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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256) (Sphingomonas alaskensis)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-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 bindingi255Magnesium or manganese 1UniRule annotation1
Metal bindingi271Magnesium or manganese 1UniRule annotation1
Metal bindingi271Magnesium or manganese 2UniRule annotation1
Metal bindingi273Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi131 – 187ATPUniRule annotationAdd BLAST57

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:Sala_1878
OrganismiSphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256) (Sphingomonas alaskensis)
Taxonomic identifieri317655 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingopyxis
Proteomesi
  • UP000006578 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003411771 – 308D-alanine--D-alanine ligaseAdd BLAST308

Interactioni

Protein-protein interaction databases

STRINGi317655.Sala_1878.

Structurei

3D structure databases

ProteinModelPortaliQ1GRY2.
SMRiQ1GRY2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini104 – 304ATP-graspUniRule annotationAdd BLAST201

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

Gene3Di3.30.1490.20. 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.

Q1GRY2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRGPWHVAV LMGGWSAERE VSLMSGKGVA DALESRGHKV TRIDMDRDVA
60 70 80 90 100
LRLAEAKPDV VFNALHGVPG EDGTVQGMLD LMGFRYTHSG LVTSVIAIDK
110 120 130 140 150
ELTKQALVPH GIPMPTGTMV DSESLFSVDP LPRPYVLKPV NEGSSVGVAI
160 170 180 190 200
VRDDSNYGNP ISRDALGPWQ QFDRLLAEPF IKGRELTVAV LGDTALAVTE
210 220 230 240 250
LRVKSGFYDY DAKYTDGLTE HVCPADVPDD VAQRMKDLAL QAHRLLGCKG
260 270 280 290 300
ASRSDFRWDD EHGLAGIFLL EVNTQPGMTP LSLVPEQARA VGMDYAELVE

RIVEEALT
Length:308
Mass (Da):33,521
Last modified:June 27, 2006 - v1
Checksum:i867191BFEA5D2EC2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000356 Genomic DNA. Translation: ABF53590.1.
RefSeqiWP_011542168.1. NC_008048.1.

Genome annotation databases

EnsemblBacteriaiABF53590; ABF53590; Sala_1878.
KEGGisal:Sala_1878.

Similar proteinsi

Entry informationi

Entry nameiDDL_SPHAL
AccessioniPrimary (citable) accession number: Q1GRY2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: June 27, 2006
Last modified: November 22, 2017
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

Documents

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