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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Stackebrandtia nassauensis (strain DSM 44728 / NRRL B-16338 / NBRC 102104 / LLR-40K-21)
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 annotationSAAS annotation, Mn2+UniRule annotationSAAS annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi308 – 3081Magnesium or manganese 1UniRule annotation
Metal bindingi321 – 3211Magnesium or manganese 1UniRule annotation
Metal bindingi321 – 3211Magnesium or manganese 2UniRule annotation
Metal bindingi323 – 3231Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi176 – 23156ATPUniRule 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

BioCyciSNAS446470:GHHC-5022-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:Snas_4988Imported
OrganismiStackebrandtia nassauensis (strain DSM 44728 / NRRL B-16338 / NBRC 102104 / LLR-40K-21)Imported
Taxonomic identifieri446470 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesGlycomycineaeGlycomycetaceaeStackebrandtia
ProteomesiUP000000844 Componenti: 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

ProteinModelPortaliD3Q9S9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini149 – 354206ATP-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

HOGENOMiHOG000011593.
KOiK01921.
OMAiWENSTEN.

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]
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.

D3Q9S9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKTKVAVVL GGRSVEHPVS CASAAGVIAA LDPEQYEVVA VGITQAGQWL
60 70 80 90 100
SVDARSAKLA LGDGNVPEIS ADSGQHVVLA ADPTMKDVAI TDAAGGARVL
110 120 130 140 150
SDVDVVFPVL HGAYGEDGTI QGLLEMADVP YVGSNVLSSA ASMDKDFMKR
160 170 180 190 200
LLKAEGIPVG DYVVLKRDQT LSEAEKQRLG LPVFVKPSRA GSSLGISKVT
210 220 230 240 250
DWDDLDKAIA TARAVDPKVL VEAAFTGVRE LECGVLERED GGAPDTTPPF
260 270 280 290 300
EVLIAGTEGW FDFEAKYLAS GSPYDLAPDL PEGTAERIRE LAARVFTVMD
310 320 330 340 350
CSDLARVDFF LASDGTVYVN EINTMPGLTP GSGVPVAWAN AGVDYPELVA
360
RLVRLAANRG TGLR
Length:364
Mass (Da):38,257
Last modified:April 19, 2010 - v1
Checksum:iEBC995B5C7248003
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001778 Genomic DNA. Translation: ADD44625.1.
RefSeqiYP_003513718.1. NC_013947.1.

Genome annotation databases

EnsemblBacteriaiADD44625; ADD44625; Snas_4988.
KEGGisna:Snas_4988.
PATRICi35372287. VBIStaNas43420_4945.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001778 Genomic DNA. Translation: ADD44625.1.
RefSeqiYP_003513718.1. NC_013947.1.

3D structure databases

ProteinModelPortaliD3Q9S9.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADD44625; ADD44625; Snas_4988.
KEGGisna:Snas_4988.
PATRICi35372287. VBIStaNas43420_4945.

Phylogenomic databases

HOGENOMiHOG000011593.
KOiK01921.
OMAiWENSTEN.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciSNAS446470:GHHC-5022-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]
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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 44728 / NRRL B-16338 / NBRC 102104 / LLR-40K-21Imported.

Entry informationi

Entry nameiD3Q9S9_STANL
AccessioniPrimary (citable) accession number: D3Q9S9
Entry historyi
Integrated into UniProtKB/TrEMBL: April 19, 2010
Last sequence update: April 19, 2010
Last modified: March 31, 2015
This is version 40 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.