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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Rhodopseudomonas palustris (strain BisA53)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Cell wall formation.UniRule annotation

Catalytic activityi

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

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule 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 bindingi252Magnesium or manganese 1UniRule annotation1
Metal bindingi269Magnesium or manganese 1UniRule annotation1
Metal bindingi269Magnesium or manganese 2UniRule annotation1
Metal bindingi271Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi130 – 184ATPUniRule annotationAdd BLAST55

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, 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:RPE_2113
OrganismiRhodopseudomonas palustris (strain BisA53)
Taxonomic identifieri316055 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeRhodopseudomonas
Proteomesi
  • UP000000654 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003411661 – 308D-alanine--D-alanine ligaseAdd BLAST308

Interactioni

Protein-protein interaction databases

STRINGi316055.RPE_2113.

Structurei

3D structure databases

ProteinModelPortaliQ07PS7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini103 – 302ATP-graspUniRule annotationAdd BLAST200

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011592.
KOiK01921.
OMAiTKYTEGF.
OrthoDBiPOG091H00GT.

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. 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]
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.

Q07PS7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKRKHVAVL LGGWSSEREV SLRSGNACAD ALERRGFEVT RIDVARDIAT
60 70 80 90 100
VLDQLRPDSA LMMLHGHPGE DGSIQGVLET LAIPYSHSGV LASALAMQKD
110 120 130 140 150
LAKTVMKTAG VPVAEGLTLS RDEIARGHVM EPPYVIKPVA DGSSVGVYII
160 170 180 190 200
TEQHQHPPQE LFRDDWAYGD KLLVEKYVAG KELTCAVVKG EPTDVIEIVP
210 220 230 240 250
MVRFYDYEAK YSPGASKHVL PASLLPFVYQ EVRRLTLAAH VALGCRGVSR
260 270 280 290 300
ADFRFDDRIE GTGGLVCLEV NTQPGMTETS LVPELAAYAG ITFDELVQWM

VEDASLDR
Length:308
Mass (Da):33,660
Last modified:October 31, 2006 - v1
Checksum:iD4443B1871BBD940
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000463 Genomic DNA. Translation: ABJ06057.1.
RefSeqiWP_011663540.1. NC_008435.1.

Genome annotation databases

EnsemblBacteriaiABJ06057; ABJ06057; RPE_2113.
KEGGirpe:RPE_2113.
PATRICi23258810. VBIRhoPal93214_2157.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000463 Genomic DNA. Translation: ABJ06057.1.
RefSeqiWP_011663540.1. NC_008435.1.

3D structure databases

ProteinModelPortaliQ07PS7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi316055.RPE_2113.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABJ06057; ABJ06057; RPE_2113.
KEGGirpe:RPE_2113.
PATRICi23258810. VBIRhoPal93214_2157.

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011592.
KOiK01921.
OMAiTKYTEGF.
OrthoDBiPOG091H00GT.

Enzyme and pathway databases

UniPathwayiUPA00219.

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. 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]
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 nameiDDL_RHOP5
AccessioniPrimary (citable) accession number: Q07PS7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: October 31, 2006
Last modified: November 2, 2016
This is version 70 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

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.