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Protein

D-alanine--D-alanine ligase B

Gene

ddlB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

GO - Biological processi

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

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:DALADALALIGB-MONOMER.
ECOL316407:JW0090-MONOMER.
MetaCyc:DALADALALIGB-MONOMER.
BRENDAi6.3.2.4. 2026.
UniPathwayiUPA00219.

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

  • cytosol Source: EcoCyc
Complete GO annotation...

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. 304 interactors.
IntActiP07862. 4 interactors.
STRINGi511145.b0092.

Structurei

Secondary structure

1306
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 8Combined sources5
Helixi16 – 32Combined sources17
Beta strandi36 – 40Combined sources5
Turni42 – 44Combined sources3
Helixi47 – 49Combined sources3
Turni50 – 54Combined sources5
Beta strandi57 – 60Combined sources4
Turni65 – 67Combined sources3
Beta strandi68 – 70Combined sources3
Helixi71 – 79Combined sources9
Beta strandi83 – 85Combined sources3
Helixi88 – 95Combined sources8
Helixi97 – 106Combined sources10
Beta strandi114 – 118Combined sources5
Helixi119 – 124Combined sources6
Helixi128 – 136Combined sources9
Beta strandi139 – 147Combined sources9
Turni150 – 153Combined sources4
Beta strandi155 – 157Combined sources3
Helixi160 – 162Combined sources3
Helixi163 – 171Combined sources9
Beta strandi175 – 181Combined sources7
Beta strandi187 – 193Combined sources7
Beta strandi201 – 204Combined sources4
Beta strandi206 – 209Combined sources4
Helixi212 – 216Combined sources5
Beta strandi222 – 226Combined sources5
Helixi231 – 248Combined sources18
Beta strandi252 – 260Combined sources9
Beta strandi266 – 274Combined sources9
Helixi282 – 289Combined sources8
Helixi294 – 303Combined sources10

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...

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
Contains 1 ATP-grasp domain.Curated

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011592.
InParanoidiP07862.
KOiK01921.
OMAiFQHDDEV.
PhylomeDBiP07862.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig. 1 hit.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
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.
[Graphical view]
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

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.
PATRICi32115289. VBIEscCol129921_0096.

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. 304 interactors.
IntActiP07862. 4 interactors.
STRINGi511145.b0092.

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.
PATRICi32115289. VBIEscCol129921_0096.

Organism-specific databases

EchoBASEiEB0210.
EcoGeneiEG10214. ddlB.

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011592.
InParanoidiP07862.
KOiK01921.
OMAiFQHDDEV.
PhylomeDBiP07862.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciEcoCyc:DALADALALIGB-MONOMER.
ECOL316407:JW0090-MONOMER.
MetaCyc:DALADALALIGB-MONOMER.
BRENDAi6.3.2.4. 2026.

Miscellaneous databases

EvolutionaryTraceiP07862.
PROiP07862.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig. 1 hit.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
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.
[Graphical view]
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDDLB_ECOLI
AccessioniPrimary (citable) accession number: P07862
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 160 of the entry and version 3 of the sequence. [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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.