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Protein

tRNA pseudouridine synthase D

Gene

truD

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-13 in transfer RNAs.1 Publication

Catalytic activityi

tRNA uridine(13) = tRNA pseudouridine(13).2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei27 – 271SubstrateBy similarity
Active sitei31 – 311Proton acceptorSequence analysis
Active sitei80 – 801Nucleophile1 Publication
Binding sitei129 – 1291SubstrateCurated
Binding sitei329 – 3291SubstrateBy similarity

GO - Molecular functioni

  • pseudouridine synthase activity Source: EcoCyc
  • RNA binding Source: InterPro

GO - Biological processi

  • pseudouridine synthesis Source: EcoCyc
  • tRNA pseudouridine synthesis Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

tRNA processing

Enzyme and pathway databases

BioCyciEcoCyc:G7422-MONOMER.
ECOL316407:JW2715-MONOMER.
MetaCyc:G7422-MONOMER.
BRENDAi5.4.99.27. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA pseudouridine synthase D (EC:5.4.99.27)
Alternative name(s):
tRNA pseudouridine(13) synthase
tRNA pseudouridylate synthase D
tRNA-uridine isomerase D
Gene namesi
Name:truD
Synonyms:ygbO
Ordered Locus Names:b2745, JW2715
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13109. truD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi31 – 311E → D: 3-fold decrease in activity. 1 Publication
Mutagenesisi31 – 311E → Q: Loss of activity. 1 Publication
Mutagenesisi79 – 791K → L: 20-fold decrease in activity. 1 Publication
Mutagenesisi79 – 791K → R: 10-fold decrease in activity. 1 Publication
Mutagenesisi80 – 801D → N or T: Loss of activity. 1 Publication
Mutagenesisi87 – 871Q → E: 3-fold decrease in activity. 1 Publication
Mutagenesisi129 – 1291N → K: Loss of activity. 1 Publication
Mutagenesisi131 – 1311F → Y: 1.5-fold decrease in activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 349349tRNA pseudouridine synthase DPRO_0000152495Add
BLAST

Proteomic databases

PaxDbiQ57261.
PRIDEiQ57261.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi4262278. 7 interactions.
IntActiQ57261. 9 interactions.
STRINGi511145.b2745.

Structurei

Secondary structure

1
349
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 63Combined sources
Beta strandi15 – 173Combined sources
Beta strandi19 – 235Combined sources
Helixi24 – 263Combined sources
Beta strandi27 – 326Combined sources
Beta strandi41 – 5313Combined sources
Helixi55 – 6511Combined sources
Helixi70 – 723Combined sources
Beta strandi73 – 764Combined sources
Beta strandi83 – 9210Combined sources
Helixi101 – 1033Combined sources
Beta strandi109 – 11911Combined sources
Beta strandi128 – 13710Combined sources
Helixi141 – 15414Combined sources
Helixi162 – 1654Combined sources
Helixi167 – 1693Combined sources
Helixi170 – 17910Combined sources
Helixi189 – 21022Combined sources
Beta strandi213 – 2153Combined sources
Beta strandi224 – 2274Combined sources
Beta strandi233 – 2353Combined sources
Helixi238 – 2403Combined sources
Helixi241 – 2499Combined sources
Beta strandi252 – 2598Combined sources
Helixi269 – 27810Combined sources
Turni279 – 2813Combined sources
Helixi283 – 2919Combined sources
Beta strandi297 – 3037Combined sources
Beta strandi306 – 3149Combined sources
Beta strandi317 – 3259Combined sources
Helixi330 – 3345Combined sources
Turni335 – 3373Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SB7X-ray2.20A/B1-349[»]
1SI7X-ray2.20A1-349[»]
1SZWX-ray2.00A/B1-349[»]
ProteinModelPortaliQ57261.
SMRiQ57261. Positions 1-340.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ57261.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini155 – 303149TRUDAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni180 – 1878RNA bindingCurated

Sequence similaritiesi

Belongs to the pseudouridine synthase TruD family.Curated
Contains 1 TRUD domain.Curated

Phylogenomic databases

eggNOGiENOG4106NZV. Bacteria.
COG0585. LUCA.
HOGENOMiHOG000224848.
InParanoidiQ57261.
KOiK06176.
OMAiLWLWVEK.
PhylomeDBiQ57261.

