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Protein

Ribosomal large subunit pseudouridine synthase D

Gene

rluD

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA.By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei139 – 1391By similarity

GO - Molecular functioni

  1. pseudouridine synthase activity Source: InterPro
  2. RNA binding Source: UniProtKB-KW

GO - Biological processi

  1. pseudouridine synthesis Source: InterPro
  2. rRNA processing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-571-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
Ordered Locus Names:VP0559
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000002493: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 325325Ribosomal large subunit pseudouridine synthase DPRO_0000162703Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi223926.VP0559.

Structurei

3D structure databases

ProteinModelPortaliQ87S65.
SMRiQ87S65. Positions 2-319.
ModBaseiSearch...
MobiDBiSearch...

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.
KOiK06180.
OMAiTYGGRPR.
OrthoDBiEOG6P070X.

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.

Q87S65-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAQQIVLTNT VKDSQLGQRL DQAIAELFAD FSRSRLKEWL LDGKVQVNGE
60 70 80 90 100
VVTKPRTKVM GGEEITLQAE LEDEERWEAQ DIPLDIVYED DDIIVINKPR
110 120 130 140 150
DFVVHPGAGT PDGTVLNALL HHYPDIAEVP RAGIVHRLDK DTTGLMVVAK
160 170 180 190 200
TVPAQTRLVR ALQKRNITRE YEAIAIGRMT AGGKVDQPIG RHSTKRTLMA
210 220 230 240 250
VAPLGKPAVT HYRVAEHFRE HTRIRLRLET GRTHQIRVHM SYLQHPLLGD
260 270 280 290 300
TAYGGRARIP TGASQELTDM IRGFDRQALH AVMLRFEHPI TGEELEFHAP
310 320
VPDDMVAMTE ALRKDTEEYG LPDEF
Length:325
Mass (Da):36,604
Last modified:June 1, 2003 - v1
Checksum:iD3359215265F1156
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC58822.1.
RefSeqiNP_796938.1. NC_004603.1.

Genome annotation databases

EnsemblBacteriaiBAC58822; BAC58822; BAC58822.
GeneIDi1188027.
KEGGivpa:VP0559.
PATRICi20139314. VBIVibPar50997_0531.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000031 Genomic DNA. Translation: BAC58822.1.
RefSeqiNP_796938.1. NC_004603.1.

3D structure databases

ProteinModelPortaliQ87S65.
SMRiQ87S65. Positions 2-319.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi223926.VP0559.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC58822; BAC58822; BAC58822.
GeneIDi1188027.
KEGGivpa:VP0559.
PATRICi20139314. VBIVibPar50997_0531.

Phylogenomic databases

eggNOGiCOG0564.
HOGENOMiHOG000275919.
KOiK06180.
OMAiTYGGRPR.
OrthoDBiEOG6P070X.

Enzyme and pathway databases

BioCyciVPAR223926:GHK4-571-MONOMER.

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

  1. "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae."
    Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.
    Lancet 361:743-749(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RIMD 2210633.

Entry informationi

Entry nameiRLUD_VIBPA
AccessioniPrimary (citable) accession number: Q87S65
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 29, 2003
Last sequence update: June 1, 2003
Last modified: January 7, 2015
This is version 67 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.