DescriptionActionsGraphical viewLength
Sequence conflicti271 – 326LRKFD…EVDWL → AGVSLTARRYMQPCCVFITR SPASKWNGMRLFHKIWWS (PubMed:9205837).CuratedAdd BLAST56

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.
WP_000079100.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75643; AAC75643; b2594.
BAA16479; BAA16479; BAA16479.
GeneIDi947087.
KEGGiecj:JW2576.
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.
WP_000079100.1. NZ_LN832404.1.

3D structure databases

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

Protein-protein interaction databases

BioGridi4263197. 29 interactors.
DIPiDIP-10721N.
IntActiP33643. 18 interactors.
STRINGi511145.b2594.

Proteomic databases

PaxDbiP33643.
PRIDEiP33643.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75643; AAC75643; b2594.
BAA16479; BAA16479; BAA16479.
GeneIDi947087.
KEGGiecj:JW2576.
eco:b2594.
PATRICi32120591. VBIEscCol129921_2694.

Organism-specific databases

EchoBASEiEB2022.
EcoGeneiEG12098. rluD.

Phylogenomic databases

eggNOGiENOG4105C34. Bacteria.
COG0564. LUCA.
HOGENOMiHOG000275919.
InParanoidiP33643.
KOiK06180.
OMAiSRIYECI.
PhylomeDBiP33643.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP33643.
PROiP33643.

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...

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: November 2, 2016
This is version 144 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

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 one 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.