truB:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

truB

Gene Synonym(s)

ECK3155, b3166, JW3135, yhbA, P35[1]

Product Desc.

tRNA pseudouridine 55 synthase[2][3]

tRNA U55 pseudouridine synthase[4]

Product Synonyms(s)

tRNA pseudouridine synthase[1], B3166[2][1], YhbA[2][1], TruB[2][1] , ECK3155, JW3135, yhbA, b3166

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Mutants are sensitive to extreme heat shock[4]



Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

truB

Mnemonic

tRNA uridine

Synonyms

ECK3155, b3166, JW3135, yhbA, P35[1]

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

71.34 minutes 

MG1655: 3310799..3309855
<gbrowseImage> name=NC_000913:3309855..3310799 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3248011..3247067
<gbrowseImage> name=NC_012967:3247067..3248011 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3197003..3197947
<gbrowseImage> name=NC_012759:3197003..3197947 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3312632..3311688
<gbrowseImage> name=NC_007779:3311688..3312632 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3408544..3407600
<gbrowseImage> name=NC_010473:3407600..3408544 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

3309858

Edman degradation

PMID:7489483


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔtruB (Keio:JW3135)

deletion

deletion

PMID:16738554

Shigen
CGSC10386[5]

truB::Tn5KAN-I-SceI (FB21052)

Insertion at nt 735 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21052

contains pKD46

truBC193A

C193A

Slight increase in activity; when associated with A-58 and A-174

seeded from UniProt:P60340

truBC193V

C193V

Slight increase in activity

seeded from UniProt:P60340

truBD48C

D48C

Loss of activity

seeded from UniProt:P60340

truBK19M,R

K19M,R

Reduced structural stability and decrease in activity

seeded from UniProt:P60340

truBC58A

C58A

Slight increase in activity. Slight increase in activity; when associated with A-174 and A-193

seeded from UniProt:P60340

truBH43N

H43N

180-fold decrease in catalytic efficiency

seeded from UniProt:P60340

truBH43Q

H43Q

50-fold decrease in catalytic efficiency

seeded from UniProt:P60340

truBP20G,L

P20G,L

Reduced structural stability and no change in activity

seeded from UniProt:P60340

truBH43A

H43A

330-fold decrease in catalytic efficiency

seeded from UniProt:P60340

truBH43F

H43F

2-fold decrease in catalytic efficiency

seeded from UniProt:P60340

truBH43G

H43G

250-fold decrease in catalytic efficiency

seeded from UniProt:P60340

truBC174A

C174A

Slight increase in activity. Slight increase in activity; when associated with A-58 and A-193

seeded from UniProt:P60340

ΔtruB778::kan

PMID:16738554

CGSC:103238


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW3135

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGTCGTCCTCGTCGTCGCGG

Primer 2:CCgGCCGGGTATTCAACCACCAG

E4G11S

Kohara Phage

Genobase

PMID:3038334

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[5]

est. P1 cotransduction: % [6]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[5]

est. P1 cotransduction: 45% [6]
Synonyms:zgj-203::Tn10, zha-203::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11177

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11177

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001159

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947687

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1164

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010404

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

TruB

Synonyms

tRNA pseudouridine synthase[1], B3166[2][1], YhbA[2][1], TruB[2][1] , ECK3155, JW3135, yhbA, b3166

Product description

tRNA pseudouridine 55 synthase[2][3]

tRNA U55 pseudouridine synthase[4]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0001522

pseudouridine synthesis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014780

P

Seeded from EcoCyc (v14.0)

complete

GO:0001522

pseudouridine synthesis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015240

P

Seeded from EcoCyc (v14.0)

complete

GO:0001522

pseudouridine synthesis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020103

