hupB: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

hupB

Gene Synonym(s)

ECK0434, b0440, JW0430, dpeA, hopD, dbhB, gsp*[1][2]

Product Desc.

DNA-binding protein HU-β, NS1 (HU-1)[2]; Transcriptional dual regulator HU-β, NS1 (HU-1)[3];

Component of HU Transcriptional dual regulator[3]

Histone-like protein HU-beta, HU-1[4]

Product Synonyms(s)

HU, DNA-binding transcriptional regulator, beta subunit[1], B0440[2][1], DpeA[2][1], HopD[2][1], DbhB[2][1], HupB[2][1] , dpeA, ECK0434, hopD, JW0430, b0440

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): hupB[2]

Regulation/Activity
Quick Links



        

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Notes

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HU concentration in the cell determines the mechanical effect; flexible bends responsible for compaction occur at concentrations <100nM, while increased concentrations result in the formation of a rigid nucleoprotein filament and no significant concentration. Binds TrxA (Kumar, 2004).[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

hupB

Mnemonic

HU protein

Synonyms

ECK0434, b0440, JW0430, dpeA, hopD, dbhB, gsp*[1][2]

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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.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

9.93 minutes 

MG1655: 460675..460947
<gbrowseImage> name=NC_000913:460675..460947 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 433506..433778
<gbrowseImage> name=NC_012967:433506..433778 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 363434..363706
<gbrowseImage> name=NC_012759:363434..363706 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 460675..460947
<gbrowseImage> name=NC_007779:460675..460947 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 400006..400278
<gbrowseImage> name=NC_010473:400006..400278 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

460675

Edman degradation

PMID:215461
PMID:350619
PMID:6987059
PMID:9298646


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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

hupBA30D

A30D

No effect

seeded from UniProt:P0ACF4

hupBRTGR58GTGG

RTGR58GTGG

Reduced DNA-binding

seeded from UniProt:P0ACF4

hupBF47T

F47T

Reduced DNA-binding

seeded from UniProt:P0ACF4

hupBK37Q

K37Q

No effect

seeded from UniProt:P0ACF4

hupB(del) (Keio:JW0430)

deletion

deletion

PMID:16738554

Shigen

CGSC8593[5]

hupB::Tn5KAN-2 (FB20176)

Insertion at nt 210 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20176

does not contain pKD46

hupB(del)::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938

hupB726(del)::kan

PMID:16738554

CGSC:101442


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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

JW0430

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAATAAATCTCAATTGATCGA

Primer 2:CCGTTTACCGCGTCTTTCAGTGC

3B6

Kohara Phage

Genobase

PMID:3038334

7E2

Kohara Phage

Genobase

PMID:3038334

zaj-3054::Tn10

Linked marker

CAG12017 = CGSC7339[5]

est. P1 cotransduction: 96% [6]
Synonyms:zba-3054::Tn10

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[5]

est. P1 cotransduction: 18% [6]
Synonyms:zbb-30-55::TnlO, zba-3055::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:EG10467

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10467

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000460

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949095

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0462

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001527

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

HupB

Synonyms

HU, DNA-binding transcriptional regulator, beta subunit[1], B0440[2][1], DpeA[2][1], HopD[2][1], DbhB[2][1], HupB[2][1] , dpeA, ECK0434, hopD, JW0430, b0440

Product description

DNA-binding protein HU-β, NS1 (HU-1)[2]; Transcriptional dual regulator HU-β, NS1 (HU-1)[3];

Component of HU Transcriptional dual regulator[3]

Histone-like protein HU-beta, HU-1[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.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000119

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010992

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020816

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

Contributes to

GO:0003677

DNA binding

PMID:10551881[7]

IDA: Inferred from Direct Assay

F

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 HU Transcriptional dual regulator

could be indirect

Protein

hsdM

PMID:15690043[8]

Experiment(s):EBI-886990

Protein

malP

PMID:15690043[8]

Experiment(s):EBI-886990, EBI-884415

Protein

malQ

PMID:15690043[8]

Experiment(s):EBI-886990, EBI-884415

Protein

polA

PMID:15690043[8]

