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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)DescriptionActionsGraphical viewLength
Binding sitei27SubstrateBy similarity1
Active sitei31Proton acceptorSequence analysis1
Active sitei80Nucleophile1 Publication1
Binding sitei129SubstrateCurated1
Binding sitei329SubstrateBy similarity1

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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)DescriptionActionsGraphical viewLength
Mutagenesisi31E → D: 3-fold decrease in activity. 1 Publication1
Mutagenesisi31E → Q: Loss of activity. 1 Publication1
Mutagenesisi79K → L: 20-fold decrease in activity. 1 Publication1
Mutagenesisi79K → R: 10-fold decrease in activity. 1 Publication1
Mutagenesisi80D → N or T: Loss of activity. 1 Publication1
Mutagenesisi87Q → E: 3-fold decrease in activity. 1 Publication1
Mutagenesisi129N → K: Loss of activity. 1 Publication1
Mutagenesisi131F → Y: 1.5-fold decrease in activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001524951 – 349tRNA pseudouridine synthase DAdd BLAST349

Proteomic databases

PaxDbiQ57261.
PRIDEiQ57261.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

BioGridi4262278. 7 interactors.
IntActiQ57261. 9 interactors.
STRINGi511145.b2745.

Structurei

Secondary structure

1349
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 6Combined sources3
Beta strandi15 – 17Combined sources3
Beta strandi19 – 23Combined sources5
Helixi24 – 26Combined sources3
Beta strandi27 – 32Combined sources6
Beta strandi41 – 53Combined sources13
Helixi55 – 65Combined sources11
Helixi70 – 72Combined sources3
Beta strandi73 – 76Combined sources4
Beta strandi83 – 92Combined sources10
Helixi101 – 103Combined sources3
Beta strandi109 – 119Combined sources11
Beta strandi128 – 137Combined sources10
Helixi141 – 154Combined sources14
Helixi162 – 165Combined sources4
Helixi167 – 169Combined sources3
Helixi170 – 179Combined sources10
Helixi189 – 210Combined sources22
Beta strandi213 – 215Combined sources3
Beta strandi224 – 227Combined sources4
Beta strandi233 – 235Combined sources3
Helixi238 – 240Combined sources3
Helixi241 – 249Combined sources9
Beta strandi252 – 259Combined sources8
Helixi269 – 278Combined sources10
Turni279 – 281Combined sources3
Helixi283 – 291Combined sources9
Beta strandi297 – 303Combined sources7
Beta strandi306 – 314Combined sources9
Beta strandi317 – 325Combined sources9
Helixi330 – 334Combined sources5
Turni335 – 337Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ57261.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini155 – 303TRUDAdd BLAST149

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni180 – 187RNA bindingCurated8

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SB7X-ray2.20A/B1-349[»]
1SI7X-ray2.20A1-349[»]
1SZWX-ray2.00A/B1-349[»]
ProteinModelPortaliQ57261.
SMRiQ57261.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262278. 7 interactors.
IntActiQ57261. 9 interactors.
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: November 2, 2016
This is version 130 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.