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B3DTT9

- DDL_BIFLD

UniProt

B3DTT9 - DDL_BIFLD

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Protein

D-alanine--D-alanine ligase

Gene
ddl, BLD_1112
Organism
Bifidobacterium longum (strain DJO10A)
Status
Reviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

Functioni

Cell wall formation By similarity.UniRule annotation

Catalytic activityi

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

Cofactori

Binds 2 magnesium or manganese ions per subunit By similarity.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi345 – 3451Magnesium or manganese 1 By similarity
Metal bindingi358 – 3581Magnesium or manganese 1 By similarity
Metal bindingi358 – 3581Magnesium or manganese 2 By similarity
Metal bindingi360 – 3601Magnesium or manganese 2 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi204 – 26663ATP By similarityAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. D-alanine-D-alanine ligase activity Source: UniProtKB-HAMAP
  3. magnesium ion binding Source: UniProtKB-HAMAP
  4. manganese ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  2. 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

BioCyciBLON205913:GJB4-1148-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligase (EC:6.3.2.4)
Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase
Gene namesi
Name:ddl
Ordered Locus Names:BLD_1112
OrganismiBifidobacterium longum (strain DJO10A)
Taxonomic identifieri205913 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeBifidobacterialesBifidobacteriaceaeBifidobacterium
ProteomesiUP000002419: Chromosome

Subcellular locationi

Cytoplasm By similarity UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 395395D-alanine--D-alanine ligaseUniRule annotationPRO_1000202194Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi205913.BLD_1112.

Structurei

3D structure databases

ProteinModelPortaliB3DTT9.

Family & Domainsi

Domains and Repeats

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

Sequence similaritiesi

Contains 1 ATP-grasp domain.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiQIDVIFP.
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]
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

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MAKKRVVVLY GGRADEHSIS CISTAGVLGA MDTERFEPIP VGITKDGKWI    50
INGEDPRGWN LDGGELPTVK ITPESRPVML DPSRGQDGFF IGEPSHINSA 100
DSGFGTSFVS MSDPEMHHVL TSLGHVDAVL PVLHGPYGED GTVQGLLEMM 150
GVPYVGCGVF ASAACMDKHY TKVVLDAAGI PTAPGVTVDA RNFTAADVLA 200
EIEDAGLTYP LFVKPSRAGS SFGVTKVEKA DDRETQQDRL AAAIATAGEH 250
DWKVLVEQGI DGREIECAVL CPKAGDEPEA SWPGEIVLDH QNDDQFYDFD 300
SKYMDASASH VEVPANLPVS VLEDVRDVAR RAFKAVDGVG LSRVDTFVTP 350
DGTVMVNEIN TMPGFTPISM YPKAWDATGV SYTELITRLI EGVLR 395
Length:395
Mass (Da):42,397
Last modified:July 22, 2008 - v1
Checksum:iD062392B3C4665CF
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000605 Genomic DNA. Translation: ACD98558.1.
RefSeqiYP_001955056.1. NC_010816.1.

Genome annotation databases

EnsemblBacteriaiACD98558; ACD98558; BLD_1112.
GeneIDi6364071.
KEGGiblj:BLD_1112.
PATRICi21115190. VBIBifLon134794_1127.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000605 Genomic DNA. Translation: ACD98558.1 .
RefSeqi YP_001955056.1. NC_010816.1.

3D structure databases

ProteinModelPortali B3DTT9.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 205913.BLD_1112.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACD98558 ; ACD98558 ; BLD_1112 .
GeneIDi 6364071.
KEGGi blj:BLD_1112.
PATRICi 21115190. VBIBifLon134794_1127.

Phylogenomic databases

eggNOGi COG1181.
HOGENOMi HOG000011593.
KOi K01921.
OMAi QIDVIFP.
OrthoDBi EOG64BQ73.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci BLON205913:GJB4-1148-MONOMER.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 2 hits.
HAMAPi MF_00047. Dala_Dala_lig.
InterProi IPR011761. 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 ]
PANTHERi PTHR23132. PTHR23132. 1 hit.
Pfami PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 2 hits.
TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: May 14, 2014
This is version 44 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

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