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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Francisella philomiragia subsp. philomiragia (strain ATCC 25017)
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 bindingi247Magnesium or manganese 1UniRule annotation1
Metal bindingi260Magnesium or manganese 1UniRule annotation1
Metal bindingi260Magnesium or manganese 2UniRule annotation1
Metal bindingi262Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi129 – 180ATPUniRule annotationAdd BLAST52

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:Fphi_0663
OrganismiFrancisella philomiragia subsp. philomiragia (strain ATCC 25017)
Taxonomic identifieri484022 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaThiotrichalesFrancisellaceaeFrancisella
Proteomesi
  • UP000001320 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_00003410931 – 297D-alanine--D-alanine ligaseAdd BLAST297

Interactioni

Protein-protein interaction databases

STRINGi484022.Fphi_0663.

Structurei

3D structure databases

ProteinModelPortaliB0TVX5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini103 – 293ATP-graspUniRule annotationAdd BLAST191

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]
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.

B0TVX5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQKEKIVVLY GGDSPEREVS LKSGKAVLDS LLNQGYDAVG LDASSKDLVV
60 70 80 90 100
KLLELNPDKC FIALHGEDGE NGRVAALLEL LGIKHTGSTM KSCVVTMDKM
110 120 130 140 150
ISKEILMHHR MPTPMAKFLT DRLVEADEIS FPVAVKPSSG GSSIATFKVK
160 170 180 190 200
SLEELENAYQ QASKHGEVMI EQWVTGKEIT VAIVNNDVYS SVWIEPLNEF
210 220 230 240 250
YDYESKYSGK SIYHAPSGLC EQKELEVRQL AKKAYDLLGC KGHARVDFIY
260 270 280 290
DDKGDFYIME INSSPGMTEN SLSPKSAAAE GIDFDSFVKS ILEQAQC
Length:297
Mass (Da):32,760
Last modified:April 8, 2008 - v1
Checksum:i63F9A5B759DCDF7B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000937 Genomic DNA. Translation: ABZ86883.1.
RefSeqiWP_012280102.1. NC_010336.1.

Genome annotation databases

EnsemblBacteriaiABZ86883; ABZ86883; Fphi_0663.
KEGGifph:Fphi_0663.
PATRICi17938175. VBIFraPhi43880_0687.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000937 Genomic DNA. Translation: ABZ86883.1.
RefSeqiWP_012280102.1. NC_010336.1.

3D structure databases

ProteinModelPortaliB0TVX5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi484022.Fphi_0663.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABZ86883; ABZ86883; Fphi_0663.
KEGGifph:Fphi_0663.
PATRICi17938175. VBIFraPhi43880_0687.

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]
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 nameiDDL_FRAP2
AccessioniPrimary (citable) accession number: B0TVX5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: April 8, 2008
Last modified: November 2, 2016
This is version 59 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.