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Gene ddlB from Escherichia coli str. K-12 substr. MG1655: D-alanine:D-alanine ligase
Member of NCBI Protein Clusters PRK01372(See COMBREX Page ) (See NCBI page)
NCBI Entrez GeneID 946324
UniProtKB accession
RefSeq Protein accession NP_414634.1 (PROVISIONAL)
Gene Symbol(s)
  • symbol: ddlB
  • locus tag: b0092
  • aliases: ECK0093, JW0090, ddl
Organism Escherichia coli str. K-12 substr. MG1655 (NCBI TaxID: 511145)
Other Cross References:
  • S
    Structure(s) available in PDB: 1IOV 1IOW 2DLN
  • C
    Gene cloned by a participant in the Protein Structure Initiative (PSI): TargetDB. (To obtain a clone, please contact the PSI:Biology-Materials Repository.)
  • U
    Protein purified by a participant in the Protein Structure Initiative (PSI): TargetDB. (If you are interested in collaborating to obtain the protein, please contact the Northeast Structural Genomics consortium).
  • Protein described in EcoCyc: EG10214
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Contribute a predicted function for this gene (free text, GO terms, or EC number) (info). Be sure to check the list of current predicted functions in the section immediately below beforehand.
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Post a comment about this gene to appear on this page (info).
Source Predicted function(s)
NCBI Protein Cluster Prediction D-alanine--D-alanine ligase
Source References Functional description
GSDB
[PMID: 1554356]
[PMID: 7939684]
[PMID: 9054558]
D-alanine--D-alanine ligase B (source organism: Escherichia coli (strain K12).; strain specific ID: )
Functional Status greenGreen (experimental evidence, uncurated)
EC number
GO terms
  • MF: GO:0046872 : metal ion binding : IEA
  • CC: GO:0005618 : cell wall : IEA
  • MF: GO:0003824 : catalytic activity : IEA
  • MF: GO:0005524 : ATP binding : IEA
  • MF: GO:0016874 : ligase activity : IEA
  • MF: GO:0030145 : manganese ion binding : IEA
  • MF: GO:0008716 : D-alanine-D-alanine ligase activity : IEA
  • BP: GO:0009252 : peptidoglycan biosynthetic process : IEA
  • BP: GO:0008360 : regulation of cell shape : IEA
  • MF: GO:0000166 : nucleotide binding : IEA
  • MF: GO:0000287 : magnesium ion binding : IEA
  • CC: GO:0005737 : cytoplasm : IEA
  • BP: GO:0007047 : cellular cell wall organization : IEA
  • MF: GO:0008716 : D-alanine-D-alanine ligase activity : IDA
Domain Structure from CDD
  • ddl: D-alanine--D-alanine ligase; Reviewed
  • Dala_Dala_lig_N: D-ala D-ala ligase N-terminus. This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme EC.... (More)
  • CPSase_L_D2: Carbamoyl-phosphate synthase L chain, ATP binding domain. Members of this protein family contain a region of homology to.... (More)

See domain structure on NCBI Conserved Domain Database
Domain structure from Pfam
See domain structure on Pfam Database
Based on the function of this gene, COMBREX predictions were made to the following related genes (mouse over gene symbol for details) [Download ]
ddl (49) , ddlB
The table at right lists genes that may be "functionally linked to" (i.e., participate in a common biological process, or form a protein complex with) the subject gene of this page, as determined by two sequence-independent methods, including phylogenetic profiling and operon membership (determined by OperonDB). (Info.) These linkages may also be viewed graphically using the program VisANT, by clicking on the headers of the table. Note: VisANT requires Java. To install the latest version of Java, see www.java.com
 gene neighbourhoods
phylogenetic profile
domain fusion
ftsQmembrane anchored protein involved in growth of wa
 
  
murCUDP-N-acetylmuramate:L-alanine ligase
 
 
 
cpxRDNA-binding response regulator in two-component re 
 
 
radADNA repair protein 
 
 
murAUDP-N-acetylglucosamine 1-carboxyvinyltransferase 
 
 
rsuA16S rRNA U516 pseudouridine synthase 
 
 
mrdBcell wall shape-determining protein 
 
 
rstAmulticopy supressor of yjeE, yeaZ or ygjD deletion 
 
 
cusRDNA-binding response regulator in two-component re 
 
 
ftsItranspeptidase involved in septal peptidoglycan sy 
 
 
mfdtranscription-repair coupling factor 
 
 
baeRDNA-binding response regulator in two-component re 
 
 
ftsWintegral membrane protein involved in stabilizing  
 
 
rluE23S rRNA U2457 pseudouridine synthase 
 
 
qseBquorum sensing DNA-binding response regulator in t 
 
 
kdpEDNA-binding response regulator in two-component re 
 
 
mplUDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-mes 
 
 
mrdAtranspeptidase involved in peptidoglycan synthesis 
 
 
murGN-acetylglucosaminyl transferase 
 
 
phoBDNA-binding response regulator in two-component re 
 
 
ompRDNA-binding response regulator in two-component re 
 
 
polAfused DNA polymerase I 5'->3' polymerase/3'->5' ex 
 
 
rluB23S rRNA pseudouridylate synthase 
 
 
clpXATPase and specificity subunit of ClpX-ClpP ATP-de 
 
 
basRDNA-binding response regulator in two-component re 
 
 
recGATP-dependent DNA helicase 
 
 
torRDNA-binding response regulator in two-component re 
 
 
rluF23S rRNA U2604 pseudouridine synthase 
 
 
yedWpredicted DNA-binding response regulator in two-co 
 
 
murBUDP-N-acetylenolpyruvoylglucosamine reductase, FAD 
 
 
priAPrimosome factor n' (replication factor Y) 
 
 
clpPproteolytic subunit of ClpA-ClpP and ClpX-ClpP ATP 
 
 
phoPDNA-binding response regulator in two-component re 
 
 
arcADNA-binding response regulator in two-component re 
 
 
creBDNA-binding response regulator in two-component re 
 
 
Metabolic Annotation from Palsson Lab

Metabolic Reaction: ALAALAr

Name
D-alanine-D-alanine ligase (reversible)
Formula
2 ala-DASH-D[c] + atp[c] <=> adp[c] + alaala[c] + h[c] + pi[c]
Pathway
Cell Envelope Biosynthesis
Other Genes

Source: Ported to COMBREX by Segre's Lab
KEGG
Phenotype Description Expression
Class
Reference(s)
Ampicillin sensitivity Knockout confers increased sensitivity to ampicillin Knock out
PMID: 20065048
Candidate essential gene Identified as essential gene in one or more studies (see references) Knock out
PMID: 13129938
(candidate essential)
PMID: 17700540
(not essential)
PMID: 20029369
(not essential)
Cefoxitin sensitivity Knockout confers increased sensitivity to cefoxitin Knock out
PMID: 20065048
Cephradine sensitivity Knockout confers increased sensitivity to cephradine Knock out
PMID: 20065048
Gentamicin sensitivity Knockout confers increased sensitivity to gentamicin Knock out
PMID: 20065048
Neomycin sensitivity Knockout confers increased sensitivity to neomycin Knock out
PMID: 20065048
Nitrofurantoin sensitivity Knockout confers increased sensitivity to nitrofurantoin Knock out
PMID: 20065048
Streptomycin sensitivity Knockout confers increased sensitivity to streptomycin Knock out
PMID: 20065048
Tobramycin sensitivity Knockout confers increased sensitivity to tobramycin Knock out
PMID: 20065048
Triclosan sensitivity Knockout confers increased sensitivity to triclosan Knock out
PMID: 20065048