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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Methylacidiphilum infernorum (isolate V4) (Methylokorus infernorum (strain V4))
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Cell wall formation.

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
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 bindingi247Magnesium or manganese 11
Metal bindingi260Magnesium or manganese 11
Metal bindingi260Magnesium or manganese 21
Metal bindingi262Magnesium or manganese 21

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi130 – 179ATPAdd BLAST50

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis
LigandATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligase (EC:6.3.2.4)
Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase
Gene namesi
Name:ddl
Ordered Locus Names:Minf_1408
OrganismiMethylacidiphilum infernorum (isolate V4) (Methylokorus infernorum (strain V4))
Taxonomic identifieri481448 [NCBI]
Taxonomic lineageiBacteriaVerrucomicrobiaMethylacidiphilaeMethylacidiphilalesMethylacidiphilaceaeMethylacidiphilum
Proteomesi
  • UP000009149 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000911941 – 303D-alanine--D-alanine ligaseAdd BLAST303

Interactioni

Protein-protein interaction databases

STRINGi481448.Minf_1408.

Structurei

3D structure databases

ProteinModelPortaliB3DVV9.
SMRiB3DVV9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini103 – 293ATP-graspAdd BLAST191

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011592.
KOiK01921.
OMAiYETKYTE.
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_sf.
PfamiView protein in Pfam
PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiView protein in PROSITE
PS50975. ATP_GRASP. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.

Sequencei

Sequence statusi: Complete.

B3DVV9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNPALPRHIA VLKGGPSEER EISLRTAKAV EDALSSLGYE ISSIDVTTEK
60 70 80 90 100
FEIPRDAEIC FLCIHGSFGE DGQIQRLLMR RGIPFTGSDA SSSEKAFDKA
110 120 130 140 150
WSKTLFIKGG IPTPPFCVVG DGKKIPFDPP YVIKPSRQGS SIGIEFVYDI
160 170 180 190 200
KELDQAIKKS TQYDHVVLAE ALITGKELTV GILDGKALPV VEIKPKEGFY
210 220 230 240 250
DYHHKYTKGA STYFCPAPLT VDQTSAVQKT ALDAFNVLGC SVYGRVDIIL
260 270 280 290 300
SDNGIPWVLE INTIPGMTET SLFPMAAKAS GMNFAQLCEK ILEISYLRWK

AHG
Length:303
Mass (Da):33,194
Last modified:July 22, 2008 - v1
Checksum:i4B0BC4D8738D0BEA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000975 Genomic DNA. Translation: ACD83462.1.
RefSeqiWP_012463744.1. NC_010794.1.

Genome annotation databases

EnsemblBacteriaiACD83462; ACD83462; Minf_1408.
KEGGimin:Minf_1408.

Similar proteinsi

Entry informationi

Entry nameiDDL_METI4
AccessioniPrimary (citable) accession number: B3DVV9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 22, 2008
Last modified: November 22, 2017
This is version 67 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families