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Standard Name

gadB

Gene Synonym(s)

ECK1487, b1493, JW1488[1]

Product Desc.

glutamate decarboxylase B subunit[2][3];

Component of glutamate decarboxylase B[2][3]

Glutamate decarboxylase B, vitamin B6-dependent; hexameric[4]

Product Synonyms(s)

glutamate decarboxylase B, PLP-dependent[1], B1493[2][1], GadB[2][1]

Function from GO

Molecular Function

Cellular Component

Biological Process

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): gadBC[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(gadB)    Textpresso(gadB)

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Notes

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RpoS regulon. EvgAS regulon. H-NS repressed. Repressed during biofilm formation. Induced by acid shock and salt stress. At low pH, cytoplasmic GadB is recruited to the membrane. GadB helps E. coli survive stomach acids.[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

gadB

Mnemonic

Glutamic acid decarboxylase

Synonyms

ECK1487, b1493, JW1488[1]

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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.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

33.81 minutes 

MG1655: 1570069..1568669
gbrowse_img.php?coord=1568669..1570069&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 1545996..1544596
gbrowse_img.php?coord=1544596..1545996&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 1573759..1572359
gbrowse_img.php?coord=1572359..1573759&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 1660664..1659264
gbrowse_img.php?coord=1659264..1660664&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 1460728..1462128
gbrowse_img.php?coord=1460728..1462128&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

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

gadBK276A

K276A

Strongly reduces pyridoxal phosphate binding and increases stability of the polypeptide

seeded from UniProt:P69910

gadBK276H

K276H

Abolishes pyridoxal phosphate binding

seeded from UniProt:P69910

ΔgadB (Keio:JW1488)

deletion

deletion

PMID:16738554

Shigen
CGSC9292[5]

gadB

PMID:12519969

ASAP

At position 820 in Minus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20337

gadB

PMID:12519969

ASAP

At position 820 in Minus orientation, contains plasmid pKD46.
ASAP strain name: FB20338

ΔgadB786::kan

PMID:16738554

CGSC:101070


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Notes

Genetic Resources

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

ResourceResource TypeSourceNotes/Reference

JW1488

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGATAAGAAGCAAGTAACGGA

Primer 2:CCGGTATGTTTAAAGCTGTTCTG

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: 27% [6]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[5]

est. P1 cotransduction: % [6]
Synonyms:zdh-925::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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11490

EchoBASE (EcoliWiki Page)

EchoBASE:EB1453

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1493

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C1922

EcoGene (EcoliWiki Page)

EcoGene:EG11490

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:GADB

CGSC (EcoliWiki Page)

CGSC:32194

ASAP (EcoliWikiPage)

ASAP:ABE-0004976


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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

GadB

Synonyms

glutamate decarboxylase B, PLP-dependent[1], B1493[2][1], GadB[2][1]

Product description

glutamate decarboxylase B subunit[2][3];

Component of glutamate decarboxylase B[2][3]

Glutamate decarboxylase B, vitamin B6-dependent; hexameric[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.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0004351

glutamate decarboxylase activity

PMID:8954890

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0005515

protein binding

PMID:15690043

IPI: Inferred from Physical Interaction

UniProtKB:P36879

F

Seeded from EcoCyc [8]

complete

GO:0005624

membrane fraction

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc [8]

complete

GO:0051454

intracellular pH elevation

PMID:10348866

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc [8]

complete

GO:0004351

glutamate decarboxylase activity

GO_REF:0000002
GO_REF:0000003

IEA: Inferred from Electronic Annotation

InterPro:IPR010107
EC:4.1.1.15

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0005737

cytoplasm

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc 12.5 [7]

complete

GO:0006536

glutamate metabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010107

P

Seeded from EcoCyc [8]

complete

GO:0016020

membrane

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc 12.5 [7]

complete

GO:0019752

carboxylic acid metabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002129

P

Seeded from EcoCyc [8]

complete

GO:0030170

pyridoxal phosphate binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002129
InterPro:IPR010107
InterPro:IPR015421

F

Seeded from EcoCyc [8]

complete

GO:0003824

catalytic activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015421

F

Seeded from EcoCyc [8]

complete

GO:0005739

mitochondrion

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc [8]

complete

GO:0005829

cytosol

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc [8]

complete

GO:0016829

lyase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0456

F

Seeded from EcoCyc [8]

complete

GO:0016831

carboxy-lyase activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR002129
SP_KW:KW-0210

F

Seeded from EcoCyc [8]

complete

GO:0009063

amino acid catabolic process

P

Seeded from EcoCyc 10.6[2].

required fields missing

GO:0006520

amino acid metabolic process

P

Seeded from EcoCyc 10.6[2].

required fields missing

GO:0051454

intracellular pH elevation

PMID:10348866

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc 11.1[3].

complete

GO:0004351

glutamate decarboxylase activity

PMID:8954890

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc 11.1[3].

