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Latest revision as of 05:20, 29 July 2007

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

Quickview

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Standard Name

lrp

Gene Synonym(s)

ECK0880, b0889, JW0872, ihb, livR, lrs, lss, lstR, mbf, oppI, rblA, g[1][2], alsB

Product Desc.

Lrp transcriptional dual regulator[2][3]

Global regulatory protein, Leu responsive; regulator of high-affinity branched-chain amino acid transport system; octameric or hexadecameric functional state[4]

Product Synonyms(s)

DNA-binding transcriptional dual regulator, leucine-binding[1], B0889[2][1], LstR[2][1], Mbf[2][1], OppI[2][1], RblA[2][1], Lss[2][1], Lrs[2][1], Ihb[2][1], Lrp[2][1], LivR[2][1], regulator for leucine (or lrp) regulon and high-affinity branched-chain amino acid transport system.[2][1] , alsB, ECK0880, ihb, JW0872, livR, lrs, lss, lstR, mbf, oppI, rblA, b0889

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): lrp[2], OP00251

Regulation/Activity
Quick Links



        

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See Help:Quickview for help with entering information in the Quickview table.

Notes

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Feast/famine regulatory protein. Homodimers bind adjacent DNA binding sites to form functional octameric state. Lrp wraps DNA and probably plays a role in chromatin organization.[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

lrp

Mnemonic

Leucine regulatory protein

Synonyms

ECK0880, b0889, JW0872, ihb, livR, lrs, lss, lstR, mbf, oppI, rblA, g[1][2], alsB

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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

20.08 minutes 

MG1655: 931818..932312
<gbrowseImage> name=NC_000913:931818..932312 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 949653..950147
<gbrowseImage> name=NC_012967:949653..950147 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 834786..835280
<gbrowseImage> name=NC_012759:834786..835280 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 933017..933511
<gbrowseImage> name=NC_007779:933017..933511 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 985746..986240
<gbrowseImage> name=NC_010473:985746..986240 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

931821

Edman degradation

PMID:2115869


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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

lrp(del) (Keio:JW0872)

deletion

deletion

PMID:16738554

Shigen

CGSC8901[5]

lrpD114E

D114E

(in lrp-1 mutant)

Strain variation; seeded from UniProt:P0ACJ0

lrp-1

CGSC:10310

lrp-787(del)::kan

PMID:16738554

CGSC:101692

Irp787(del)::FRT

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554

Parental Strain: SMR4562

Experimental Strain: PJH1276

Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.

CAG45114 lrp787(del)::FRTKanFRT

deletion

SigmaE activity

Decrease in SigmaE activity

PMID:23224554

Parental Strain: CAG45114 Experimental Strain: SMR15265

See table S11 for full experimental results.

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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

JW0872

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGTAGATAGCAAGAAGCGCCC

Primer 2:CCGCGCGTCTTAATAACCAGACG

1H1

Kohara Phage

Genobase

PMID:3038334

1F10

Kohara Phage

Genobase

PMID:3038334

E6H3

Kohara Phage

Genobase

PMID:3038334

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[5]

est. P1 cotransduction: % [6]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[5]

est. P1 cotransduction: 60% [6]
Synonyms:zbj-1230::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:EG10547

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10547

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000540

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949051

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0542

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003023

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

Lrp

Synonyms

DNA-binding transcriptional dual regulator, leucine-binding[1], B0889[2][1], LstR[2][1], Mbf[2][1], OppI[2][1], RblA[2][1], Lss[2][1], Lrs[2][1], Ihb[2][1], Lrp[2][1], LivR[2][1], regulator for leucine (or lrp) regulon and high-affinity branched-chain amino acid transport system.[2][1] , alsB, ECK0880, ihb, JW0872, livR, lrs, lss, lstR, mbf, oppI, rblA, b0889

Product description

Lrp transcriptional dual regulator[2][3]

