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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)
Status
Reviewed-Annotation score: -Protein inferred from homologyi

Functioni

Cell wall formation.UniRule annotation

Catalytic activityi

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

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.UniRule 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 bindingi284Magnesium or manganese 1UniRule annotation1
Metal bindingi297Magnesium or manganese 1UniRule annotation1
Metal bindingi297Magnesium or manganese 2UniRule annotation1
Metal bindingi299Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi154 – 209ATPUniRule annotationAdd BLAST56

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

BioCyciSDEN318161:G1G6C-2475-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:ddlUniRule annotation
Ordered Locus Names:Sden_2354
OrganismiShewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)
Taxonomic identifieri318161 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
Proteomesi
  • UP000001982 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000747861 – 335D-alanine--D-alanine ligaseAdd BLAST335

Interactioni

Protein-protein interaction databases

STRINGi318161.Sden_2354

Structurei

3D structure databases

ProteinModelPortaliQ12LP2
SMRiQ12LP2
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini124 – 330ATP-graspUniRule annotationAdd BLAST207

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CPF Bacteria
COG1181 LUCA
HOGENOMiHOG000011592
KOiK01921
OMAiRCDFFVI
OrthoDBiPOG091H06GK

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
PS00843 DALA_DALA_LIGASE_1, 1 hit
PS00844 DALA_DALA_LIGASE_2, 1 hit

Sequencei

Sequence statusi: Complete.

Q12LP2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKINVLLLC GGGGAEHDIS LMSARFFETS LAKSDQFSVL TLTLDKQGRY
60 70 80 90 100
HTQDGNLCSL TNRREIRFED PSIAPWAVDY VIPCIHGFPG ETGDIQSYFN
110 120 130 140 150
LIQLPYFGCE SEASSNCFNK ITAKMWFSAL GVPNTPYIFL HQFDQEAIAQ
160 170 180 190 200
TQAAFDTWGS VFIKAASQGS SVGCYKVDVR DNIAKVLEEA FGYAPYVVVE
210 220 230 240 250
KTIKARELEV AVYEYQGDII ATLPGEIICD TNKFYSFDEK YAKDSKARTD
260 270 280 290 300
VVASNLSPKL CLQIQDYAIK AFKGMKLRHL SRIDFFLTQD DEILLNEINT
310 320 330
FPGLTPISMF PKMLQNHGHD FTEYLSDVIS QQLGR
Length:335
Mass (Da):37,585
Last modified:August 22, 2006 - v1
Checksum:i112BC8E7C0123B8D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000302 Genomic DNA Translation: ABE55634.1
RefSeqiWP_011496785.1, NC_007954.1

Genome annotation databases

EnsemblBacteriaiABE55634; ABE55634; Sden_2354
KEGGisdn:Sden_2354

Similar proteinsi

Entry informationi

Entry nameiDDL_SHEDO
AccessioniPrimary (citable) accession number: Q12LP2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: August 22, 2006
Last modified: March 28, 2018
This is version 83 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

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