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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)
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

Pathwayi: 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)DescriptionActionsGraphical viewLength
Metal bindingi328Magnesium or manganese 1UniRule annotation1
Metal bindingi341Magnesium or manganese 1UniRule annotation1
Metal bindingi341Magnesium or manganese 2UniRule annotation1
Metal bindingi343Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi189 – 247ATPUniRule annotationAdd BLAST59

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

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:BAD_0186
OrganismiBifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)
Taxonomic identifieri367928 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaBifidobacterialesBifidobacteriaceaeBifidobacterium
Proteomesi
  • UP000008702 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000304321 – 378D-alanine--D-alanine ligaseAdd BLAST378

Interactioni

Protein-protein interaction databases

STRINGi367928.BAD_0186.

Structurei

3D structure databases

ProteinModelPortaliA0ZZT4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini149 – 374ATP-graspUniRule annotationAdd BLAST226

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011593.
KOiK01921.
OMAiMDKIAMK.
OrthoDBiPOG091H06GK.

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.

A0ZZT4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKKRIVVMY GGKADEHSIS CISAASALRA LDTDKFEAIP VGITKDGKWI
60 70 80 90 100
VNGENPLGWS LDEGLPTVEK TPGAKDVVLE VALGQDGFFA REDDGTMTPF
110 120 130 140 150
GHVDAVFPVL HGPYGEDGTI QGLFEMMGVP YVGCGVLASA ACMDKHYTKV
160 170 180 190 200
LLAAAGIPVA PGITLDARSF DKASEFKTDA DAIMAQVSEA GLQYPLFVKP
210 220 230 240 250
SRAGSSFGVT KVEHEGDAAE LAAAVYEASR HDWRILVEQG IDAREIECAV
260 270 280 290 300
LCPKAGEAPQ ASWPGEIVLD KRAEGDDQFY DFDSKYMDAA ASHVEVPANL
310 320 330 340 350
PEETLNLVRE TAKKAFVAVD GAGLSRVDTF VTKDGKVMVN EINTMPGFTS
360 370
ISMYPKAWEA TGVRYTDLIT KLIEGVLR
Length:378
Mass (Da):40,528
Last modified:January 23, 2007 - v1
Checksum:iBBDC4977384B8C56
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009256 Genomic DNA. Translation: BAF38967.1.
RefSeqiWP_011742720.1. NC_008618.1.

Genome annotation databases

EnsemblBacteriaiBAF38967; BAF38967; BAD_0186.
GeneIDi4556245.
KEGGibad:BAD_0186.
PATRICi21099595. VBIBifAdo27973_0199.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009256 Genomic DNA. Translation: BAF38967.1.
RefSeqiWP_011742720.1. NC_008618.1.

3D structure databases

ProteinModelPortaliA0ZZT4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi367928.BAD_0186.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAF38967; BAF38967; BAD_0186.
GeneIDi4556245.
KEGGibad:BAD_0186.
PATRICi21099595. VBIBifAdo27973_0199.

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011593.
KOiK01921.
OMAiMDKIAMK.
OrthoDBiPOG091H06GK.

Enzyme and pathway databases

UniPathwayiUPA00219.

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 nameiDDL_BIFAA
AccessioniPrimary (citable) accession number: A0ZZT4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 68 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, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.