Family and domain databases

HAMAPiMF_01082. TruD. 1 hit.
InterProiIPR020103. PsdUridine_synth_cat_dom.
IPR001656. PsdUridine_synth_TruD.
IPR020119. PsdUridine_synth_TruD_CS.
IPR011760. PsdUridine_synth_TruD_insert.
[Graphical view]
PANTHERiPTHR13326. PTHR13326. 1 hit.
PfamiPF01142. TruD. 2 hits.
[Graphical view]
SUPFAMiSSF55120. SSF55120. 1 hit.
TIGRFAMsiTIGR00094. tRNA_TruD_broad. 1 hit.
PROSITEiPS50984. TRUD. 1 hit.
PS01268. UPF0024. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q57261-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIEFDNLTYL HGKPQGTGLL KANPEDFVVV EDLGFEPDGE GEHILVRILK
60 70 80 90 100
NGCNTRFVAD ALAKFLKIHA REVSFAGQKD KHAVTEQWLC ARVPGKEMPD
110 120 130 140 150
LSAFQLEGCQ VLEYARHKRK LRLGALKGNA FTLVLREVSN RDDVEQRLID
160 170 180 190 200
ICVKGVPNYF GAQRFGIGGS NLQGAQRWAQ TNTPVRDRNK RSFWLSAARS
210 220 230 240 250
ALFNQIVAER LKKADVNQVV DGDALQLAGR GSWFVATTEE LAELQRRVND
260 270 280 290 300
KELMITAALP GSGEWGTQRE ALAFEQAAVA AETELQALLV REKVEAARRA
310 320 330 340
MLLYPQQLSW NWWDDVTVEI RFWLPAGSFA TSVVRELINT TGDYAHIAE
Length:349
Mass (Da):39,091
Last modified:November 1, 1996 - v1
Checksum:i45282BA3F2CCD64B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L07942 Genomic DNA. Translation: AAA79838.1.
U29579 Genomic DNA. Translation: AAA69255.1.
U00096 Genomic DNA. Translation: AAC75787.1.
AP009048 Genomic DNA. Translation: BAE76822.1.
PIRiI69731.
RefSeqiNP_417225.1. NC_000913.3.
WP_000568943.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75787; AAC75787; b2745.
BAE76822; BAE76822; BAE76822.
GeneIDi947214.
KEGGiecj:JW2715.
eco:b2745.
PATRICi32120896. VBIEscCol129921_2840.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L07942 Genomic DNA. Translation: AAA79838.1.
U29579 Genomic DNA. Translation: AAA69255.1.
U00096 Genomic DNA. Translation: AAC75787.1.
AP009048 Genomic DNA. Translation: BAE76822.1.
PIRiI69731.
RefSeqiNP_417225.1. NC_000913.3.
WP_000568943.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SB7X-ray2.20A/B1-349[»]
1SI7X-ray2.20A1-349[»]
1SZWX-ray2.00A/B1-349[»]
ProteinModelPortaliQ57261.
SMRiQ57261. Positions 1-340.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262278. 7 interactions.
IntActiQ57261. 9 interactions.
STRINGi511145.b2745.

Proteomic databases

PaxDbiQ57261.
PRIDEiQ57261.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75787; AAC75787; b2745.
BAE76822; BAE76822; BAE76822.
GeneIDi947214.
KEGGiecj:JW2715.
eco:b2745.
PATRICi32120896. VBIEscCol129921_2840.

Organism-specific databases

EchoBASEiEB2912.
EcoGeneiEG13109. truD.

Phylogenomic databases

eggNOGiENOG4106NZV. Bacteria.
COG0585. LUCA.
HOGENOMiHOG000224848.
InParanoidiQ57261.
KOiK06176.
OMAiLWLWVEK.
PhylomeDBiQ57261.

Enzyme and pathway databases

BioCyciEcoCyc:G7422-MONOMER.
ECOL316407:JW2715-MONOMER.
MetaCyc:G7422-MONOMER.
BRENDAi5.4.99.27. 2026.

Miscellaneous databases

EvolutionaryTraceiQ57261.
PROiQ57261.

Family and domain databases

HAMAPiMF_01082. TruD. 1 hit.
InterProiIPR020103. PsdUridine_synth_cat_dom.
IPR001656. PsdUridine_synth_TruD.
IPR020119. PsdUridine_synth_TruD_CS.
IPR011760. PsdUridine_synth_TruD_insert.
[Graphical view]
PANTHERiPTHR13326. PTHR13326. 1 hit.
PfamiPF01142. TruD. 2 hits.
[Graphical view]
SUPFAMiSSF55120. SSF55120. 1 hit.
TIGRFAMsiTIGR00094. tRNA_TruD_broad. 1 hit.
PROSITEiPS50984. TRUD. 1 hit.
PS01268. UPF0024. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTRUD_ECOLI
AccessioniPrimary (citable) accession number: Q57261
Secondary accession number(s): Q2MA84
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: September 7, 2016
This is version 128 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

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
  4. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

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.