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Protein

D-alanine--D-alanine ligase B

Gene

ddlB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Cell wall formation.

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei151
Active sitei1501
Metal bindingi257Magnesium or manganese 1By similarity1
Metal bindingi270Magnesium or manganese 1By similarity1
Metal bindingi270Magnesium or manganese 2By similarity1
Metal bindingi272Magnesium or manganese 2By similarity1
Active sitei2811

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi134 – 189ATPBy similarityAdd BLAST56

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • D-alanine-D-alanine ligase activity Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • cell wall organization Source: UniProtKB-KW
  • peptidoglycan biosynthetic process Source: EcoCyc
  • regulation of cell shape Source: UniProtKB-KW

Keywordsi

Molecular functionLigase
Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis
LigandATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:DALADALALIGB-MONOMER
MetaCyc:DALADALALIGB-MONOMER
BRENDAi6.3.2.4 2026
UniPathwayi
UPA00219

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligase B (EC:6.3.2.4)
Alternative name(s):
D-Ala-D-Ala ligase B
D-alanylalanine synthetase B
Gene namesi
Name:ddlB
Synonyms:ddl
Ordered Locus Names:b0092, JW0090
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10214 ddlB

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL1956

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved
ChainiPRO_00001778182 – 306D-alanine--D-alanine ligase BAdd BLAST305

Proteomic databases

EPDiP07862
PaxDbiP07862
PRIDEiP07862

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

BioGridi4261114, 306 interactors
IntActiP07862, 4 interactors
STRINGi316385.ECDH10B_0074

Structurei

Secondary structure

1306
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP07862
SMRiP07862
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07862

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini101 – 303ATP-graspAdd BLAST203

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.Curated

Phylogenomic databases

eggNOGiENOG4105CPF Bacteria
COG1181 LUCA
HOGENOMiHOG000011592
InParanoidiP07862
KOiK01921
OMAiYETKYTE
PhylomeDBiP07862

Family and domain databases

Gene3Di3.30.1490.20, 1 hit
HAMAPiMF_00047 Dala_Dala_lig, 1 hit
InterProiView protein in InterPro
IPR011761 ATP-grasp
IPR013815 ATP_grasp_subdomain_1
IPR000291 D-Ala_lig_Van_CS
IPR005905 D_ala_D_ala
IPR011095 Dala_Dala_lig_C
IPR011127 Dala_Dala_lig_N
IPR016185 PreATP-grasp_dom_sf
PfamiView protein in Pfam
PF07478 Dala_Dala_lig_C, 1 hit
PF01820 Dala_Dala_lig_N, 1 hit
PIRSFiPIRSF039102 Ddl/VanB, 1 hit
SUPFAMiSSF52440 SSF52440, 1 hit
TIGRFAMsiTIGR01205 D_ala_D_alaTIGR, 1 hit
PROSITEiView protein in PROSITE
PS50975 ATP_GRASP, 1 hit
PS00843 DALA_DALA_LIGASE_1, 1 hit
PS00844 DALA_DALA_LIGASE_2, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P07862-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTDKIAVLLG GTSAEREVSL NSGAAVLAGL REGGIDAYPV DPKEVDVTQL
60 70 80 90 100
KSMGFQKVFI ALHGRGGEDG TLQGMLELMG LPYTGSGVMA SALSMDKLRS
110 120 130 140 150
KLLWQGAGLP VAPWVALTRA EFEKGLSDKQ LAEISALGLP VIVKPSREGS
160 170 180 190 200
SVGMSKVVAE NALQDALRLA FQHDEEVLIE KWLSGPEFTV AILGEEILPS
210 220 230 240 250
IRIQPSGTFY DYEAKYLSDE TQYFCPAGLE ASQEANLQAL VLKAWTTLGC
260 270 280 290 300
KGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR

