ddlA: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

ddlA

Gene Synonym(s)

ECK0376, b0381, JW0372[1], JW0372

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] , ECK0376, JW0372, b0381

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ddlA[3]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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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], JW0372

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Notes

Location(s) and DNA Sequence

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<protect> 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

8.6 minutes 

MG1655: 400147..399053
<gbrowseImage> name=NC_000913:399053..400147 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 368569..367475
<gbrowseImage> name=NC_012967:367475..368569 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 301812..302906
<gbrowseImage> name=NC_012759:301812..302906 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 400147..399053
<gbrowseImage> name=NC_007779:399053..400147 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 339478..338384
<gbrowseImage> name=NC_010473:338384..339478 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
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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

ddlA(del) (Keio:JW0372)

deletion

deletion

PMID:16738554

Shigen

CGSC8550[4]

ddlA746(del)::kan

PMID:16738554

CGSC:100552


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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

JW0372

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGAAAAACTGCGGGTAGGAAT

Primer 2:CCCATTGTGGTTTTCAATGCGTT

6E2

Kohara Phage

Genobase

PMID:3038334

1A10

Kohara Phage

Genobase

PMID:3038334

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.

Database Accession Notes

EcoCyc

EcoCyc:EG10213

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10213

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000207

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945313

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0209

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001309

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

DdlA

Synonyms

D-alanine-D-alanine ligase A[1], B0381[3][1], DdlA[3][1] , ECK0376, JW0372, b0381

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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<protect> 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:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

PMID:1993184

IDA: Inferred from Direct Assay

F

Table II and Table III.

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011761

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013816

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013817

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016185

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011761

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013816

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013817

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016185

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005618

cell wall

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011127

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00047

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005905

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0007047

cellular cell wall organization

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0961

P

Seeded from EcoCyc (v14.0)

complete

GO:0008360

regulation of cell shape

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0133

P

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00047

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000291

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005905

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011095

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011127

F

Seeded from EcoCyc (v14.0)

complete

GO:0008716

D-alanine-D-alanine ligase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:6.3.2.4

F

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00047

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000291

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005905

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011095

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011127

P

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0573

P

Seeded from EcoCyc (v14.0)

complete

GO:0016874

ligase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0436

F

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

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

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

Protein

proA

PMID:19402753

MALDI(Z-score):24.143708

Protein

yafC

PMID:19402753

LCMS(ID Probability):99.0

Protein

ddpA

PMID:19402753

LCMS(ID Probability):99.0

Protein

viaA

PMID:19402753

LCMS(ID Probability):99.0

Protein

ftsI

PMID:19402753

LCMS(ID Probability):99.0

Protein

apt

PMID:19402753

MALDI(Z-score):18.893511

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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

cytoplasm

From EcoCyc[6]


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Notes

Structure and Physical Properties

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<protect> 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 

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.

Type Residues Description Notes References

Domain

4..130

PF01820 D-ala D-ala ligase N-terminus

PMID:19920124

Domain

147..348

PF07478 D-ala D-ala ligase C-terminus

PMID:19920124

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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=ddlA taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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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:16128366

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945313

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001309

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A6J8

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10213

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10213

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945313

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000207

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0209

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

9.39E+02

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

25.582+/-0.144

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.072669104

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

4072

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

296

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

3589

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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<protect>

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

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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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<protect><gbrowseImage> name=NC_000913:400127..400167 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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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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<protect> 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: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 Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (400075..400665) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ19; Well:B1[7]

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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.

Database Accession Notes

EcoCyc

EcoCyc:EG10213

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0209

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0381

EcoGene

EcoGene:EG10213

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000207

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001309

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

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

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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)

PF01820 D-ala D-ala ligase N-terminus

Superfamily (EcoliWiki Page)

SUPERFAMILY:52440

Superfamily (EcoliWiki Page)

SUPERFAMILY:56059

Pfam (EcoliWiki Page)

PF07478 D-ala D-ala ligase C-terminus

EcoCyc

EcoCyc:EG10213

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10213

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000207

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0209

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001309

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. ↑ 1.0 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. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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