EcoliHub logo

Try the new EcoliHub and let us know what you'd like to see.

leuB:On One Page

From EcoliWiki

Jump to: navigation, search
Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]



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

Standard Name

leuB

Gene Synonym(s)

ECK0075, b0073, JW5807[1]

Product Desc.

LeuB[2][3];

Component of 3-isopropylmalate dehydrogenase[2][3]

beta-Isopropylmalate dehydrogenase[4]

Product Synonyms(s)

3-isopropylmalate dehydrogenase[1], B0073[2][1], LeuB[2][1]

Function from GO

Molecular Function

Biological Process

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): leuLABCD[2], OP00249, leu, leuABCD

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(leuB)    Textpresso(leuB)

edit table

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

Notes

[back to top]





Gene

[back to top]


Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

leuB

Mnemonic

Leucine (biosynthesis)

Synonyms

ECK0075, b0073, JW5807[1]

edit table

Notes

Location(s) and DNA Sequence

[back to top]


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

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

1.74 minutes 

MG1655: 81958..80867
gbrowse_img.php?coord=80867..81958&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 84762..83671
gbrowse_img.php?coord=83671..84762&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 81958..80867
gbrowse_img.php?coord=80867..81958&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

BW2952

NC_012759: 80866..81957
gbrowse_img.php?coord=80866..81957&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

edit table

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature typeLocationDescription
edit table

Notes

Alleles and Phenotypes

[back to top]


See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

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

ΔleuB (Keio:JW5807)

deletion

deletion

PMID:16738554

Shigen

leuB6(Am)

CGSC:4494

amber (UAG) mutation

leuB401

CGSC:6568

leuB61

CGSC:6570

leuB19

CGSC:8331


edit table

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW5807

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCGAAGAATTACCATATTGC

Primer 2:CCaACCCCTTCTGCTACATAGCG

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 11% [6]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 92% [6]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

edit table

Notes

Accessions in Other Databases

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11577

EchoBASE (EcoliWiki Page)

EchoBASE:EB1537

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0073

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0090

EcoGene (EcoliWiki Page)

EcoGene:EG11577

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:LEUB

CGSC (EcoliWiki Page)

CGSC:571

ASAP (EcoliWikiPage)

ASAP:ABE-0000265


edit table

Notes

Links

[back to top]



Product(s)

[back to top]



Nomenclature

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

Standard name

LeuB

Synonyms

3-isopropylmalate dehydrogenase[1], B0073[2][1], LeuB[2][1]

Product description

LeuB[2][3];

Component of 3-isopropylmalate dehydrogenase[2][3]

beta-Isopropylmalate dehydrogenase[4]

EC number (for enzymes)
edit table

Notes

Function

[back to top]


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:0003862

3-isopropylmalate dehydrogenase activity

PMID:9003442

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0009098

leucine biosynthetic process

PMID:9003442

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc 12.5 [7]

complete

GO:0000287

magnesium ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc [8]

complete

GO:0003862

3-isopropylmalate dehydrogenase activity

GO_REF:0000002
GO_REF:0000003
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR004429
EC:1.1.1.85
HAMAP:MF_01033

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0005737

cytoplasm

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR004429
SP_KW:KW-0963

C

Seeded from EcoCyc 12.5 [7]

complete

GO:0009098

leucine biosynthetic process

GO_REF:0000002
GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR004429
SP_KW:KW-0432
HAMAP:MF_01033

P

Seeded from EcoCyc 12.5 [7]

complete

GO:0030145

manganese ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc [8]

complete

GO:0046872

metal ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc [8]

complete

GO:0008152

metabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001804

P

Seeded from EcoCyc [8]

complete

GO:0008652

amino acid biosynthetic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0028

P

Seeded from EcoCyc [8]

complete

GO:0009082

branched chain family amino acid biosynthetic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0100

P

Seeded from EcoCyc [8]

complete

GO:0016491

oxidoreductase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc [8]

complete

GO:0016616

oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001804

F

Seeded from EcoCyc [8]

complete

GO:0055114

oxidation reduction

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc [8]

complete

GO:0009098

leucine biosynthetic process

PMID:9003442

IDA

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0003862

3-isopropylmalate dehydrogenase activity

PMID:9003442

IDA

F

Seeded from EcoCyc 11.1[3].

