ddlB: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

ddlB

Gene Synonym(s)

ECK0093, b0092, JW0090, ddl[1], ddl

Product Desc.

ddlB[2][3];

Component of D-alanine-D-alanine ligase B[2][3]

D-alanine:D-alanine ligase B, ADP-forming[4]

Product Synonyms(s)

D-alanine:D-alanine ligase[1], B0092[2][1], Ddl[2][1], DdlB[2][1] , ddl, ECK0093, JW0090, b0092

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): mraZW-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ[2]

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

ddlB

Mnemonic

D-alanine D-alanine Ligase B

Synonyms

ECK0093, b0092, JW0090, ddl[1], ddl

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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

2.2 minutes 

MG1655: 102233..103153
<gbrowseImage> name=NC_000913:102233..103153 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 105037..105957
<gbrowseImage> name=NC_012967:105037..105957 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 102232..103152
<gbrowseImage> name=NC_012759:102232..103152 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 102233..103153
<gbrowseImage> name=NC_007779:102233..103153 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 76337..77257
<gbrowseImage> name=NC_010473:76337..77257 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

102236

Edman degradation

PMID:1554356


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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

ddlB(del) (Keio:JW0090)

deletion

deletion

PMID:16738554

Shigen

ddlB1(ts)

temperature sensitive

CGSC:9824


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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

JW0090

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACTGATAAAATCGCGGTCCT

Primer 2:CCGTCCGCCAGTTCCAGAATTCG

6F3

Kohara Phage

Genobase

PMID:3038334

15B8

Kohara Phage

Genobase

PMID:3038334

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 51% [6]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[5]

est. P1 cotransduction: 13% [6]

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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:EG10214

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10214

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000208

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946324

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0210

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000326

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

DdlB

Synonyms

D-alanine:D-alanine ligase[1], B0092[2][1], Ddl[2][1], DdlB[2][1] , ddl, ECK0093, JW0090, b0092

Product description

ddlB[2][3];

Component of D-alanine-D-alanine ligase B[2][3]

D-alanine:D-alanine ligase B, ADP-forming[4]

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:0008716

D-alanine-D-alanine ligase activity

PMID:8756703

IMP: Inferred from Mutant Phenotype

F

complete

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

Tables II and III

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: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

GO:0008716

D-alanine-D-alanine ligase activity

PMID:1554356

IDA: Inferred from Direct Assay

F

Table 1, Fig. 3

complete

GO:0008716

D-alanine-D-alanine ligase activity

PMID:1993184

IDA: Inferred from Direct Assay

F

Tables II and III

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

Subunits of D-alanine-D-alanine ligase B

could be indirect


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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[3]


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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 

MTDKIAVLLG GTSAEREVSL NSGAAVLAGL REGGIDAYPV DPKEVDVTQL KSMGFQKVFI
ALHGRGGEDG TLQGMLELMG LPYTGSGVMA SALSMDKLRS KLLWQGAGLP VAPWVALTRA
EFEKGLSDKQ LAEISALGLP VIVKPSREGS SVGMSKVVAE NALQDALRLA FQHDEEVLIE
KWLSGPEFTV AILGEEILPS IRIQPSGTFY DYEAKYLSDE TQYFCPAGLE ASQEANLQAL
VLKAWTTLGC KGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR
ILELAD
Length

306

Mol. Wt

32.84 kDa

pI

4.6 (calculated)

Extinction coefficient

37,930 - 38,180 (calc based on 7 Y, 5 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:P07862

Domain

3..54

PF01820 D-ala D-ala ligase N-terminus

PMID:19920124

Domain

43..86

PF01820 D-ala D-ala ligase N-terminus

PMID:19920124

Domain

103..303

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=ddlB 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:16128085

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946324

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000326

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P07862

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10214

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10214

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946324

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000208

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0210

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

3.92E+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

E. coli K-12 MG1655

844

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

824

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)

mraZW-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ

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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_000913:102213..102253 source=MG1655 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:b0092 (EcoliWiki Page)

NCBI GEO profiles for ddlB

microarray

GenExpDB:b0092 (EcoliWiki Page)

Summary of data for ddlB 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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Notes

Accessions Related to ddlB Expression

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Database Accession Notes

EcoCyc

EcoCyc:EG10214

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0210

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0092

EcoGene

EcoGene:EG10214

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000208

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000326

Escherichia coli str. K-12 substr. MG1655

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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.

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

DDLB

From SHIGELLACYC

E. coli O157

DDLB

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

Pfam (EcoliWiki Page)

PF01820 D-ala D-ala ligase N-terminus

Superfamily (EcoliWiki Page)

SUPERFAMILY:52440

Panther (EcoliWiki Page)

PTHR23132:SF0

Superfamily (EcoliWiki Page)

SUPERFAMILY:56059

Pfam (EcoliWiki Page)

PF07478 D-ala D-ala ligase C-terminus

EcoCyc

EcoCyc:EG10214

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10214

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000208

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0210

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000326

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 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 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).

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