ILELAD
Length:306
Mass (Da):32,840
Last modified:January 23, 2007 - v3
Checksum:iF2D401C323A04471
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M14029 Genomic DNA Translation: AAA23672.1
K02668 Genomic DNA Translation: AAA23815.1
X52644 Genomic DNA Translation: CAA36869.1
X55034 Genomic DNA Translation: CAA38869.1
U00096 Genomic DNA Translation: AAC73203.1
AP009048 Genomic DNA Translation: BAB96660.1
PIRiA30289 CEECDL
RefSeqiNP_414634.1, NC_000913.3
WP_000130056.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC73203; AAC73203; b0092
BAB96660; BAB96660; BAB96660
GeneIDi946324
KEGGiecj:JW0090
eco:b0092
PATRICifig|1411691.4.peg.2188

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M14029 Genomic DNA Translation: AAA23672.1
K02668 Genomic DNA Translation: AAA23815.1
X52644 Genomic DNA Translation: CAA36869.1
X55034 Genomic DNA Translation: CAA38869.1
U00096 Genomic DNA Translation: AAC73203.1
AP009048 Genomic DNA Translation: BAB96660.1
PIRiA30289 CEECDL
RefSeqiNP_414634.1, NC_000913.3
WP_000130056.1, NZ_LN832404.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IOVX-ray2.20A1-306[»]
1IOWX-ray1.90A1-306[»]
2DLNX-ray2.30A1-306[»]
4C5AX-ray1.65A/B1-306[»]
4C5BX-ray1.50A/B1-306[»]
4C5CX-ray1.40A/B1-306[»]
ProteinModelPortaliP07862
SMRiP07862
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261114, 306 interactors
IntActiP07862, 4 interactors
STRINGi316385.ECDH10B_0074

Chemistry databases

ChEMBLiCHEMBL1956

Proteomic databases

EPDiP07862
PaxDbiP07862
PRIDEiP07862

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73203; AAC73203; b0092
BAB96660; BAB96660; BAB96660
GeneIDi946324
KEGGiecj:JW0090
eco:b0092
PATRICifig|1411691.4.peg.2188

Organism-specific databases

EchoBASEiEB0210
EcoGeneiEG10214 ddlB

Phylogenomic databases

eggNOGiENOG4105CPF Bacteria
COG1181 LUCA
HOGENOMiHOG000011592
InParanoidiP07862
KOiK01921
OMAiYETKYTE
PhylomeDBiP07862

Enzyme and pathway databases

UniPathwayi
UPA00219

BioCyciEcoCyc:DALADALALIGB-MONOMER
MetaCyc:DALADALALIGB-MONOMER
BRENDAi6.3.2.4 2026

Miscellaneous databases

EvolutionaryTraceiP07862
PROiPR:P07862

Family and domain databases

Gene3Di3.30.1490.20, 1 hit
HAMAPiMF_00047 Dala_Dala_lig, 1 hit
InterProiView protein in InterPro
IPR011761 ATP-grasp
IPR013815 ATP_grasp_subdomain_1
IPR000291 D-Ala_lig_Van_CS
IPR005905 D_ala_D_ala
IPR011095 Dala_Dala_lig_C
IPR011127 Dala_Dala_lig_N
IPR016185 PreATP-grasp_dom_sf
PfamiView protein in Pfam
PF07478 Dala_Dala_lig_C, 1 hit
PF01820 Dala_Dala_lig_N, 1 hit
PIRSFiPIRSF039102 Ddl/VanB, 1 hit
SUPFAMiSSF52440 SSF52440, 1 hit
TIGRFAMsiTIGR01205 D_ala_D_alaTIGR, 1 hit
PROSITEiView protein in PROSITE
PS50975 ATP_GRASP, 1 hit
PS00843 DALA_DALA_LIGASE_1, 1 hit
PS00844 DALA_DALA_LIGASE_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDDLB_ECOLI
AccessioniPrimary (citable) accession number: P07862
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: January 23, 2007
Last modified: March 28, 2018
This is version 171 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  4. PATHWAY comments
    Index of metabolic and biosynthesis pathways
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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