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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

Protein has several cofactor binding sites:
  • Mg2+UniRule annotation, Mn2+UniRule annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotation
  • Mn2+SAAS annotation

Pathwayi: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotationSAAS 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 bindingi308Magnesium or manganese 1UniRule annotation1
Metal bindingi321Magnesium or manganese 1UniRule annotation1
Metal bindingi321Magnesium or manganese 2UniRule annotation1
Metal bindingi323Magnesium or manganese 2UniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

LigaseUniRule annotationSAAS annotationImported

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

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:Snas_4988Imported
OrganismiStackebrandtia nassauensis (strain DSM 44728 / NRRL B-16338 / NBRC 102104 / LLR-40K-21)Imported
Taxonomic identifieri446470 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaGlycomycetalesGlycomycetaceaeStackebrandtia
Proteomesi
  • UP000000844 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 24Sequence analysisAdd BLAST24
ChainiPRO_500304879525 – 364D-alanine--D-alanine ligaseSequence analysisAdd BLAST340

Interactioni

Protein-protein interaction databases

STRINGi446470.Snas_4988.

Structurei

3D structure databases

ProteinModelPortaliD3Q9S9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini149 – 354ATP-graspInterPro annotationAdd BLAST206

Sequence similaritiesi

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

Keywords - Domaini

SignalSequence analysis

Phylogenomic databases

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

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. 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.

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 20, 2010 - v1
Checksum:iEBC995B5C7248003
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001778 Genomic DNA. Translation: ADD44625.1.
RefSeqiWP_013020196.1. 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.
RefSeqiWP_013020196.1. NC_013947.1.

3D structure databases

ProteinModelPortaliD3Q9S9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi446470.Snas_4988.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00219.

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. 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 nameiD3Q9S9_STANL
AccessioniPrimary (citable) accession number: D3Q9S9
Entry historyi
Integrated into UniProtKB/TrEMBL: April 20, 2010
Last sequence update: April 20, 2010
Last modified: November 30, 2016
This is version 55 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

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.