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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Thermincola potens (strain JR)
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 bindingi300Magnesium or manganese 1UniRule annotation1
Metal bindingi314Magnesium or manganese 1UniRule annotation1
Metal bindingi314Magnesium or manganese 2UniRule annotation1
Metal bindingi316Magnesium 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:TherJR_1176Imported
OrganismiThermincola potens (strain JR)Imported
Taxonomic identifieri635013 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesPeptococcaceaeThermincola
Proteomesi
  • UP000002377 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

STRINGi635013.TherJR_1176.

Structurei

3D structure databases

ProteinModelPortaliD5XEG9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini141 – 347ATP-graspInterPro annotationAdd BLAST207

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.UniRule annotationSAAS 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. 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.

D5XEG9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKNRVAVIF GGKSGEHEVS LASANSVLQA LNKEKYEIIP IKISREGKWY
60 70 80 90 100
ILSSLNTFDS NIKCEAAILA DPTGDNLVNL QEKEPGQIFF TRESVDVVLP
110 120 130 140 150
VLHGTFGEDG TLQGLLELAN IPYVGCGVAA SSVGMDKAMM KAMFAQHNLP
160 170 180 190 200
QGKYLTFLRK EWEKDQDPIC DEIETALGYP VFVKPANLGS SVGISKAANR
210 220 230 240 250
DELVKAMHLA CLYDRKVVVE ENINGREIEV AVLGNDEPEA SIAGEIVPCN
260 270 280 290 300
DFYDYEAKYI SGTSELKIPA PLDDKTMNEV RKLAVKAFKA IDGAGLSRVD
310 320 330 340 350
FFIKKDTGEI LINEINTLPG FTEISMYPKL WAATGLPYDK LLDRLIELAI
360
ERHQDKNRNK TVYSE
Length:365
Mass (Da):40,380
Last modified:July 13, 2010 - v1
Checksum:i536F4F38DB8BBB94
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002028 Genomic DNA. Translation: ADG82040.1.
RefSeqiWP_013120059.1. NC_014152.1.

Genome annotation databases

EnsemblBacteriaiADG82040; ADG82040; TherJR_1176.
KEGGitjr:TherJR_1176.
PATRICi38273925. VBITheSp141296_1261.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002028 Genomic DNA. Translation: ADG82040.1.
RefSeqiWP_013120059.1. NC_014152.1.

3D structure databases

ProteinModelPortaliD5XEG9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi635013.TherJR_1176.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADG82040; ADG82040; TherJR_1176.
KEGGitjr:TherJR_1176.
PATRICi38273925. VBITheSp141296_1261.

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. 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 nameiD5XEG9_THEPJ
AccessioniPrimary (citable) accession number: D5XEG9
Entry historyi
Integrated into UniProtKB/TrEMBL: July 13, 2010
Last sequence update: July 13, 2010
Last modified: November 30, 2016
This is version 46 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.