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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (Silicibacter pomeroyi)
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 bindingi251Magnesium or manganese 1UniRule annotation1
Metal bindingi267Magnesium or manganese 1UniRule annotation1
Metal bindingi267Magnesium or manganese 2UniRule annotation1
Metal bindingi269Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi134 – 184ATPUniRule annotationAdd BLAST51

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 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:SPO1201
OrganismiRuegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (Silicibacter pomeroyi)
Taxonomic identifieri246200 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRuegeria
Proteomesi
  • UP000001023 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003411731 – 306D-alanine--D-alanine ligaseAdd BLAST306

Interactioni

Protein-protein interaction databases

STRINGi246200.SPO1201

Structurei

3D structure databases

ProteinModelPortaliQ5LU57
SMRiQ5LU57
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini107 – 300ATP-graspUniRule annotationAdd BLAST194

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CPF Bacteria
COG1181 LUCA
HOGENOMiHOG000011592
KOiK01921
OMAiYETKYTE
OrthoDBiPOG091H00GT

Family and domain databases

Gene3Di3.30.1490.201 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.

Q5LU57-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGMSSRTNPK VAVLMGGPSA EREVSLVSGR ECAAALRGEG FEVVELDAGS
60 70 80 90 100
DLCDRLRASA PDVVFNALHG RWGEDGCVQG LLEWLRIPYT SSGVLASALA
110 120 130 140 150
MDKERSKEAY RAAGLPVAAS QLADRAAIEA AHVMQPPYVV KPYNEGSSVG
160 170 180 190 200
VYIVTEAANG PPVLAPDLPA TLMVEEYVPG RELSTTVLGD RALNVTDIIT
210 220 230 240 250
DGWYDYHAKY SPGGSRHVIP ADLPPEIFEL CLDYALRAHK ALGCRGLSRT
260 270 280 290 300
DFRWDESRGA AGLFLLETNT QPGMTPTSLA PEQALAAGMS FGQLCAWMVE

DASCDR
Length:306
Mass (Da):32,716
Last modified:February 1, 2005 - v1
Checksum:iF7056B1A09A3675B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000031 Genomic DNA Translation: AAV94497.1

Genome annotation databases

EnsemblBacteriaiAAV94497; AAV94497; SPO1201
KEGGisil:SPO1201

Similar proteinsi

Entry informationi

Entry nameiDDL_RUEPO
AccessioniPrimary (citable) accession number: Q5LU57
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: February 1, 2005
Last modified: November 22, 2017
This is version 93 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