required fields missing

edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner TypePartnerNotesReferencesEvidence

Protein

Subunits of 3-isopropylmalate dehydrogenase

could be indirect


edit table

Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
edit table

Notes

Structure and Physical Properties

[back to top]


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

Sequence

at EcoCyc 

MMSKNYHIAV LPGDGIGPEV MTQALKVLDA VRNRFAMRIT TSHYDVGGAA IDNHGQPLPP
ATVEGCEQAD AVLFGSVGGP KWEHLPPDQQ PERGALLPLR KHFKLFSNLR PAKLYQGLEA
FCPLRADIAA NGFDILCVRE LTGGIYFGQP KGREGSGQYE KAFDTEVYHR FEIERIARIA
FESARKRRHK VTSIDKANVL QSSILWREIV NEIATEYPDV ELAHMYIDNA TMQLIKDPSQ
FDVLLCSNLF GDILSDECAM ITGSMGMLPS ASLNEQGFGL YEPAGGSAPD IAGKNIANPI
AQILSLALLL RYSLDADDAA CAIERAINRA LEEGIRTGDL ARGAAAVSTD EMGDIIARYV AEGV
Length

364

Mol. Wt

39.649 kDa

pI

5.0 (calculated)

Extinction coefficient

27,390 - 28,140 (calc based on 11 Y, 2 W, and 6 C residues)

edit table


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:P30125


edit table


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

Structures
Models

View models at:

edit table

Structure figures

Notes

Gene Product Resources

[back to top]


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

Resource typeSourceNotes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:3-ISOPROPYLMALDEHYDROG-MONOMER

UniProt (EcoliWiki Page)

UniProt:P30125

PFAM (EcoliWiki Page)

PFAM:PF00180

RefSeq (EcoliWiki Page)

RefSeq:NP_414615


edit table

Notes

Links

[back to top]




Expression

[back to top]



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

[back to top]


See Help:Cellular levels

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

Notes

Transcription and Transcriptional Regulation

[back to top]


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

Transcription unit(s)

leuLABCD

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

[back to top]


gbrowse_img.php?coord=81938..81978&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

[back to top]


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

Allele NameMutationPhenotypeReference
edit table


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

TypeReferenceNotes

microarray

GEO Profiles:b0073 (EcoliWiki Page)

NCBI GEO profiles for leuB

microarray

GenExpDB:b0073 (EcoliWiki Page)

Summary of data for leuB from multiple microarray studies

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource NameResource TypeDescriptionSourceNotes
edit table

Notes

Accessions Related to leuB Expression

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11577

EchoBASE (EcoliWiki Page)

EchoBASE:EB1537

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0073

EcoGene (EcoliWiki Page)

EcoGene:EG11577


edit table

Notes

Links

[back to top]



Evolution

[back to top]



Homologs in Other Organisms

[back to top]


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

OrganismHomologs (Statistics)Comments

Arabidopsis thaliana

  • AT1G80560 (score: 1.000; bootstrap: 100%)
  • AT1G31180 (score: 0.761)
  • AT5G14200 (score: 0.756)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00036287 (score: 1.000; bootstrap: 100%)
  • WBGene00026699 (score: 0.257)
  • WBGene00037537 (score: 0.253)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00007993 (score: 1.000; bootstrap: 100%)
  • WBGene00016266 (score: 0.262)
  • WBGene00009440 (score: 0.252)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000015535 (score: 1.000; bootstrap: 100%)
  • ENSMMUP00000028091 (score: 0.212)

From Inparanoid:20070104

Oryza gramene

  • Q6AT60 (score: 1.000; bootstrap: 100%)
  • Q7Y096 (score: 0.994)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YCL018W (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC1A42c (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000014804 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Shigella flexneri

LEUB

From SHIGELLACYC

E. coli O157

LEUB

From ECOO157CYC

edit table


Do-It-Yourself Web Tools

Notes

Families

[back to top]


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

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00180


edit table

Notes

Links

[back to top]



References

[back to top]


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 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 3.3 3.4 3.5 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. ↑ 7.0 7.1 7.2 7.3 7.4 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 8.8 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70

Categories

[back to top]


Retrieved from "http://ecoliwiki.net/colipedia/index.php/leuB:On_One_Page"
Personal tools