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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Vibrio cholerae serotype O1 (strain MJ-1236)
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

Protein has several cofactor binding sites:
  • Mg2+UniRule annotationSAAS annotation, Mn2+UniRule annotationSAAS annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation
  • Mg2+, Mn2+Note: Binds 2 magnesium or manganese ions per subunit.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi281 – 2811Magnesium or manganese 1UniRule annotation
Metal bindingi294 – 2941Magnesium or manganese 1UniRule annotation
Metal bindingi294 – 2941Magnesium or manganese 2UniRule annotation
Metal bindingi296 – 2961Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi151 – 20656ATPUniRule 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

BioCyciVCHO593588:GI2R-3641-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:VCD_000746Imported
OrganismiVibrio cholerae serotype O1 (strain MJ-1236)Imported
Taxonomic identifieri593588 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
ProteomesiUP000001618 Componenti: Chromosome 2

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Protein-protein interaction databases

STRINGi593588.VCD_000746.

Structurei

3D structure databases

ProteinModelPortaliC3NX60.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini121 – 327207ATP-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

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG6ND0KB.

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

Sequencei

Sequence statusi: Complete.

C3NX60-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKTTILLLC GGGSSEHEIS LVSANYIQQQ LELTPEFHVI RVEMKKEGWF
60 70 80 90 100
SEQGALVYLD TNSATLNSDK ASYPIDFVVP CIHGFPGETG DIQSMLELAG
110 120 130 140 150
IPYLGCGPEA SANSFNKITS KLWYDALDIP NTPYLFLTQN TPSSIDKAKQ
160 170 180 190 200
AFGHWGSIFV KAARQGSSVG CYKVTTEDQI APAIEAAFGF SEQVLVEQAV
210 220 230 240 250
KPRELEVSAY EMNGKLYISK PGEVIAPEGT FYSYEEKYSA NSHARTVLEA
260 270 280 290 300
ENLTEKHKEL IQTYAERVFI HMKLRHLSRI DFFLTQEGQI YLNEVNTFPG
310 320 330
MTPISMFPKM LEHNGHRFSE FLVQCVTNTL VNAK
Length:334
Mass (Da):37,318
Last modified:June 16, 2009 - v1
Checksum:iB7581B22D766818B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001486 Genomic DNA. Translation: ACQ62706.1.
RefSeqiWP_000169444.1. NC_012667.1.
YP_002876502.1. NC_012667.1.

Genome annotation databases

EnsemblBacteriaiACQ62706; ACQ62706; VCD_000746.
KEGGivcj:VCD_000746.
PATRICi20072651. VBIVibCho20143_0747.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001486 Genomic DNA. Translation: ACQ62706.1.
RefSeqiWP_000169444.1. NC_012667.1.
YP_002876502.1. NC_012667.1.

3D structure databases

ProteinModelPortaliC3NX60.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi593588.VCD_000746.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACQ62706; ACQ62706; VCD_000746.
KEGGivcj:VCD_000746.
PATRICi20072651. VBIVibCho20143_0747.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciVCHO593588:GI2R-3641-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.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: MJ-1236Imported.

Entry informationi

Entry nameiC3NX60_VIBCJ
AccessioniPrimary (citable) accession number: C3NX60
Entry historyi
Integrated into UniProtKB/TrEMBL: June 16, 2009
Last sequence update: June 16, 2009
Last modified: May 27, 2015
This is version 47 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.