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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Frankia symbiont subsp. Datisca glomerata
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Cell wall formation.UniRule annotationSAAS annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi329 – 3291Magnesium or manganese 1UniRule annotation
Metal bindingi342 – 3421Magnesium or manganese 1UniRule annotation
Metal bindingi342 – 3421Magnesium or manganese 2UniRule annotation
Metal bindingi344 – 3441Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi196 – 25055ATPUniRule 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

LigaseUniRule annotationSAAS annotation

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradationUniRule annotationSAAS annotation, Peptidoglycan synthesisUniRule annotationSAAS annotation

Keywords - Ligandi

ATP-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotationSAAS annotation, ManganeseUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding

Enzyme and pathway databases

BioCyciFSYM656024:GHLT-3728-MONOMER.
UniPathwayiUPA00219.
UPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligaseUniRule annotationSAAS annotation (EC:6.3.2.4UniRule annotationSAAS annotation)
Alternative name(s):
D-Ala-D-Ala ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:FsymDg_3700Imported
OrganismiFrankia symbiont subsp. Datisca glomerataImported
Taxonomic identifieri656024 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesFrankineaeFrankiaceaeFrankia
ProteomesiUP000001549: Chromosome

Subcellular locationi

Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Structurei

3D structure databases

ProteinModelPortaliF8AVM7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini168 – 375208ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

KOiK01921.
OMAiWFPILHG.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
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.

F8AVM7-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MPGSPPRRTR IAVLYGGRST EHAISCVSAG SVLRALDRRR YDVVAVGITP
60 70 80 90 100
DGRWVLGPDD PDALAVRDGV LPAVDATARP VVLPGDPTVG GLIALDGVAV
110 120 130 140 150
SAGPGPADRG TADLGAVGLG AVDVVFPLLH GPFGEDGTVQ GLLEMAAVPY
160 170 180 190 200
VGSGVFASAA AMDKQYMKIL LAAAGLDIGP YTVLRAGQAL SGDDRERLGL
210 220 230 240 250
PVFVKPARGG SSIGISRVDA WDDLATALKA ARAVDPKVLV EAAVVGREVE
260 270 280 290 300
CGVLGSLDGG GPEASLPAEV TVASSAGSAG FYDFEAKYLS DAARFDVPAN
310 320 330 340 350
LPAEVTAAVR QIAVRAFVAL DCAGLARVDV FVRPDGSVVV NEVNTMPGFT
360 370 380
PTSMFPRMWA ATGLDYPRLV DRLVALATRH GTGLH
Length:385
Mass (Da):39,480
Last modified:September 21, 2011 - v1
Checksum:iF8A2F8921914D4D7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002801 Genomic DNA. Translation: AEH10977.1.
RefSeqiWP_013874858.1. NC_015656.1.
YP_004584898.1. NC_015656.1.

Genome annotation databases

EnsemblBacteriaiAEH10977; AEH10977; FsymDg_3700.
GeneIDi10784385.
KEGGifsy:FsymDg_3700.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002801 Genomic DNA. Translation: AEH10977.1.
RefSeqiWP_013874858.1. NC_015656.1.
YP_004584898.1. NC_015656.1.

3D structure databases

ProteinModelPortaliF8AVM7.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAEH10977; AEH10977; FsymDg_3700.
GeneIDi10784385.
KEGGifsy:FsymDg_3700.

Phylogenomic databases

KOiK01921.
OMAiWFPILHG.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciFSYM656024:GHLT-3728-MONOMER.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
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]
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of chromosome of Frankia symbiont of Datisca glomerata."
    US DOE Joint Genome Institute
    Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S., Peters L., Mikhailova N., Chertkov O., Teshima H., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Ivanova N., Pagani I., Berry A.
    , Pawlowski K., Persson T., Vanden Heuvel B., Benson D., Woyke T.
    Submitted (MAY-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 4085684Imported.

Entry informationi

Entry nameiF8AVM7_FRADG
AccessioniPrimary (citable) accession number: F8AVM7
Entry historyi
Integrated into UniProtKB/TrEMBL: September 21, 2011
Last sequence update: September 21, 2011
Last modified: February 4, 2015
This is version 27 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

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.