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D2RC91

- D2RC91_GARV4

UniProt

D2RC91 - D2RC91_GARV4

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Protein

D-alanine--D-alanine ligase

Gene
ddl, HMPREF0424_1233
Organism
Gardnerella vaginalis (strain 409-05)
Status
Unreviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

Functioni

Cell wall formation By similarity.UniRule annotationSAAS annotations

Catalytic activityi

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

Cofactori

Binds 2 magnesium or manganese ions per subunit By similarity.UniRule annotationSAAS annotations

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi330 – 3301Magnesium or manganese 1 By similarityUniRule annotation
Metal bindingi343 – 3431Magnesium or manganese 1 By similarityUniRule annotation
Metal bindingi343 – 3431Magnesium or manganese 2 By similarityUniRule annotation
Metal bindingi345 – 3451Magnesium or manganese 2 By similarityUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi192 – 24958ATP By similarityUniRule 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. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  2. regulation of cell shape Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

LigaseUniRule annotationSAAS annotationsImported

Keywords - Biological processi

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

Keywords - Ligandi

ATP-bindingUniRule annotationSAAS annotations, MagnesiumUniRule annotationSAAS annotations, ManganeseUniRule annotationSAAS annotations, Metal-bindingUniRule annotationSAAS annotations, 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 ligase
D-alanylalanine synthetase
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 By similarity UniRule annotationSAAS annotations

GO - Cellular componenti

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

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotations

Structurei

3D structure databases

ProteinModelPortaliD2RC91.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini150 – 376227ATP-grasp By similarityUniRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.UniRule annotation
Contains ATP-grasp domain.SAAS annotations

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

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MTKKRVVFLY GGKADEHSIS CISAAGVLSA VDENRFDIVR IAITKQGEWI    50
VGGEDPRNFH MEEGELPVIT KTAGTRDVVL DPAKGADGFL ARENDGTLTS 100
LGHIDAVFPV LHGPNGEDGT LQGLLEMMQV PYVGCGVLAS AACMDKYYAK 150
QLFKAAGIDV APGIALDARK FASDAENRFD AYAEEILAQV EAAKLEYPLF 200
VKPSRAGSSF GVTKVESRDA KALAEAIFEA SEHDWRVLVE QGIDAREIEC 250
AVLAARDGEE PKASWPGEVV LDKREAGEDQ FYDFDSKYMD SAASHVEVPA 300
NLPAETLERV RKTALAAFKA ADGRGLSRVD SFVTKDGRVI LNEINTMPGF 350
TPISMYPKAW EATGISYSDL ITKLIEGVLK 380
Length:380
Mass (Da):41,170
Last modified:March 2, 2010 - v1
Checksum:i4A0BE9B630852FAA
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001849 Genomic DNA. Translation: ADB14041.1.
RefSeqiWP_012914489.1. NC_013721.1.
YP_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:
EMBL
GenBank
DDBJ
Links Updated
CP001849 Genomic DNA. Translation: ADB14041.1 .
RefSeqi WP_012914489.1. NC_013721.1.
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: 409-05.

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: September 3, 2014
This is version 34 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome

External Data

Dasty 3

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