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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Variovorax paradoxus (strain S110)
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 annotation, Mn2+UniRule annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotation
  • Mn2+SAAS annotation

Pathwayi: peptidoglycan 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.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi265Magnesium or manganese 1UniRule annotation1
Metal bindingi279Magnesium or manganese 1UniRule annotation1
Metal bindingi279Magnesium or manganese 2UniRule annotation1
Metal bindingi281Magnesium or manganese 2UniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLigaseUniRule annotationSAAS annotationImported
Biological processCell shape, Cell wall biogenesis/degradationUniRule annotationSAAS annotation, Peptidoglycan synthesisUniRule annotationSAAS annotation
LigandATP-bindingPROSITE-ProRule annotationSAAS annotation, MagnesiumUniRule annotationSAAS annotation, ManganeseUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding

Enzyme and pathway databases

UniPathwayiUPA00219.

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:Vapar_0921Imported
OrganismiVariovorax paradoxus (strain S110)Imported
Taxonomic identifieri543728 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeVariovorax
Proteomesi
  • UP000000453 Componenti: Chromosome 1

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Protein-protein interaction databases

STRINGi543728.Vapar_0921.

Structurei

3D structure databases

ProteinModelPortaliC5CNF6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini108 – 312ATP-graspInterPro annotationAdd BLAST205

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.UniRule annotationSAAS annotation

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011592.
KOiK01921.
OMAiMQGLLEC.
OrthoDBiPOG091H00GT.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig. 1 hit.
InterProiView protein in InterPro
IPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
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.
PfamiView protein in Pfam
PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
PIRSFiPIRSF039102. Ddl/VanB. 2 hits.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiView protein in PROSITE
PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.

Sequencei

Sequence statusi: Complete.

C5CNF6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLQDPKQFG KVAVLFGGSS AEREISLLSG NGVLEALRSR GVDAHAFDPA
60 70 80 90 100
ERDLVELRRE GFARCFIALH GRHGEDGTVQ GALELLGIPY TGSGVMASSV
110 120 130 140 150
AMDKVMTKRI WQADGLPTPR YVRLAFDQQS REQVRAVPDV LGLPLIVKPP
160 170 180 190 200
REGSSIGVTK VEGYSQMQDA VTLSARYDAD VLCEEFIEGE EVTCAVLGQG
210 220 230 240 250
LDARALPVVR IAAPEGAYDY QNKYFTDDVK YHCPSGLPEA EEHEIQRITL
260 270 280 290 300
AAYHTLGCRG WGRADVMIRA SDRKPFLLEM NTSPGMTSHS LVPMSARASG
310 320
IAYEDLCLRV LASASLDAAG GAQ
Length:323
Mass (Da):34,942
Last modified:July 28, 2009 - v1
Checksum:i4157FC4255F962A1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001635 Genomic DNA. Translation: ACS17572.1.
RefSeqiWP_012746071.1. NC_012791.1.

Genome annotation databases

EnsemblBacteriaiACS17572; ACS17572; Vapar_0921.
KEGGivap:Vapar_0921.

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 one 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.

Entry informationi

Entry nameiC5CNF6_VARPS
AccessioniPrimary (citable) accession number: C5CNF6
Entry historyiIntegrated into UniProtKB/TrEMBL: July 28, 2009
Last sequence update: July 28, 2009
Last modified: July 5, 2017
This is version 62 of the entry and version 1 of the sequence. See complete history.
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported