dusC: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

dusC

Gene Synonym(s)

ECK2133, b2140, JW2128, yohI[1], yohI

Product Desc.

tRNA dihydrouridine synthase[2][3]

tRNA-dihydrouridine synthase C[4]

Product Synonyms(s)

tRNA-dihydrouridine synthase C[1], B2140[2][1], DusC[2][1], YohI[2][1] , ECK2133, JW2128, yohI, b2140

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): dusC[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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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

dusC

Mnemonic

Dihydrouridine synthase C

Synonyms

ECK2133, b2140, JW2128, yohI[1], yohI

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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

48.01 minutes, 48.01 minutes 

MG1655: 2228407..2227460
<gbrowseImage> name=NC_000913:2227460..2228407 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2180677..2181624
<gbrowseImage> name=NC_012967:2180677..2181624 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2119943..2120890
<gbrowseImage> name=NC_012759:2119943..2120890 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2233719..2232772
<gbrowseImage> name=NC_007779:2232772..2233719 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2319415..2318468
<gbrowseImage> name=NC_010473:2318468..2319415 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
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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

ΔdusC (Keio:JW2128)

deletion

deletion

PMID:16738554

Shigen
CGSC9724[5]

yohI::Tn5KAN-I-SceI (FB20641)

Insertion at nt 219 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20641

contains pKD46

yohI::Tn5KAN-I-SceI (FB20642)

Insertion at nt 219 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20642

does not contain pKD46

ΔdusC767::kan

PMID:16738554

CGSC:100668


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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

JW2128

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCGTGTGTTACTGGCACCGAT

Primer 2:CCGAGTTTCTCGATATCAATTGC

1E1

Kohara Phage

Genobase

PMID:3038334

2B2

Kohara Phage

Genobase

PMID:3038334

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[5]

est. P1 cotransduction: 9% [6]
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[5]

est. P1 cotransduction: 1% [6]
Synonyms:zeg-722, zei-722::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:EG12022

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12022

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001939

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945458

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1957

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007074

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

DusC

Synonyms

tRNA-dihydrouridine synthase C[1], B2140[2][1], DusC[2][1], YohI[2][1] , ECK2133, JW2128, yohI, b2140

Product description

tRNA dihydrouridine synthase[2][3]

tRNA-dihydrouridine synthase C[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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013785

F

Seeded from EcoCyc (v14.0)

complete

GO:0008033

tRNA processing

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001269

P

Seeded from EcoCyc (v14.0)

complete

GO:0008033

tRNA processing

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018517

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:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013785

P

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc (v14.0)

complete

GO:0017150

tRNA dihydrouridine synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001269

F

Seeded from EcoCyc (v14.0)

complete

GO:0017150

tRNA dihydrouridine synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018517

F

Seeded from EcoCyc (v14.0)

complete

GO:0050660

FAD binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001269

F

Seeded from EcoCyc (v14.0)