P

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014780

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015240

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020103

F

Seeded from EcoCyc (v14.0)

complete

GO:0006396

RNA processing

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002501

P

Seeded from EcoCyc (v14.0)

complete

GO:0008033

tRNA processing

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0819

P

Seeded from EcoCyc (v14.0)

complete

GO:0009982

pseudouridine synthase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01080

F

Seeded from EcoCyc (v14.0)

complete

GO:0009982

pseudouridine synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014780

F

Seeded from EcoCyc (v14.0)

complete

GO:0009982

pseudouridine synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015240

F

Seeded from EcoCyc (v14.0)

complete

GO:0009982

pseudouridine synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020103

F

Seeded from EcoCyc (v14.0)

complete

GO:0016853

isomerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0413

F

Seeded from EcoCyc (v14.0)

complete

GO:0031119

tRNA pseudouridine synthesis

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01080

P

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

rplJ

PMID:16606699

Experiment(s):EBI-1144986

Protein

rplQ

PMID:16606699

Experiment(s):EBI-1144986

Protein

rplB

PMID:16606699

Experiment(s):EBI-1144986

Protein

yggW

PMID:16606699

Experiment(s):EBI-1144986

Protein

rplO

PMID:16606699

Experiment(s):EBI-1144986
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

cytoplasm

From EcoCyc[3]


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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MSRPRRRGRD INGVLLLDKP QGMSSNDALQ KVKRIYNANR AGHTGALDPL ATGMLPICLG
EATKFSQYLL DSDKRYRVIA RLGQRTDTSD ADGQIVEERP VTFSAEQLAA ALDTFRGDIE
QIPSMYSALK YQGKKLYEYA RQGIEVPREA RPITVYELLF IRHEGNELEL EIHCSKGTYI
RTIIDDLGEK LGCGAHVIYL RRLAVSKYPV ERMVTLEHLR ELVEQAEQQD IPAAELLDPL
LMPMDSPASD YPVVNLPLTS SVYFKNGNPV RTSGAPLEGL VRVTEGENGK FIGMGEIDDE
GRVAPRRLVV EYPA
Length

314

Mol. Wt

35.087 kDa

pI

5.8 (calculated)

Extinction coefficient

20,860 - 21,235 (calc based on 14 Y, 0 W, and 3 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

33..180

PF01509 TruB family pseudouridylate synthase (N terminal domain)

PMID:19920124

Domain

252..309

PF09157 Pseudouridine synthase II TruB, C-terminal

PMID:19920124

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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=truB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16131058

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947687

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010404

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P60340

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11177

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11177

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947687

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001159

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1164

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

1.86E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

1527

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

214

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

754

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp

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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:3310779..3310819 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b3166 (EcoliWiki Page)

NCBI GEO profiles for truB

microarray

GenExpDB:b3166 (EcoliWiki Page)

Summary of data for truB from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes
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Notes

Accessions Related to truB Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11177

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1164

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3166

EcoGene

EcoGene:EG11177

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001159

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010404

Escherichia coli str. K-12 substr. MG1655

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Notes

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000017710 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT5G14460 (score: 1.000; bootstrap: 97%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000017209 (score: 1.000; bootstrap: 85%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00037760 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00010478 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000017180 (score: 1.000; bootstrap: 91%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000009497 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-050828-5 (score: 1.000; bootstrap: 77%)
  • ZDB-CDNA-050828-8 (score: 1.000; bootstrap: 77%)
  • ZDB-GENE-031118-120 (score: 0.968)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0204297 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0023184 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000014785 (score: 1.000; bootstrap: 87%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000298746 (score: 1.000; bootstrap: 91%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000002541 (score: 1.000; bootstrap: 91%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000012096 (score: 1.000; bootstrap: 90%)

From Inparanoid:20070104

Mus musculus

  • MGI:1919383 (score: 1.000; bootstrap: 89%)

From Inparanoid:20070104

Oryza gramene

  • Q94HL3 (score: 1.000; bootstrap: 97%)
  • Q65X25 (score: 1.000; bootstrap: 97%)
  • Q84ZW4 (score: 0.912)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000005235 (score: 1.000; bootstrap: 89%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000023309 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YLR175W (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC29A44c (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000140014 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000051364 (score: 1.000; bootstrap: 90%)

From Inparanoid:20070104

Shigella flexneri

TRUB

From SHIGELLACYC

E. coli O157

TRUB

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

Panther (EcoliWiki Page)

PTHR13767:SF2

Superfamily (EcoliWiki Page)

SUPERFAMILY:55120

Superfamily (EcoliWiki Page)

SUPERFAMILY:88697

Pfam (EcoliWiki Page)

PF01509 TruB family pseudouridylate synthase (N terminal domain)

Pfam (EcoliWiki Page)

PF09157 Pseudouridine synthase II TruB, C-terminal

EcoCyc

EcoCyc:EG11177

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11177

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001159

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1164

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010404

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

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