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rluA:On One Page

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Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

rluA

Gene Synonym(s)

ECK0059, b0058, JW0057, yabO[1]

Product Desc.

23S rRNA and tRNA pseudouridine synthase[2][3]

Dual specificity tRNA and rRNA pseudouridine synthase; specific to 23S rRNA U746 and tRNAphe U32; non-essential gene[4]

Product Synonyms(s)

pseudouridine synthase for 23S rRNA (position 746) and tRNAphe(position 32)[1], B0058[2][1], YabO[2][1], RluA[2][1]

Function from GO

Biological Process

Molecular Function

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rluA[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(rluA)    Textpresso(rluA)

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Notes

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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

rluA

Mnemonic

rRNA, large, uridine

Synonyms

ECK0059, b0058, JW0057, yabO[1]

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Notes

Location(s) and DNA Sequence

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

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

1.29 minutes 

MG1655: 60346..59687
gbrowse_img.php?coord=59687..60346&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 63150..62491
gbrowse_img.php?coord=62491..63150&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 60346..59687
gbrowse_img.php?coord=59687..60346&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 60346..59687
gbrowse_img.php?coord=59687..60346&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 59687..60346
gbrowse_img.php?coord=59687..60346&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

yabO::Tn5KAN

PMID:12519969

ASAP

At position 454 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB20005

ΔrluA (Keio:JW0057)

deletion

deletion

PMID:16738554

Shigen
CGSC8365[5]

rluAK28M,R

K28M,R

Forms inclusion bodies, indicating precipitation even within the cell

seeded from UniProt:P0AA37

rluAP29G,L

P29G,L

Reduced structural stability and decrease in activity

seeded from UniProt:P0AA37

rluAC128A

C128A

No change in activity

seeded from UniProt:P0AA37

rluAC117A

C117A

No change in activity

seeded from UniProt:P0AA37

rluAD64N,T

D64N,T

Loss of activity

seeded from UniProt:P0AA37

ΔrluA768::kan

PMID:16738554

CGSC:102730


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Notes

Genetic Resources

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ResourceResource TypeSourceNotes/Reference

JW0057

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGGGATGGAAAACTACAATCC

Primer 2:CCAAAATCCGCTGGCGCTTTAAA

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 35% [6]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 41% [6]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

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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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG12609

EchoBASE (EcoliWiki Page)

EchoBASE:EB2493

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0058

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0069

EcoGene (EcoliWiki Page)

EcoGene:EG12609

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YABO

CGSC (EcoliWiki Page)

CGSC:36966

ASAP (EcoliWikiPage)

ASAP:ABE-0000196


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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

RluA

Synonyms

pseudouridine synthase for 23S rRNA (position 746) and tRNAphe(position 32)[1], B0058[2][1], YabO[2][1], RluA[2][1]

Product description

23S rRNA and tRNA pseudouridine synthase[2][3]

Dual specificity tRNA and rRNA pseudouridine synthase; specific to 23S rRNA U746 and tRNAphe U32; non-essential gene[4]

EC number (for enzymes)
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Notes

Function

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

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0016853

isomerase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0413

F

Seeded from EcoCyc [7]

complete

GO:0009982

pseudouridine synthase activity

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006145
InterPro:IPR006224

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0008033

tRNA processing

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0819

P

Seeded from EcoCyc [7]

complete

GO:0006364

rRNA processing

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0698

P

Seeded from EcoCyc [7]

complete

GO:0031119

tRNA pseudouridine synthesis

PMID:10383384

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc [7]

complete

GO:0001522

pseudouridine synthesis

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006145
InterPro:IPR006224

P

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

required fields missing

GO:0000455

enzyme-directed rRNA pseudouridine synthesis

PMID:10383384

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc [7]

complete

GO:0009451

RNA modification

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0031118

rRNA pseudouridine synthesis

PMID:10383384

IMP: Inferred from Mutant Phenotype

P

complete

GO:0031119

tRNA pseudouridine synthesis

PMID:10383384

IMP: Inferred from Mutant Phenotype

P

complete

GO:0009451

RNA modification

PMID:10383384

IMP: Inferred from Mutant Phenotype

P

complete

GO:0009982

pseudouridine synthase activity

PMID:10383384

IMP: Inferred from Mutant Phenotype

F

complete

GO:0001522

pseudouridine synthesis

PMID:10383384

IMP: Inferred from Mutant Phenotype

P

complete

GO:0008033

tRNA processing

PMID:10383384

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006364

rRNA processing

PMID:10383384

IMP: Inferred from Mutant Phenotype

P

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 TypePartnerNotesReferencesEvidence
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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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

Sequence

at EcoCyc 

MGMENYNPPQ EPWLVILYQD DHIMVVNKPS GLLSVPGRLE EHKDSVMTRI QRDYPQAESV
HRLDMATSGV IVVALTKAAE RELKRQFRER EPKKQYVARV WGHPSPAEGL VDLPLICDWP
NRPKQKVCYE TGKPAQTEYE VVEYAADNTA RVVLKPITGR SHQLRVHMLA LGHPILGDRF
YASPEARAMA PRLLLHAEML TITHPAYGNS MTFKAPADF
Length

219

Mol. Wt

24.86 kDa

pI

8.1 (calculated)

Extinction coefficient

29,910 - 30,160 (calc based on 9 Y, 3 W, and 2 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.

TypeResiduesDescriptionNotesReferences

Initiator Methionine

1

Removed

UniProt:P0AA37


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

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG12609-MONOMER

SwissModel (EcoliWiki Page)

SwissModel:P0AA37

UniProt (EcoliWiki Page)

UniProt:P0AA37

PFAM (EcoliWiki Page)

PFAM:PF00849

RefSeq (EcoliWiki Page)

RefSeq:NP_414600


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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)

rluA

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Figure courtesy of RegulonDB

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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gbrowse_img.php?coord=60326..60366&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b0058 (EcoliWiki Page)

NCBI GEO profiles for rluA

microarray

GenExpDB:b0058 (EcoliWiki Page)

Summary of data for rluA 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 NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to rluA Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG12609

EchoBASE (EcoliWiki Page)

EchoBASE:EB2493

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0058

EcoGene (EcoliWiki Page)

EcoGene:EG12609


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Notes

Links

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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.

OrganismHomologs (Statistics)Comments

Anopheles gambiae

  • ENSANGP00000013169 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT1G56345 (score: 1.000; bootstrap: 56%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000000204 (score: 1.000; bootstrap: 75%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00038743 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000029009 (score: 1.000; bootstrap: 79%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000007760 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-040801-238 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040801-252 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0216904 (score: 1.000; bootstrap: 91%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000008504 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000007264 (score: 1.000; bootstrap: 80%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000021069 (score: 1.000; bootstrap: 74%)

From Inparanoid:20070104

Mus musculus

  • MGI:1919186 (score: 1.000; bootstrap: 79%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000007605 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000015206 (score: 1.000; bootstrap: 78%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000133004 (score: 1.000; bootstrap: 87%)

From Inparanoid:20070104

Shigella flexneri

YABO

From SHIGELLACYC

E. coli O157

YABO

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00849


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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 1.11 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 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).
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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