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ddlA:On One Page

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Standard Name

ddlA

Gene Synonym(s)

ECK0376, b0381, JW0372[1]

Product Desc.

D-alanine:D-alanine ligase A, ADP-forming[2]

Product Synonyms(s)

D-alanine-D-alanine ligase A[1], B0381[3][1], DdlA[3][1]

Function from GO

Molecular Function

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ddlA[3]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(ddlA)    Textpresso(ddlA)

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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

ddlA

Mnemonic

D-alanine D-alanine Ligase A

Synonyms

ECK0376, b0381, JW0372[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

8.6 minutes 

MG1655: 400147..399053
gbrowse_img.php?coord=399053..400147&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 368569..367475
gbrowse_img.php?coord=367475..368569&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 400147..399053
gbrowse_img.php?coord=399053..400147&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 339478..338384
gbrowse_img.php?coord=338384..339478&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 301812..302906
gbrowse_img.php?coord=301812..302906&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

ΔddlA (Keio:JW0372)

deletion

deletion

PMID:16738554

Shigen
CGSC8550[4]

ΔddlA746::kan

PMID:16738554

CGSC:100552


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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

JW0372

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGAAAAACTGCGGGTAGGAAT

Primer 2:CCCATTGTGGTTTTCAATGCGTT

zai-3053::Tn10

Linked marker

CAG18091 = CGSC7336[4]

est. P1 cotransduction: 86% [5]
Synonyms:zaj-3053::Tn10 nnnCAG18091 also carries proC9999 (CGSC).

tsx-247::Tn10

Linked marker

CAG12148 = CGSC7337[4]

est. P1 cotransduction: 28% [5]

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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:EG10213

EchoBASE (EcoliWiki Page)

EchoBASE:EB0209

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0381

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0487

EcoGene (EcoliWiki Page)

EcoGene:EG10213

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z0477

CGSC (EcoliWiki Page)

CGSC:30966

ASAP (EcoliWikiPage)

ASAP:ABE-0001309


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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

DdlA

Synonyms

D-alanine-D-alanine ligase A[1], B0381[3][1], DdlA[3][1]

Product description

D-alanine:D-alanine ligase A, ADP-forming[2]

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:0003824

catalytic activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011761
InterPro:IPR013816
InterPro:IPR013817

F

Seeded from EcoCyc 12.5 [6]

complete

GO:0005524

ATP binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011761
InterPro:IPR013816
InterPro:IPR013817

F

Seeded from EcoCyc 12.5 [6]

complete

GO:0009252

peptidoglycan biosynthetic process

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR000291
InterPro:IPR005905
InterPro:IPR011095
InterPro:IPR011127
SP_KW:KW-0573
HAMAP:MF_00047

P

Seeded from EcoCyc 12.5 [6]

complete

GO:0005618

cell wall

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011127

C

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR005905
SP_KW:KW-0963

C

Seeded from EcoCyc 12.5 [6]

complete

GO:0007047

cell wall organization

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0961

P

Seeded from EcoCyc [7]

complete

GO:0008360

regulation of cell shape

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0133

P

Seeded from EcoCyc [7]

complete

GO:0008716

D-alanine-D-alanine ligase activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000003
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR000291
InterPro:IPR005905
InterPro:IPR011095
InterPro:IPR011127
EC:6.3.2.4
HAMAP:MF_00047

F

Seeded from EcoCyc 12.5 [6]

complete

GO:0016874

ligase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0436

F

Seeded from EcoCyc [7]

complete

GO:0000166

nucleotide binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc [7]

complete

GO:0000287

magnesium ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc [7]

complete

GO:0030145

manganese ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc [7]

complete

GO:0046872

metal ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc [7]

complete

GO:0008716

D-alanine-D-alanine ligase activity

PMID: 1554356

IDA: Inferred from Direct Assay

F

Activity of D-alanyl-D-alanine ligase was determined in a coupled assay using purified DdlA enzyme (Table 1). Enzyme activity inhibition was also shown with addition of known D-alanyl-D-alanine ligase inhibitor, heptyl phosphinate (I) in Figure 3.

required field missing

GO:0008716

D-alanine-D-alanine ligase activity

PMID: 1993184

IDA: Inferred from Direct Assay

F

Table 3 shows the results of kinetic experiments, including Kcat, for assays performed on purified DdlA.

required field missing

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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

apt

PMID:15690043

Experiment(s):EBI-879997

Protein

dnaK

PMID:15690043

Experiment(s):EBI-879997

Protein

proA

PMID:15690043

Experiment(s):EBI-879997

Protein

ddpA

PMID:15690043

Experiment(s):EBI-885024

Protein

ftsI

PMID:15690043

Experiment(s):EBI-885024

Protein

yafC

PMID:15690043

Experiment(s):EBI-885024

Protein

viaA

PMID:15690043

Experiment(s):EBI-885024

Protein

alsK

PMID:15690043

Experiment(s):EBI-885024

Protein

nadE

PMID:16606699

Experiment(s):EBI-1136403

Protein

helD

PMID:16606699

Experiment(s):EBI-1136403

Protein

bglX

PMID:16606699

Experiment(s):EBI-1136403

Protein

speF

PMID:16606699

Experiment(s):EBI-1136403

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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes

cytoplasm

From EcoCyc[8]


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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 

MEKLRVGIVF GGKSAEHEVS LQSAKNIVDA IDKSRFDVVL LGIDKQGQWH VSDASNYLLN
ADDPAHIALR PSATSLAQVP GKHEHQLIDA QNGQPLPTVD VIFPIVHGTL GEDGSLQGML
RVANLPFVGS DVLASAACMD KDVTKRLLRD AGLNIAPFIT LTRANRHNIS FAEVESKLGL
PLFVKPANQG SSVGVSKVTS EEQYAIAVDL AFEFDHKVIV EQGIKGREIE CAVLGNDNPQ
ASTCGEIVLT SDFYAYDTKY IDEDGAKVVV PAAIAPEIND KIRAIAVQAY QTLGCAGMAR
VDVFLTPENE VVINEINTLP GFTNISMYPK LWQASGLGYT DLITRLIELA LERHAADNAL KTTM
Length

364

Mol. Wt

39.315 kDa

pI

5.0 (calculated)

Extinction coefficient

22,920 - 23,420 (calc based on 8 Y, 2 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.

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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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:DALADALALIGA-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0A6J8

PFAM (EcoliWiki Page)

PFAM:PF01820

RefSeq (EcoliWiki Page)

RefSeq:NP_414915


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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)

ddlA

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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=400127..400167&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:b0381 (EcoliWiki Page)

NCBI GEO profiles for ddlA

microarray

GenExpDB:b0381 (EcoliWiki Page)

Summary of data for ddlA 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 (400075..400665) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ19; Well:B1[9]

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Notes

Accessions Related to ddlA Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10213

EchoBASE (EcoliWiki Page)

EchoBASE:EB0209

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0381

EcoGene (EcoliWiki Page)

EcoGene:EG10213


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Notes

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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

Arabidopsis thaliana

  • AT3G08840 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q7XI67 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

DDLA

From SHIGELLACYC

E. coli O157

Z0477

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF01820


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Notes

Links

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References

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  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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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).
  6. ↑ 6.0 6.1 6.2 6.3 6.4 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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