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D3V4L3

- D3V4L3_XENBS

UniProt

D3V4L3 - D3V4L3_XENBS

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Protein

D-alanine--D-alanine ligase

Gene

ddlB

Organism
Xenorhabdus bovienii (strain SS-2004)
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 bindingi257 – 2571Magnesium or manganese 1UniRule annotation
Metal bindingi270 – 2701Magnesium or manganese 1UniRule annotation
Metal bindingi270 – 2701Magnesium or manganese 2UniRule annotation
Metal bindingi272 – 2721Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi134 – 18956ATPUniRule 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 division Source: UniProtKB-KW
  2. cell wall organization Source: UniProtKB-KW
  3. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  4. regulation of cell shape Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

LigaseUniRule annotationSAAS annotation

Keywords - Biological processi

Cell cycle, Cell divisionImported, 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

BioCyciXBOV406818:GHLH-3470-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:ddlBImported
Synonyms:ddlUniRule annotation
Ordered Locus Names:XBJ1_3474Imported
OrganismiXenorhabdus bovienii (strain SS-2004)Imported
Taxonomic identifieri406818 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeXenorhabdus
ProteomesiUP000002045: 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

ProteinModelPortaliD3V4L3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini101 – 303203ATP-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

HOGENOMiHOG000011592.
KOiK01921.

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. 2 hits.
[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.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

D3V4L3-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MVEKVAVLLG GTSAEREVSL QSGQSVVAGL KEAGINAYSV DTKDFDVTKL
60 70 80 90 100
KGEGFSKAFI ALHGRGGEDG TLQGVLEFLQ IPYTGSGVMA SALSMDKLRT
110 120 130 140 150
KQLWQGAKLP VSPYAAINAQ KFEQVNDFQL QEYVRELGLP LMVKPNLEGS
160 170 180 190 200
SVGMTKVNDY SELRGALELA FQHDTDVLVE KWLLGPEYTV AFLGDEVLPS
210 220 230 240 250
IRIQAPEVFY DYDAKYLSNE TKYFCPSGLS AEKELELAEI ASKAYKALGC
260 270 280 290 300
SGWGRVDIMD DGNGNFYLLE VNTSPGMTSH SLVPMAARQS GLSFSQLVVK

ILELAD
Length:306
Mass (Da):33,271
Last modified:April 20, 2010 - v1
Checksum:i8DD66453C95D8B4A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FN667741 Genomic DNA. Translation: CBJ82592.1.
RefSeqiYP_003469356.1. NC_013892.1.

Genome annotation databases

EnsemblBacteriaiCBJ82592; CBJ82592; XBJ1_3474.
GeneIDi8833097.
KEGGixbo:XBJ1_3474.
PATRICi35301631. VBIXenBov95754_3140.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FN667741 Genomic DNA. Translation: CBJ82592.1 .
RefSeqi YP_003469356.1. NC_013892.1.

3D structure databases

ProteinModelPortali D3V4L3.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CBJ82592 ; CBJ82592 ; XBJ1_3474 .
GeneIDi 8833097.
KEGGi xbo:XBJ1_3474.
PATRICi 35301631. VBIXenBov95754_3140.

Phylogenomic databases

HOGENOMi HOG000011592.
KOi K01921.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci XBOV406818:GHLH-3470-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. 2 hits.
[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.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Complete genome sequence of Xenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / LMG 1036 / NCIB 9965 / AN6)."
    Goodrich-Blair H., Barbazuk B., Bode H.B., Darby C., Du Z., Forst S., Gaudriault S., Goldman B.S., Goodner B., Henkhaus J., Latreille P., Medigue C., Miller N., Norton S., Ogier J.C., Rouy Z., Slater S., Suen G.
    Submitted (FEB-2010) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: SS-2004Imported.
  2. "The entomopathogenic bacterial endosymbionts xenorhabdus and photorhabdus: convergent lifestyles from divergent genomes."
    Chaston J.M., Suen G., Tucker S.L., Andersen A.W., Bhasin A., Bode E., Bode H.B., Brachmann A.O., Cowles C.E., Cowles K.N., Darby C., de Leon L., Drace K., Du Z., Givaudan A., Herbert Tran E.E., Jewell K.A., Knack J.J.
    , Krasomil-Osterfeld K.C., Kukor R., Lanois A., Latreille P., Leimgruber N.K., Lipke C.M., Liu R., Lu X., Martens E.C., Marri P.R., Medigue C., Menard M.L., Miller N.M., Morales-Soto N., Norton S., Ogier J.C., Orchard S.S., Park D., Park Y., Qurollo B.A., Sugar D.R., Richards G.R., Rouy Z., Slominski B., Slominski K., Snyder H., Tjaden B.C., van der Hoeven R., Welch R.D., Wheeler C., Xiang B., Barbazuk B., Gaudriault S., Goodner B., Slater S.C., Forst S., Goldman B.S., Goodrich-Blair H.
    PLoS ONE 6:e27909-e27909(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: SS-2004Imported.

Entry informationi

Entry nameiD3V4L3_XENBS
AccessioniPrimary (citable) accession number: D3V4L3
Entry historyi
Integrated into UniProtKB/TrEMBL: April 20, 2010
Last sequence update: April 20, 2010
Last modified: November 26, 2014
This is version 30 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

External Data

Dasty 3