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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
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 bindingi280Magnesium or manganese 1UniRule annotation1
Metal bindingi293Magnesium or manganese 1UniRule annotation1
Metal bindingi293Magnesium or manganese 2UniRule annotation1
Metal bindingi295Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi150 – 205ATPUniRule 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

BioCyciVPAR223926:G1GTB-4118-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:VPA0886
OrganismiVibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
Taxonomic identifieri223926 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000002493 Componenti: Chromosome 2

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001779021 – 329D-alanine--D-alanine ligaseAdd BLAST329

Interactioni

Protein-protein interaction databases

STRINGi223926.VPA0886

Structurei

3D structure databases

ProteinModelPortaliQ87HS0
SMRiQ87HS0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini120 – 326ATP-graspUniRule annotationAdd BLAST207

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CPF Bacteria
COG1181 LUCA
HOGENOMiHOG000011592
KOiK01921
OMAiRCDFFVI

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.

Q87HS0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIKNILLLCG GGSSEHEISL LSANFVEQQL NLIQNVKVTR VEIKNEGWVT
60 70 80 90 100
DQGELVYLDL NTKQLCSNES NQTIDFIVPC IHGFPGETGD IQSLFEIAGI
110 120 130 140 150
PYLGCGPEAS SNSFNKITSK LWYDALDIPN TPYLFLTRND EHAHRQAEQA
160 170 180 190 200
FEKWGKVFVK AARQGSSVGC YSVAEKQAIA KAVNDAFGYS DQVLVEKAVK
210 220 230 240 250
PRELEVAAYE MNGELHITKP GEVIAPDGAF YSYDEKYSSS SHSLTEVEAK
260 270 280 290 300
NLTQEQIDKI RHASETVFKQ MNLRHLSRID FFLTEDNEIY LNEVNTFPGM
310 320
TPISMFPKML QNNGHKFHEF LEDCINSAK
Length:329
Mass (Da):36,957
Last modified:June 1, 2003 - v1
Checksum:i00BD14677D80A2D5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000032 Genomic DNA Translation: BAC62229.1
RefSeqiNP_800396.1, NC_004605.1
WP_005455294.1, NC_004605.1

Genome annotation databases

EnsemblBacteriaiBAC62229; BAC62229; BAC62229
GeneIDi1191575
KEGGivpa:VPA0886
PATRICifig|223926.6.peg.3819

Similar proteinsi

Entry informationi

Entry nameiDDL_VIBPA
AccessioniPrimary (citable) accession number: Q87HS0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 11, 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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