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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Bacillus pumilus (strain SAFR-032)
Status
Reviewed-Annotation score: -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 bindingi298Magnesium or manganese 1UniRule annotation1
Metal bindingi311Magnesium or manganese 1UniRule annotation1
Metal bindingi311Magnesium or manganese 2UniRule annotation1
Metal bindingi313Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi172 – 227ATPUniRule annotationAdd BLAST56

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis
LigandATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciBPUM315750:G1G9U-474-MONOMER
UniPathwayi
UPA00219

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:BPUM_0427
OrganismiBacillus pumilus (strain SAFR-032)
Taxonomic identifieri315750 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001355 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000573201 – 360D-alanine--D-alanine ligaseAdd BLAST360

Proteomic databases

PRIDEiA8FA55

Interactioni

Protein-protein interaction databases

STRINGi315750.BPUM_0427

Structurei

3D structure databases

ProteinModelPortaliA8FA55
SMRiA8FA55
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini139 – 344ATP-graspUniRule annotationAdd BLAST206

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CPF Bacteria
COG1181 LUCA
HOGENOMiHOG000011593
KOiK01921
OMAiYETKYTE
OrthoDBiPOG091H06GK

Family and domain databases

Gene3Di3.30.1490.20, 1 hit
HAMAPiMF_00047 Dala_Dala_lig, 1 hit
InterProiView protein in InterPro
IPR011761 ATP-grasp
IPR013815 ATP_grasp_subdomain_1
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_sf
PfamiView protein in Pfam
PF07478 Dala_Dala_lig_C, 1 hit
PF01820 Dala_Dala_lig_N, 1 hit
PIRSFiPIRSF039102 Ddl/VanB, 1 hit
SUPFAMiSSF52440 SSF52440, 1 hit
TIGRFAMsiTIGR01205 D_ala_D_alaTIGR, 1 hit
PROSITEiView protein in PROSITE
PS50975 ATP_GRASP, 1 hit
PS00843 DALA_DALA_LIGASE_1, 1 hit
PS00844 DALA_DALA_LIGASE_2, 1 hit

Sequencei

Sequence statusi: Complete.

A8FA55-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKISLGLIYG GKSAEHNVSL QTALAVTKAL NTEKFDIHPI YITEEGEWLR
60 70 80 90 100
GEKLTEPVSN VRMLQFEQNA KTFLPTSLNE SMFPQPTSAD EKIDVVFPLL
110 120 130 140 150
HGPNGEDGTM QGLLELLNIP YVGNGVLASA AGMDKVMMKD VFAQAGLAQA
160 170 180 190 200
KHLSFNKKDY EKATPDSLEQ VEQVLGYPCF VKPANMGSSV GISKCRSKEE
210 220 230 240 250
LQTAFDLAFQ YDRRVVVEEG VVGREIEIGV LGNDEPKCSV VGEIAPKTDF
260 270 280 290 300
YDYKAKYEDG DTDLIIPASV SEDEYKTIHD MAIKAFKSLD GSGLVRADFF
310 320 330 340 350
LTEKGEVLIN EVNTMPGFTP FSMFPLLWKH TGVEYPELIE KLVSLAIERH
360
QEKQTIKTTF
Length:360
Mass (Da):39,946
Last modified:November 13, 2007 - v1
Checksum:iF436D4B60A45E6AD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000813 Genomic DNA Translation: ABV61122.1
RefSeqiWP_012008984.1, NC_009848.4

Genome annotation databases

EnsemblBacteriaiABV61122; ABV61122; BPUM_0427
KEGGibpu:BPUM_0427

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000813 Genomic DNA Translation: ABV61122.1
RefSeqiWP_012008984.1, NC_009848.4

3D structure databases

ProteinModelPortaliA8FA55
SMRiA8FA55
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi315750.BPUM_0427

Proteomic databases

PRIDEiA8FA55

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABV61122; ABV61122; BPUM_0427
KEGGibpu:BPUM_0427

Phylogenomic databases

eggNOGiENOG4105CPF Bacteria
COG1181 LUCA
HOGENOMiHOG000011593
KOiK01921
OMAiYETKYTE
OrthoDBiPOG091H06GK

Enzyme and pathway databases

UniPathwayi
UPA00219

BioCyciBPUM315750:G1G9U-474-MONOMER

Family and domain databases

Gene3Di3.30.1490.20, 1 hit
HAMAPiMF_00047 Dala_Dala_lig, 1 hit
InterProiView protein in InterPro
IPR011761 ATP-grasp
IPR013815 ATP_grasp_subdomain_1
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_sf
PfamiView protein in Pfam
PF07478 Dala_Dala_lig_C, 1 hit
PF01820 Dala_Dala_lig_N, 1 hit
PIRSFiPIRSF039102 Ddl/VanB, 1 hit
SUPFAMiSSF52440 SSF52440, 1 hit
TIGRFAMsiTIGR01205 D_ala_D_alaTIGR, 1 hit
PROSITEiView protein in PROSITE
PS50975 ATP_GRASP, 1 hit
PS00843 DALA_DALA_LIGASE_1, 1 hit
PS00844 DALA_DALA_LIGASE_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDDL_BACP2
AccessioniPrimary (citable) accession number: A8FA55
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: November 13, 2007
Last modified: October 10, 2018
This is version 72 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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Main funding by: National Institutes of Health

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