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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Bradyrhizobium sp. (strain ORS 278)
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 bindingi306Magnesium or manganese 1UniRule annotation1
Metal bindingi318Magnesium or manganese 1UniRule annotation1
Metal bindingi318Magnesium or manganese 2UniRule annotation1
Metal bindingi320Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi174 – 229ATPUniRule 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

BioCyciBSP114615:G1GI7-2701-MONOMER
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:BRADO2810
OrganismiBradyrhizobium sp. (strain ORS 278)
Taxonomic identifieri114615 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
Proteomesi

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003410651 – 367D-alanine--D-alanine ligaseAdd BLAST367

Interactioni

Protein-protein interaction databases

STRINGi114615.BRADO2810

Structurei

3D structure databases

ProteinModelPortaliA4YRU4
SMRiA4YRU4
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini145 – 351ATP-graspUniRule annotationAdd BLAST207

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CPF Bacteria
COG1181 LUCA
HOGENOMiHOG000011593
KOiK01921
OMAiRCDFFVI
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.

A4YRU4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTSERIRVAI LFGGRSAEHD VSRASAANIF RSLDAGRYAL TLIGITHDGR
60 70 80 90 100
WVLADAVNDA TSAALIVPAD GPQIVLLPAG RGRALAIDGS AAAPRELAFD
110 120 130 140 150
VIFPVLHGPN GEDGTVQGAL ELADVAYVGG RVLGSAAAMD KDVAKRLLRD
160 170 180 190 200
AGLPIVPFVT MTAASPVSYD DAARAVGSSE LFVKPANLGS SVGISKTRDA
210 220 230 240 250
AEFEAACQLA LRFDRKILIE RCIAPVREIE CAVLEHADGQ IKASELGEIV
260 270 280 290 300
PANSHGFYSY EAKYTDANGA ALHVPAQVEP AVAQRIRKMA TEVFGALCCE
310 320 330 340 350
SLARVDFFVR GDEIYVNEVN TLPGFTNISM YPKMWEAAGL PQPALMDELV
360
AHALARHARL RELASQR
Length:367
Mass (Da):39,043
Last modified:May 29, 2007 - v1
Checksum:iA356FFB24181CFA2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU234118 Genomic DNA Translation: CAL76620.1
RefSeqiWP_011925823.1, NC_009445.1

Genome annotation databases

EnsemblBacteriaiCAL76620; CAL76620; BRADO2810
KEGGibra:BRADO2810

Entry informationi

Entry nameiDDL_BRASO
AccessioniPrimary (citable) accession number: A4YRU4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: May 29, 2007
Last modified: March 28, 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

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