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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Desulfomonile tiedjei (strain ATCC 49306 / DSM 6799 / DCB-1)
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.

Pathway: 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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi302 – 3021Magnesium or manganese 1UniRule annotation
Metal bindingi315 – 3151Magnesium or manganese 1UniRule annotation
Metal bindingi315 – 3151Magnesium or manganese 2UniRule annotation
Metal bindingi317 – 3171Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi176 – 23156ATPUniRule 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

BioCyciDTIE706587:GLCI-1483-MONOMER.
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:Desti_1485Imported
OrganismiDesulfomonile tiedjei (strain ATCC 49306 / DSM 6799 / DCB-1)Imported
Taxonomic identifieri706587 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaSyntrophobacteralesSyntrophaceaeDesulfomonile
ProteomesiUP000006055 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini144 – 348205ATP-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

KOiK01921.
OMAiWFPILHG.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
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.

I4C3Q6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQNPRLRIAL VYGGQSAEHE VSLRSARSIF DAMDRSKYDP LPILITQQGS
60 70 80 90 100
WYSMPAEAAS FDPSVSPARS NRLIFSPDPQ HRGFLKVDGE SGIQPMHVDL
110 120 130 140 150
VFPVLHGTYG EDGTIQGLLE MAHMPYVGCG VLASAVGMDK ILMKKAFREN
160 170 180 190 200
GLNIGPYFWF FRAEWESDPD KITAKLKSAH FPLFVKPANL GSSVGISKVS
210 220 230 240 250
DPSGFEAAVN LAASYDRKIL VEDGIEGREL EVSVLGNDHP KASVAGEVIS
260 270 280 290 300
HSSFYDYEEK YLKDTAELVI PAELPAGMLQ KAQEAAITAF RAVDGSGLGR
310 320 330 340 350
VDMFLTPDNQ VVVNEINTLP GFTSISMYPK LWEATGLPYA QLVDRLVGLA
360
QERHREKLTI RTDRKPV
Length:367
Mass (Da):40,370
Last modified:September 5, 2012 - v1
Checksum:i160F657B5D8B912E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP003360 Genomic DNA. Translation: AFM24197.1.
RefSeqiWP_014809345.1. NC_018025.1.
YP_006446461.1. NC_018025.1.

Genome annotation databases

EnsemblBacteriaiAFM24197; AFM24197; Desti_1485.
KEGGidti:Desti_1485.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP003360 Genomic DNA. Translation: AFM24197.1.
RefSeqiWP_014809345.1. NC_018025.1.
YP_006446461.1. NC_018025.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAFM24197; AFM24197; Desti_1485.
KEGGidti:Desti_1485.

Phylogenomic databases

KOiK01921.
OMAiWFPILHG.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciDTIE706587:GLCI-1483-MONOMER.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
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: ATCC 49306 / DSM 6799 / DCB-1Imported.

Entry informationi

Entry nameiI4C3Q6_DESTA
AccessioniPrimary (citable) accession number: I4C3Q6
Entry historyi
Integrated into UniProtKB/TrEMBL: September 5, 2012
Last sequence update: September 5, 2012
Last modified: June 24, 2015
This is version 22 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

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.