Experiment(s):EBI-886990, EBI-892889, EBI-884415

Protein

fis

PMID:15690043[8]

Experiment(s):EBI-884415

Protein

ihfA

PMID:15690043[8]

Experiment(s):EBI-884415

Protein

skp

PMID:15690043[8]

Experiment(s):EBI-884415

Protein

hns

PMID:15690043[8]

Experiment(s):EBI-884415

Protein

rplC

PMID:15690043[8]

Experiment(s):EBI-884415

Protein

rpoA

PMID:15690043[8]

Experiment(s):EBI-884415

Protein

rpsG

PMID:15690043[8]

Experiment(s):EBI-884415

Protein

seqA

PMID:15690043[8]

Experiment(s):EBI-884415

Protein

rdgC

PMID:15690043[8]

Experiment(s):EBI-884415

Protein

dnaE

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

rplC

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

yghW

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

nfnB

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

rplI

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

nuoE

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

htpG

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

rpsI

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

rplS

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

rhlE

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

rpsD

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

greA

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

rplB

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

sdhA

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

rpsG

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

nadE

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

uspG

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

rplA

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

yebG

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

pepD

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

rplU

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

vsr

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

rplQ

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

dnaK

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

slyD

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

ydcP

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

rpsM

PMID:16606699[9]

Experiment(s):EBI-1136666

Protein

ihfB

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):2.338232

Protein

skp

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

fis

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

hns

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

rpoA

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

malQ

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):26.284388

Protein

hsdM

PMID:19402753[10]

MALDI(Z-score):23.699803

Protein

malP

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):24.332948

Protein

polA

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):14.532702

Protein

rdgC

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

ihfA

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):7.883297

Protein

seqA

PMID:19402753[10]

LCMS(ID Probability):99.6

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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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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 

MNKSQLIDKI AAGADISKAA AGRALDAIIA SVTESLKEGD DVALVGFGTF AVKERAARTG
RNPQTGKEIT IAAAKVPSFR AGKALKDAVN
Length

90

Mol. Wt

9.225 kDa

pI

10.1 (calculated)

Extinction coefficient

0 (calc based on 0 Y, 0 W, and 0 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

1..90

PF00216 Bacterial DNA-binding protein

PMID:19920124[11]

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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=hupB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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:16128425

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:949095

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001527

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ACF4

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10467

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10467

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:949095

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000460

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0462

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

9.52E+04

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

1146.626+/-7.15

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.43714+/-0.0137

Molecules/cell

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

by FISH

PMID:20671182

mRNA

Ecoli K-12

1.108455882

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

74002

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

28193

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

35232

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

Transcription unit(s)

hupB

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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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<gbrowseImage> name=NC_000913:460655..460695 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> 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

</protect>

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 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:b0440 (EcoliWiki Page)

NCBI GEO profiles for hupB

microarray

GenExpDB:b0440 (EcoliWiki Page)

Summary of data for hupB 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 (460388..460697) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ10; Well:C5[12]

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<protect>

Notes

Accessions Related to hupB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10467

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0462

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0440

EcoGene

EcoGene:EG10467

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000460

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001527

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

Shigella flexneri

HUPB

From SHIGELLACYC

E. coli O157

HUPB

From ECOO157CYC

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Do-It-Yourself Web Tools


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)

PF00216 Bacterial DNA-binding protein

Superfamily (EcoliWiki Page)

SUPERFAMILY:47729

EcoCyc

EcoCyc:EG10467

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10467

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000460

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0462

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001527

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 1.12 1.13 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 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).
  7. ↑ Azam, TA & Ishihama, A (1999) Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J. Biol. Chem. 274 33105-13 PubMed
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  9. ↑ 9.00 9.01 9.02 9.03 9.04 9.05 9.06 9.07 9.08 9.09 9.10 9.11 9.12 9.13 9.14 9.15 9.16 9.17 9.18 9.19 9.20 9.21 9.22 9.23 9.24 9.25 9.26 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  10. ↑ 10.00 10.01 10.02 10.03 10.04 10.05 10.06 10.07 10.08 10.09 10.10 10.11 10.12 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  11. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
  12. ↑ 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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