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 TypePartnerNotesReferencesEvidence

Protein

Subunits of glutamate decarboxylase B

could be indirect

Protein

dnaK

PMID:15690043

Experiment(s):EBI-887830, EBI-890853

Protein

gadA

PMID:15690043

Experiment(s):EBI-887830, EBI-888455, EBI-893820

Protein

groL

PMID:16606699

Experiment(s):EBI-1139975

Protein

yadG

PMID:15690043

Experiment(s):EBI-893831

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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
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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.

Sequence

at EcoCyc 

MDKKQVTDLR SELLDSRFGA KSISTIAESK RFPLHEMRDD VAFQIINDEL YLDGNARQNL
ATFCQTWDDE NVHKLMDLSI NKNWIDKEEY PQSAAIDLRC VNMVADLWHA PAPKNGQAVG
TNTIGSSEAC MLGGMAMKWR WRKRMEAAGK PTDKPNLVCG PVQICWHKFA RYWDVELREI
PMRPGQLFMD PKRMIEACDE NTIGVVPTFG VTYTGNYEFP QPLHDALDKF QADTGIDIDM
HIDAASGGFL APFVAPDIVW DFRLPRVKSI SASGHKFGLA PLGCGWVIWR DEEALPQELV
FNVDYLGGQI GTFAINFSRP AGQVIAQYYE FLRLGREGYT KVQNASYQVA AYLADEIAKL
GPYEFICTGR PDEGIPAVCF KLKDGEDPGY TLYDLSERLR LRGWQVPAFT LGGEATDIVV
MRIMCRRGFE MDFAELLLED YKASLKYLSD HPKLQGIAQQ NSFKHT
Length

466

Mol. Wt

52.669 kDa

pI

5.2 (calculated)

Extinction coefficient

84,340 - 85,590 (calc based on 16 Y, 11 W, and 10 C residues)

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Domains/Motifs/Modification Sites

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

Structures
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 typeSourceNotes/Reference

Purification protocol

PMID:8954890

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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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:GLUTDECARBOXB-MONOMER

UniProt (EcoliWiki Page)

UniProt:P69910

PFAM (EcoliWiki Page)

PFAM:PF00282

RefSeq (EcoliWiki Page)

RefSeq:NP_416010


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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

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

gadBC

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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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gbrowse_img.php?coord=1570049..1570089&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

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

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

TypeReferenceNotes

microarray

GEO Profiles:b1493 (EcoliWiki Page)

NCBI GEO profiles for gadB

microarray

GenExpDB:b1493 (EcoliWiki Page)

Summary of data for gadB 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 NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (1569975..1570435) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ06; Well:A9[9]

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Notes

Accessions Related to gadB Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11490

EchoBASE (EcoliWiki Page)

EchoBASE:EB1453

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1493

EcoGene (EcoliWiki Page)

EcoGene:EG11490


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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.

OrganismHomologs (Statistics)Comments

Anopheles gambiae

  • ENSANGP00000012191 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT2G02010 (score: 0.635)
  • AT3G17760 (score: 1.000; bootstrap: 100%)
  • AT5G17330 (score: 0.603)
  • AT2G02000 (score: 0.593)
  • AT1G65960 (score: 0.260)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000013166 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00038467 (score: 1.000; bootstrap: 100%)
  • WBGene00031909 (score: 0.294)
  • WBGene00042089 (score: 0.092)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00004981 (score: 0.298)
  • WBGene00006418 (score: 1.000; bootstrap: 100%)
  • WBGene00022427 (score: 0.231)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000020786 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000002369 (score: 1.000; bootstrap: 100%)
  • ENSCINP00000011354 (score: 0.173)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0231446 (score: 1.000; bootstrap: 100%)
  • DDB0231439 (score: 0.516)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0010591 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA21426-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000007235 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000299297 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000012828 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000010934 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1261415 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q8LLP2 (score: 0.980)
  • Q6ASV4 (score: 1.000; bootstrap: 100%)
  • Q84U04 (score: 0.773)
  • Q6YSB2 (score: 0.684)
  • Q7XV14 (score: 0.668)
  • Q9AQU4 (score: 0.662)
  • Q7XZU7 (score: 0.603)
  • Q7XV18 (score: 0.542)
  • Q9AR41 (score: 0.540)
  • Q5F1L4 (score: 0.330)
  • Q5EXM3 (score: 0.160)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000004500 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000000686 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YMR250W (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000131149 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00024535001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000017960 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

GADB

From SHIGELLACYC

E. coli O157

GADB

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00282


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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 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 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 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. ↑ 7.0 7.1 7.2 7.3 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

Categories

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