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D2RC91

- D2RC91_GARV4

UniProt

D2RC91 - D2RC91_GARV4

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Gardnerella vaginalis (strain 409-05)
Status
Unreviewed - 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

Note: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation

Pathwayi

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

  1. ATP binding Source: UniProtKB-HAMAP
  2. D-alanine-D-alanine ligase activity Source: UniProtKB-HAMAP
  3. magnesium ion binding Source: UniProtKB-HAMAP
  4. manganese ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. cell wall organization Source: UniProtKB-KW
  2. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  3. regulation of cell shape Source: UniProtKB-KW
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.

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:HMPREF0424_1233Imported
OrganismiGardnerella vaginalis (strain 409-05)Imported
Taxonomic identifieri553190 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeBifidobacterialesBifidobacteriaceaeGardnerella
ProteomesiUP000001888: Chromosome

Subcellular locationi

Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

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
Contains ATP-grasp domain.SAAS annotation

Phylogenomic databases

HOGENOMiHOG000011593.
KOiK01921.
OMAiIECGVLG.
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]
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.
RefSeqiYP_003374426.1. NC_013721.1.

Genome annotation databases

EnsemblBacteriaiADB14041; ADB14041; HMPREF0424_1233.
GeneIDi8709920.
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 .
RefSeqi YP_003374426.1. NC_013721.1.

3D structure databases

ProteinModelPortali D2RC91.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ADB14041 ; ADB14041 ; HMPREF0424_1233 .
GeneIDi 8709920.
KEGGi gva:HMPREF0424_1233.
PATRICi 32148266. VBIGarVag136958_1087.

Phylogenomic databases

HOGENOMi HOG000011593.
KOi K01921.
OMAi IECGVLG.
OrthoDBi EOG64BQ73.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci GVAG553190:GJPT-1227-MONOMER.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPi MF_00047. Dala_Dala_lig.
InterProi IPR011761. 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 ]
PANTHERi PTHR23132. PTHR23132. 1 hit.
Pfami PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 1 hit.
TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: November 26, 2014
This is version 37 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