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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Planctopirus limnophilus (strain ATCC 43296 / DSM 3776 / IFAM 1008 / 290) (Planctomyces limnophilus)
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

Pathway: 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.

Pathway: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi266 – 2661Magnesium or manganese 1UniRule annotation
Metal bindingi279 – 2791Magnesium or manganese 1UniRule annotation
Metal bindingi279 – 2791Magnesium or manganese 2UniRule annotation
Metal bindingi281 – 2811Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi143 – 19856ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

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

BioCyciPLIM521674:GKE7-9-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:Plim_0009Imported
OrganismiPlanctopirus limnophilus (strain ATCC 43296 / DSM 3776 / IFAM 1008 / 290) (Planctomyces limnophilus)Imported
Taxonomic identifieri521674 [NCBI]
Taxonomic lineageiBacteriaPlanctomycetesPlanctomycetiaPlanctomycetalesPlanctomycetaceaePlanctopirus
ProteomesiUP000002220 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Protein-protein interaction databases

STRINGi521674.Plim_0009.

Structurei

3D structure databases

ProteinModelPortaliD5SME2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini114 – 312199ATP-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

HOGENOMiHOG000011592.
KOiK01921.
OMAiPFLLEMN.

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.
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. 2 hits.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

D5SME2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRGNIQSAA TNPPRWNIAL LAGGDSDERS ISLRSGQAVC QALQERGHFI
60 70 80 90 100
LPIDPAIVSL KGMDWNGFDA VFIALHGRFG EDGGVQTLLE ESGIPYTGSS
110 120 130 140 150
SQASRLAFDK RIAKQNFDRM QVPTPAWCEL SPHESFDSLL MKAKELGWPV
160 170 180 190 200
VIKPASQGSS LGVSIVRQPE QLQSAYERAR HYDEALIMEA AIVGSEWTVG
210 220 230 240 250
LHDDEILPPI CIETDREFFD WVAKYEDDHT RYIFDKPLPA TCRQKLETAC
260 270 280 290 300
RGAVHALGVT GISRVDLMLD SEGNPWVLEI NTIPGLTDHS LVPKAAQQAG
310 320 330
WSLGELCEES IHRAIQRRPR RPHLLRRASF STQARQRP
Length:338
Mass (Da):37,544
Last modified:July 13, 2010 - v1
Checksum:i89F692F5E89B1E8B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001744 Genomic DNA. Translation: ADG65862.1.
RefSeqiWP_013108293.1. NC_014148.1.
YP_003628061.1. NC_014148.1.

Genome annotation databases

EnsemblBacteriaiADG65862; ADG65862; Plim_0009.
KEGGiplm:Plim_0009.
PATRICi38235438. VBIPlaLim6916_0010.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001744 Genomic DNA. Translation: ADG65862.1.
RefSeqiWP_013108293.1. NC_014148.1.
YP_003628061.1. NC_014148.1.

3D structure databases

ProteinModelPortaliD5SME2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi521674.Plim_0009.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADG65862; ADG65862; Plim_0009.
KEGGiplm:Plim_0009.
PATRICi38235438. VBIPlaLim6916_0010.

Phylogenomic databases

HOGENOMiHOG000011592.
KOiK01921.
OMAiPFLLEMN.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciPLIM521674:GKE7-9-MONOMER.

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.
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. 2 hits.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43296 / DSM 3776 / IFAM 1008 / 290Imported.

Entry informationi

Entry nameiD5SME2_PLAL2
AccessioniPrimary (citable) accession number: D5SME2
Entry historyi
Integrated into UniProtKB/TrEMBL: July 13, 2010
Last sequence update: July 13, 2010
Last modified: June 24, 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.