complete

GO:0050660

FAD binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018517

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001269

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018517

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

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

groL

PMID:16606699

Experiment(s):EBI-1142015

Protein

aceE

PMID:15690043

Experiment(s):EBI-894927

Protein

ampE

PMID:15690043

Experiment(s):EBI-894927

Protein

cynT

PMID:15690043

Experiment(s):EBI-894927

Protein

entE

PMID:15690043

Experiment(s):EBI-894927

Protein

fumC

PMID:15690043

Experiment(s):EBI-894927

Protein

hupA

PMID:15690043

Experiment(s):EBI-894927

Protein

intA

PMID:15690043

Experiment(s):EBI-894927

Protein

lpdA

PMID:15690043

Experiment(s):EBI-894927

Protein

nfo

PMID:15690043

Experiment(s):EBI-894927

Protein

recG

PMID:15690043

Experiment(s):EBI-894927

Protein

rplM

PMID:15690043

Experiment(s):EBI-894927

Protein

rplN

PMID:15690043

Experiment(s):EBI-894927

Protein

rplR

PMID:15690043

Experiment(s):EBI-894927

Protein

rplV

PMID:15690043

Experiment(s):EBI-894927

Protein

rpsB

PMID:15690043

Experiment(s):EBI-894927

Protein

rpsE

PMID:15690043

Experiment(s):EBI-894927

Protein

rpsG

PMID:15690043

Experiment(s):EBI-894927

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-894927

Protein

secA

PMID:15690043

Experiment(s):EBI-894927

Protein

ydaY

PMID:15690043

Experiment(s):EBI-894927

Protein

ydiB

PMID:15690043

Experiment(s):EBI-894927

Protein

yfjW

PMID:15690043

Experiment(s):EBI-894927

Protein

intA

PMID:19402753

LCMS(ID Probability):99.0

Protein

recG

PMID:19402753

LCMS(ID Probability):99.0

Protein

entE

PMID:19402753

LCMS(ID Probability):99.0

Protein

fumC

PMID:19402753

LCMS(ID Probability):99.0

Protein

nfo

PMID:19402753

LCMS(ID Probability):99.0

Protein

ydiB

PMID:19402753

LCMS(ID Probability):99.0

Protein

ampE

PMID:19402753

LCMS(ID Probability):99.0

Protein

cynT

PMID:19402753

LCMS(ID Probability):99.0

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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
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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 

MRVLLAPMEG VLDSLVRELL TEVNDYDLCI TEFVRVVDQL LPVKVFHRIC PELQNASRTP
SGTLVRVQLL GQFPQWLAEN AARAVELGSW GVDLNCGCPS KTVNGSGGGA TLLKDPELIY
QGAKAMREAV PAHLPVSVKV RLGWDSGEKK FEIADAVQQA GATELVVHGR TKEQGYRAEH
IDWQAIGDIR QRLNIPVIAN GEIWDWQSAQ QCMAISGCDA VMIGRGALNI PNLSRVVKYN
EPRMPWPEVV ALLQKYTRLE KQGDTGLYHV ARIKQWLSYL RKEYDEATEL FQHVRVLNNS
PDIARAIQAI DIEKL
Length

315

Mol. Wt

35.198 kDa

pI

6.5 (calculated)

Extinction coefficient

55,920 - 56,670 (calc based on 8 Y, 8 W, and 6 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

4..309

PF01207 Dihydrouridine synthase (Dus)

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=dusC 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:16130078

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945458

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007074

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P33371

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12022

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12022

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945458

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001939

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1957

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

Ecoli K-12

0.114+/-0.035

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

Protein

E. coli K-12 MG1655

196

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

25

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

62

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)

dusC

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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_000913:2228387..2228427 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:b2140 (EcoliWiki Page)

NCBI GEO profiles for dusC

microarray

GenExpDB:b2140 (EcoliWiki Page)

Summary of data for dusC 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

GFP Fusion

Intergenic region (2228311..2228676) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ10; Well:E1[7]

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Notes

Accessions Related to dusC Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12022

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1957

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2140

EcoGene

EcoGene:EG12022

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001939

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007074

Escherichia coli str. K-12 substr. MG1655

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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

  • ENSANGP00000000609 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00041459 (score: 1.000; bootstrap: 100%)
  • WBGene00033329 (score: 0.050)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00016674 (score: 1.000; bootstrap: 83%)
  • WBGene00009452 (score: 0.055)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000005834 (score: 1.000; bootstrap: 66%)
  • ENSCAFP00000008929 (score: 0.108)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000003786 (score: 1.000; bootstrap: 100%)
  • ENSCINP00000015347 (score: 0.124)
  • ENSCINP00000014945 (score: 0.119)

From Inparanoid:20070104

Danio rerio

  • ZDB-CDNA-040801-247 (score: 1.000; bootstrap: 100%)
  • ZDB-GENE-040801-233 (score: 0.998)
  • ZDB-CDNA-040425-1158 (score: 0.127)
  • ZDB-GENE-030131-1435 (score: 0.127)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000020448 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000004101 (score: 0.099)
  • ENSMODP00000006529 (score: 0.052)

From Inparanoid:20070104

Mus musculus

  • MGI:1919166 (score: 1.000; bootstrap: 78%)
  • MGI:1915980 (score: 0.114)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000011068 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YOHI

From SHIGELLACYC

E. coli O157

YOHI

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

Pfam (EcoliWiki Page)

PF01207 Dihydrouridine synthase (Dus)

Superfamily (EcoliWiki Page)

SUPERFAMILY:51395

EcoCyc

EcoCyc:EG12022

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12022

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001939

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1957

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007074

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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 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 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. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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