ribB: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

ribB

Gene Synonym(s)

ECK3032, b3041, JW3009, htrP, luxH-I, luxH, luxH-, luxH-l[1][2]

Product Desc.

3,4-dihydroxy-2-butanone 4-phosphate synthase[2][3];

Component of 3,4-dihydroxy-2-butanone 4-phosphate synthase[2][3]

3,4-dihydroxy-2-butanone 4-phosphate synthase; riboflavin biosynthesis; acid-inducible; homodimeric[4]

Product Synonyms(s)

3,4-dihydroxy-2-butanone-4-phosphate synthase[1], B3041[2][1], LuxH[2][1], HtrP[2][1], RibB[2][1] , ECK3032, htrP, JW3009, luxH, b3041

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ribB[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

ribB

Mnemonic

Riboflavin

Synonyms

ECK3032, b3041, JW3009, htrP, luxH-I, luxH, luxH-, luxH-l[1][2]

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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

68.58 minutes 

MG1655: 3182488..3181835
<gbrowseImage> name=NC_000913:3181835..3182488 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3118638..3117985
<gbrowseImage> name=NC_012967:3117985..3118638 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3068983..3069636
<gbrowseImage> name=NC_012759:3068983..3069636 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3183122..3182469
<gbrowseImage> name=NC_007779:3182469..3183122 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3280233..3279580
<gbrowseImage> name=NC_010473:3279580..3280233 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

3181835

Edman degradation

PMID:1597419


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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

ribBD33S

D33S

Loss of activity

seeded from UniProt:P0A7J0

ribBE35S

E35S

Reduces activity by 85%

seeded from UniProt:P0A7J0

ribBR37E

R37E

Loss of activity

seeded from UniProt:P0A7J0

ribBD42S

D42S

Loss of activity

seeded from UniProt:P0A7J0

ribBC67S

C67S

Reduces activity by 80%

seeded from UniProt:P0A7J0

ribBT107S

T107S

Loss of activity

seeded from UniProt:P0A7J0

ribBS110A

S110A

Reduces activity by 85%

seeded from UniProt:P0A7J0

ribBD113S

D113S

Reduces activity by 88%

seeded from UniProt:P0A7J0

ribBT117A

T117A

Reduces activity by 75%

seeded from UniProt:P0A7J0

ribBE40S

E40S

Loss of activity

seeded from UniProt:P0A7J0

ribBE38S

E38S

Loss of activity

seeded from UniProt:P0A7J0

ribBH136S

H136S

Loss of activity

seeded from UniProt:P0A7J0

ribBR150S

R150S

Loss of activity

seeded from UniProt:P0A7J0

ribBH153S

H153S

Loss of activity

seeded from UniProt:P0A7J0

ribBE155S

E155S

Reduces activity by 83%

seeded from UniProt:P0A7J0

ribBE174S

E174S

Loss of activity

seeded from UniProt:P0A7J0

ribB30::Tn5

CGSC:9049

ribB11::Tn5

CGSC:9029


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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

JW3009

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAATCAGACGCTACTTTCCTC

Primer 2:CCGCTGGCTTTACGCTCATGTGC

6B12

Kohara Phage

Genobase

PMID:3038334

tolC210::Tn10

Linked marker

CAG12184 = CGSC7437[5]

est. P1 cotransduction: 89% [6]

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[5]

est. P1 cotransduction: 26% [6]
Synonyms:zgh-3075::Tn10, zgj-3075::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:EG10465

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10465

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000458

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947526

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0460

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009980

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

RibB

Synonyms

3,4-dihydroxy-2-butanone-4-phosphate synthase[1], B3041[2][1], LuxH[2][1], HtrP[2][1], RibB[2][1] , ECK3032, htrP, JW3009, luxH, b3041

Product description

3,4-dihydroxy-2-butanone 4-phosphate synthase[2][3];

Component of 3,4-dihydroxy-2-butanone 4-phosphate synthase[2][3]

3,4-dihydroxy-2-butanone 4-phosphate synthase; riboflavin biosynthesis; acid-inducible; homodimeric[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:0000287

magnesium ion binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00180

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0005829

cytosol

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0006950

response to stress

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0346

P

Seeded from EcoCyc (v14.0)

complete

GO:0008686

3,4-dihydroxy-2-butanone-4-phosphate synthase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00180

