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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Gardnerella vaginalis (strain 409-05)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Cell wall formation.UniRule annotationSAAS annotation

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotationSAAS annotation

Cofactori

Mg2+UniRule annotationSAAS annotation, Mn2+UniRule annotationSAAS annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation

Pathway:ipeptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotationSAAS annotation
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Pathway:ipeptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi330 – 3301Magnesium or manganese 1UniRule annotation
Metal bindingi343 – 3431Magnesium or manganese 1UniRule annotation
Metal bindingi343 – 3431Magnesium or manganese 2UniRule annotation
Metal bindingi345 – 3451Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi192 – 24958ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

LigaseUniRule annotationSAAS annotation

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradationUniRule annotationSAAS annotation, Peptidoglycan synthesisUniRule annotationSAAS annotation

Keywords - Ligandi

ATP-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotationSAAS annotation, ManganeseUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding

Enzyme and pathway databases

BioCyciGVAG553190:GJPT-1227-MONOMER.
UniPathwayiUPA00219.
UPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligaseUniRule annotationSAAS annotation (EC:6.3.2.4UniRule annotationSAAS annotation)
Alternative name(s):
D-Ala-D-Ala ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:HMPREF0424_1233Imported
OrganismiGardnerella vaginalis (strain 409-05)Imported
Taxonomic identifieri553190 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaBifidobacterialesBifidobacteriaceaeGardnerella
ProteomesiUP000001888 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Protein-protein interaction databases

STRINGi553190.HMPREF0424_1233.

Structurei

3D structure databases

ProteinModelPortaliD2RC91.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini150 – 376227ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.UniRule annotation
Contains 1 ATP-grasp domain.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000011593.
KOiK01921.
OMAiMDKIAMK.
OrthoDBiEOG64BQ73.

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.
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]
PANTHERiPTHR23132. PTHR23132. 1 hit.
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.
[Graphical view]

Sequencei

Sequence statusi: Complete.

D2RC91-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKKRVVFLY GGKADEHSIS CISAAGVLSA VDENRFDIVR IAITKQGEWI
60 70 80 90 100
VGGEDPRNFH MEEGELPVIT KTAGTRDVVL DPAKGADGFL ARENDGTLTS
110 120 130 140 150
LGHIDAVFPV LHGPNGEDGT LQGLLEMMQV PYVGCGVLAS AACMDKYYAK
160 170 180 190 200
QLFKAAGIDV APGIALDARK FASDAENRFD AYAEEILAQV EAAKLEYPLF
210 220 230 240 250
VKPSRAGSSF GVTKVESRDA KALAEAIFEA SEHDWRVLVE QGIDAREIEC
260 270 280 290 300
AVLAARDGEE PKASWPGEVV LDKREAGEDQ FYDFDSKYMD SAASHVEVPA
310 320 330 340 350
NLPAETLERV RKTALAAFKA ADGRGLSRVD SFVTKDGRVI LNEINTMPGF
360 370 380
TPISMYPKAW EATGISYSDL ITKLIEGVLK
Length:380
Mass (Da):41,170
Last modified:March 2, 2010 - v1
Checksum:i4A0BE9B630852FAA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001849 Genomic DNA. Translation: ADB14041.1.
RefSeqiWP_012914489.1. NC_013721.1.

Genome annotation databases

EnsemblBacteriaiADB14041; ADB14041; HMPREF0424_1233.
KEGGigva:HMPREF0424_1233.
PATRICi32148266. VBIGarVag136958_1087.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001849 Genomic DNA. Translation: ADB14041.1.
RefSeqiWP_012914489.1. NC_013721.1.

3D structure databases

ProteinModelPortaliD2RC91.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi553190.HMPREF0424_1233.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADB14041; ADB14041; HMPREF0424_1233.
KEGGigva:HMPREF0424_1233.
PATRICi32148266. VBIGarVag136958_1087.

Phylogenomic databases

HOGENOMiHOG000011593.
KOiK01921.
OMAiMDKIAMK.
OrthoDBiEOG64BQ73.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciGVAG553190:GJPT-1227-MONOMER.

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.
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]
PANTHERiPTHR23132. PTHR23132. 1 hit.
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.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential."
    Yeoman C.J., Yildirim S., Thomas S.M., Durkin A.S., Torralba M., Sutton G., Buhay C.J., Ding Y., Dugan-Rocha S.P., Muzny D.M., Qin X., Gibbs R.A., Leigh S.R., Stumpf R., White B.A., Highlander S.K., Nelson K.E., Wilson B.A.
    PLoS ONE 5:E12411-E12411(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 409-05Imported.

Entry informationi

Entry nameiD2RC91_GARV4
AccessioniPrimary (citable) accession number: D2RC91
Entry historyi
Integrated into UniProtKB/TrEMBL: March 2, 2010
Last sequence update: March 2, 2010
Last modified: July 22, 2015
This is version 44 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

External Data

Dasty 3

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 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.