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Protein

Ribosomal large subunit pseudouridine synthase D

Gene

rluD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionIsomerase, RNA-binding
Biological processrRNA processing

Enzyme and pathway databases

BioCyciEcoCyc:EG12098-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

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

Show more details

Protein-protein interaction databases

BioGridi4263197, 106 interactors
DIPiDIP-10721N
IntActiP33643, 18 interactors
STRINGi316385.ECDH10B_2762

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

Phylogenomic databases

eggNOGiENOG4105C34 Bacteria
COG0564 LUCA
HOGENOMiHOG000275919
InParanoidiP33643
KOiK06180
OMAiAHPSPGW
PhylomeDBiP33643

Family and domain databases

CDDicd02869 PseudoU_synth_RluCD_like, 1 hit
cd00165 S4, 1 hit
Gene3Di3.10.290.10, 1 hit
InterProiView protein in InterPro
IPR020103 PsdUridine_synth_cat_dom_sf
IPR006225 PsdUridine_synth_RluC/D
IPR006224 PsdUridine_synth_RluC/D_CS
IPR006145 PsdUridine_synth_RsuA/RluD
IPR002942 S4_RNA-bd
IPR036986 S4_RNA-bd_sf
PfamiView protein in Pfam
PF00849 PseudoU_synth_2, 1 hit
PF01479 S4, 1 hit
SMARTiView protein in SMART
SM00363 S4, 1 hit
SUPFAMiSSF55120 SSF55120, 1 hit
TIGRFAMsiTIGR00005 rluA_subfam, 1 hit
PROSITEiView protein in PROSITE
PS01129 PSI_RLU, 1 hit
PS50889 S4, 1 hit

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
PATRICifig|1411691.4.peg.4143

Similar proteinsi

Entry informationi

Entry nameiRLUD_ECOLI
AccessioniPrimary (citable) accession number: P33643
Secondary accession number(s): P77003
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: January 23, 2007
Last modified: March 28, 2018
This is version 153 of the entry and version 4 of the sequence. See 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
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Main funding by: National Institutes of Health