F

Seeded from EcoCyc (v14.0)

complete

GO:0008686

3,4-dihydroxy-2-butanone-4-phosphate synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000422

F

Seeded from EcoCyc (v14.0)

complete

GO:0008686

3,4-dihydroxy-2-butanone-4-phosphate synthase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.1.99.12

F

Seeded from EcoCyc (v14.0)

complete

GO:0009231

riboflavin biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00180

P

Seeded from EcoCyc (v14.0)

complete

GO:0009231

riboflavin biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000422

P

Seeded from EcoCyc (v14.0)

complete

GO:0009231

riboflavin biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0686

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0019898

extrinsic to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9903

C

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00180

F

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

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

Subunits of 3,4-dihydroxy-2-butanone 4-phosphate synthase

could be indirect

Protein

arcB

PMID:15690043

Experiment(s):EBI-894222

Protein

atpD

PMID:15690043

Experiment(s):EBI-894222

Protein

oxc

PMID:15690043

Experiment(s):EBI-894222

Protein

ybaL

PMID:15690043

Experiment(s):EBI-894222

Protein

phnN

PMID:16606699

Experiment(s):EBI-1144639

Protein

greB

PMID:16606699

Experiment(s):EBI-1144639

Protein

ppx

PMID:16606699

Experiment(s):EBI-1144639

Protein

phnJ

PMID:16606699

Experiment(s):EBI-1144639

Protein

lldR

PMID:16606699

Experiment(s):EBI-1144639

Protein

pepD

PMID:16606699

Experiment(s):EBI-1144639

Protein

purC

PMID:16606699

Experiment(s):EBI-1144639

Protein

caiD

PMID:16606699

Experiment(s):EBI-1144639

Protein

cysJ

PMID:16606699

Experiment(s):EBI-1143882

Protein

arcB

PMID:19402753

LCMS(ID Probability):99.0

Protein

oxc

PMID:19402753

LCMS(ID Probability):99.0

Protein

ybaL

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 

MNQTLLSSFG TPFERVENAL AALREGRGVM VLDDEDRENE GDMIFPAETM TVEQMALTIR
HGSGIVCLCI TEDRRKQLDL PMMVENNTSA YGTGFTVTIE AAEGVTTGVS AADRITTVRA
AIADGAKPSD LNRPGHVFPL RAQAGGVLTR GGHTEATIDL MTLAGFKPAG VLCELTNDDG
TMARAPECIE FANKHNMALV TIEDLVAYRQ AHERKAS
Length

217

Mol. Wt

23.353 kDa

pI

4.8 (calculated)

Extinction coefficient

2,980 - 3,480 (calc based on 2 Y, 0 W, and 4 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

16..209

PF00926 3,4-dihydroxy-2-butanone 4-phosphate synthase

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=ribB 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:16130937

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947526

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009980

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A7J0

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10465

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10465

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947526

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000458

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0460

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

3.09E+03

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

Ecoli K-12

178.463+/-1.254

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.11475+/-0.00792

Molecules/cell

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

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.113323124

Molecules/cell

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

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

3124

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

916

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

3439

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)

ribB

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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_000913:3182468..3182508 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:b3041 (EcoliWiki Page)

NCBI GEO profiles for ribB

microarray

GenExpDB:b3041 (EcoliWiki Page)

Summary of data for ribB 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 (3182388..3182874) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ18; Well:C6[7]

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Notes

Accessions Related to ribB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10465

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0460

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3041

EcoGene

EcoGene:EG10465

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000458

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009980

Escherichia coli str. K-12 substr. MG1655

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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.

Organism Homologs (Statistics) Comments

Arabidopsis thaliana

  • AT5G64300 (score: 1.000; bootstrap: 100%)
  • AT2G22450 (score: 0.461)

From Inparanoid:20070104

Oryza gramene

  • Q6Z234 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YDR487C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC23E66c (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000024055 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

RIBB

From SHIGELLACYC

E. coli O157

RIBB

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)

PF00926 3,4-dihydroxy-2-butanone 4-phosphate synthase

Panther (EcoliWiki Page)

PTHR21327:SF1

Superfamily (EcoliWiki Page)

SUPERFAMILY:55821

EcoCyc

EcoCyc:EG10465

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10465

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000458

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0460

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009980

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 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 2.14 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 3.3 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 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

Categories

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