Global regulatory protein, Leu responsive; regulator of high-affinity branched-chain amino acid transport system; octameric or hexadecameric functional state[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:0006355

regulation of transcription, DNA-dependent

PMID:12374860[7]

IMP: Inferred from Mutant Phenotype

P

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

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000485

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019885

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019887

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019888

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000485

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019885

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019887

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019888

C

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0043565

sequence-specific DNA binding

PMID:10551881[8]

IDA: Inferred from Direct Assay

F

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000485

P

Seeded from EcoCyc (v14.0)

complete

GO:0043201

response to leucine

PMID:1346534[9] PMID:12054800[10]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019885

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019887

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019888

P

Seeded from EcoCyc (v14.0)

complete

GO:0043565

sequence-specific DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000485

F

Seeded from EcoCyc (v14.0)

complete

GO:0043565

sequence-specific DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019885

F

Seeded from EcoCyc (v14.0)

complete

GO:0043565

sequence-specific DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019887

F

Seeded from EcoCyc (v14.0)

complete

GO:0043565

sequence-specific DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019888

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

trxB

PMID:16606699[11]

Experiment(s):EBI-1138286

Protein

nadE

PMID:16606699[11]

Experiment(s):EBI-1138286

Protein

yfhM

PMID:19402753[12]

LCMS(ID Probability):99.0

Protein

nanS

PMID:19402753[12]

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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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 

MVDSKKRPGK DLDRIDRNIL NELQKDGRIS NVELSKRVGL SPTPCLERVR RLERQGFIQG
YTALLNPHYL DASLLVFVEI TLNRGAPDVF EQFNTAVQKL EEIQECHLVS GDFDYLLKTR
VPDMSAYRKL LGETLLRLPG VNDTRTYVVM EEVKQSNRLV IKTR
Length

164

Mol. Wt

18.886 kDa

pI

9.1 (calculated)

Extinction coefficient

7,450 - 7,700 (calc based on 5 Y, 0 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.

Type Residues Description Notes References

Initiator Methionine

1

Removed

UniProt:P0ACJ0

Domain

78..152

PF01037 AsnC family

PMID:19920124[13]

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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=lrp 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:16128856

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:949051

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003023

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ACJ0

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10547

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10547

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:949051

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000540

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0542

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

1.43E+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

E. coli K-12 MG1655

4901

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

5813

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

6729

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)

lrp

edit table
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_000913:931798..931838 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:b0889 (EcoliWiki Page)

NCBI GEO profiles for lrp

microarray

GenExpDB:b0889 (EcoliWiki Page)

Summary of data for lrp 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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<protect>

Notes

Accessions Related to lrp Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10547

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0542

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0889

EcoGene

EcoGene:EG10547

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000540

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003023

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

Anopheles gambiae

  • ENSANGP00000000462 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000020115 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000015168 (score: 1.000; bootstrap: 54%)

From Inparanoid:20070104

Shigella flexneri

LRP

From SHIGELLACYC

E. coli O157

LRP

From ECOO157CYC

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF01037 AsnC family


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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 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.21 1.22 1.23 1.24 1.25 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 2.15 2.16 2.17 2.18 2.19 2.20 2.21 2.22 2.23 2.24 2.25 2.26 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 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. ↑ Tani, TH et al. (2002) Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Proc. Natl. Acad. Sci. U.S.A. 99 13471-6 PubMed
  8. ↑ 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
  9. ↑ Ernsting, BR et al. (1992) Characterization of the regulon controlled by the leucine-responsive regulatory protein in Escherichia coli. J. Bacteriol. 174 1109-18 PubMed
  10. ↑ Chen, S & Calvo, JM (2002) Leucine-induced dissociation of Escherichia coli Lrp hexadecamers to octamers. J. Mol. Biol. 318 1031-42 PubMed
  11. ↑ 11.0 11.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  12. ↑ 12.0 12.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  13. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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