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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Bifidobacterium longum (strain DJO10A)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Cell wall formation.UniRule annotation

Catalytic activityi

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

Cofactori

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

Pathway: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotation
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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi345 – 3451Magnesium or manganese 1UniRule annotation
Metal bindingi358 – 3581Magnesium or manganese 1UniRule annotation
Metal bindingi358 – 3581Magnesium or manganese 2UniRule annotation
Metal bindingi360 – 3601Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi204 – 26663ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

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

BioCyciBLON205913:GJB4-1148-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligaseUniRule annotation (EC:6.3.2.4UniRule annotation)
Alternative name(s):
D-Ala-D-Ala ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:BLD_1112
OrganismiBifidobacterium longum (strain DJO10A)
Taxonomic identifieri205913 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaBifidobacterialesBifidobacteriaceaeBifidobacterium
ProteomesiUP000002419 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 395395D-alanine--D-alanine ligasePRO_1000202194Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliB3DTT9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini172 – 391220ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.UniRule annotation
Contains 1 ATP-grasp domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 2 hits.
HAMAPiMF_00047. Dala_Dala_lig.
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]
PANTHERiPTHR23132. PTHR23132. 1 hit.
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 2 hits.
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.

B3DTT9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKKRVVVLY GGRADEHSIS CISTAGVLGA MDTERFEPIP VGITKDGKWI
60 70 80 90 100
INGEDPRGWN LDGGELPTVK ITPESRPVML DPSRGQDGFF IGEPSHINSA
110 120 130 140 150
DSGFGTSFVS MSDPEMHHVL TSLGHVDAVL PVLHGPYGED GTVQGLLEMM
160 170 180 190 200
GVPYVGCGVF ASAACMDKHY TKVVLDAAGI PTAPGVTVDA RNFTAADVLA
210 220 230 240 250
EIEDAGLTYP LFVKPSRAGS SFGVTKVEKA DDRETQQDRL AAAIATAGEH
260 270 280 290 300
DWKVLVEQGI DGREIECAVL CPKAGDEPEA SWPGEIVLDH QNDDQFYDFD
310 320 330 340 350
SKYMDASASH VEVPANLPVS VLEDVRDVAR RAFKAVDGVG LSRVDTFVTP
360 370 380 390
DGTVMVNEIN TMPGFTPISM YPKAWDATGV SYTELITRLI EGVLR
Length:395
Mass (Da):42,397
Last modified:July 22, 2008 - v1
Checksum:iD062392B3C4665CF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000605 Genomic DNA. Translation: ACD98558.1.
RefSeqiWP_010081636.1. NZ_AABM02000027.1.
YP_001955056.1. NC_010816.1.

Genome annotation databases

EnsemblBacteriaiACD98558; ACD98558; BLD_1112.
KEGGiblj:BLD_1112.
PATRICi21115190. VBIBifLon134794_1127.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000605 Genomic DNA. Translation: ACD98558.1.
RefSeqiWP_010081636.1. NZ_AABM02000027.1.
YP_001955056.1. NC_010816.1.

3D structure databases

ProteinModelPortaliB3DTT9.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACD98558; ACD98558; BLD_1112.
KEGGiblj:BLD_1112.
PATRICi21115190. VBIBifLon134794_1127.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciBLON205913:GJB4-1148-MONOMER.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 2 hits.
HAMAPiMF_00047. Dala_Dala_lig.
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]
PANTHERiPTHR23132. PTHR23132. 1 hit.
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 2 hits.
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...

Publicationsi

  1. "Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth."
    Lee J.H., Karamychev V.N., Kozyavkin S.A., Mills D., Pavlov A.R., Pavlova N.V., Polouchine N.N., Richardson P.M., Shakhova V.V., Slesarev A.I., Weimer B., O'Sullivan D.J.
    BMC Genomics 9:247-247(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DJO10A.

Entry informationi

Entry nameiDDL_BIFLD
AccessioniPrimary (citable) accession number: B3DTT9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: July 22, 2008
Last modified: June 24, 2015
This is version 51 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.