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Protein

D-alanine--D-alanine ligase B

Gene

ddlA

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
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 bindingi316Magnesium or manganese 1UniRule annotation1
Metal bindingi328Magnesium or manganese 1UniRule annotation1
Metal bindingi328Magnesium or manganese 2UniRule annotation1
Metal bindingi330Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi184 – 239ATPUniRule 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

BioCyciBDIA224911:G1G3J-3429-MONOMER
UniPathwayiUPA00219

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligase BUniRule annotation (EC:6.3.2.4UniRule annotation)
Alternative name(s):
D-Ala-D-Ala ligase BUniRule annotation
D-alanylalanine synthetase BUniRule annotation
Gene namesi
Name:ddlAUniRule annotation
Synonyms:ddlB
Ordered Locus Names:blr3405
OrganismiBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Taxonomic identifieri224911 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
Proteomesi
  • UP000002526 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001777931 – 376D-alanine--D-alanine ligase BAdd BLAST376

Interactioni

Protein-protein interaction databases

STRINGi224911.blr3405

Structurei

3D structure databases

ProteinModelPortaliQ89PS5
SMRiQ89PS5
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini155 – 361ATP-graspUniRule annotationAdd BLAST207

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CPF Bacteria
COG1181 LUCA
HOGENOMiHOG000011593
InParanoidiQ89PS5
KOiK01921
OMAiIPYVGCD
OrthoDBiPOG091H06GK
PhylomeDBiQ89PS5

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.

Q89PS5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTAYGGEMTK ERRKITVGLL FGGRSAEHEV SRASAANILR ALNSDRYDVY
60 70 80 90 100
LIGISRDGRW FACDSGNGAG TGSTALTISD EAPEIGLVPG GRGRLVHCDG
110 120 130 140 150
PTGSDAGSID VAFPILHGPN GEDGTVQGAL ELADVSFVGS SVTGSAVAMD
160 170 180 190 200
KEVSKRLMRD AGLPVVPFLT TTASSRIEYA AAVAALGTPD LFVKPANLGS
210 220 230 240 250
SVGVSRARSE EEFAASCALA FRYDRKILVE QALNGAREIE CSVLEESTGD
260 270 280 290 300
IRASGLGEIV RASEHGFYSY QAKYIDADGA ALHIPADLPL LQARRLQELA
310 320 330 340 350
VEVFNVLCCE GMARVDFFVQ GDEVFVNEAN TLPGFTSSSM YPKLWEASGL
360 370
SQTDLMDKLI AHAFARHERR RALSFG
Length:376
Mass (Da):39,991
Last modified:June 1, 2003 - v1
Checksum:iADF689A391337460
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000040 Genomic DNA Translation: BAC48670.1
RefSeqiNP_770045.1, NC_004463.1
WP_011086189.1, NZ_CP011360.1

Genome annotation databases

EnsemblBacteriaiBAC48670; BAC48670; BAC48670
GeneIDi1050703
KEGGibja:blr3405
PATRICifig|224911.5.peg.3409

Similar proteinsi

Entry informationi

Entry nameiDDLB_BRADU
AccessioniPrimary (citable) accession number: Q89PS5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: June 1, 2003
Last modified: March 28, 2018
This is version 94 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
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Main funding by: National Institutes of Health