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B3DTT9

- DDL_BIFLD

UniProt

B3DTT9 - DDL_BIFLD

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Bifidobacterium longum (strain DJO10A)
Status
Reviewed - 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

Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi

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

  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. cell wall organization Source: UniProtKB-KW
  2. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  3. 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 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 lineageiBacteriaActinobacteriaActinobacteridaeBifidobacterialesBifidobacteriaceaeBifidobacterium
ProteomesiUP000002419: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-HAMAP
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

Interactioni

Protein-protein interaction databases

STRINGi205913.BLD_1112.

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.
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 [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:
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: October 29, 2014
This is version 46 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